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Djusse ME, Gaspari V, Morselli S, Rapparini L, Foschi C, Ambretti S, Lazzarotto T, Piraccini BM, Marangoni A. Antimicrobial resistance determinants in the oropharyngeal microbiome of 'men having sex with men' attending an sexually transmitted infection clinic. Int J STD AIDS 2024; 35:803-807. [PMID: 38760931 DOI: 10.1177/09564624241255163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
BACKGROUND 'Men having sex with men' (MSM) represent a key population with a significant prevalence of pharyngeal Neisseria gonorrhoeae (NG) infections and a high rate of antimicrobial resistance genes in the pharyngeal microbiome. As NG can acquire antibiotic resistance genes from other commensal oropharyngeal bacteria, monitoring the prevalence of these resistance determinants is critical to curtail the spread of NG-resistant strains. PURPOSE AND RESEARCH DESIGN Here, we assessed the distribution of five resistance genes (pen (A), mtr (R), gyr (A), par (C), msr (D)) in the oropharynx of 164 MSM, attending an Outpatient clinic for STI screening. RESULTS The most frequently detected resistance gene was msr (D) (88.4%), followed by gyr (A) (67.1%). The distribution of resistance genes was not influenced by pharyngeal gonorrhea nor by the HIV status, whereas a younger age was associated with mtr (R) presence (p = .008). Subjects using mouthwash exhibited significantly lower levels of mtr (R) (p = .0005). Smoking habit was associated with a higher prevalence of par (C) (p = .02). A noteworthy association was observed between the presence of msr (D) gene and the use of antibiotics (p = .014). CONCLUSIONS Our findings reveal an enrichment of antimicrobial resistance genes in the oropharynx of MSM. These insights could aid in the development of screening programs and antimicrobial stewardship initiatives targeting populations at heightened risk of pharyngeal gonorrhea.
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Affiliation(s)
- Marielle Ezekielle Djusse
- Section of Microbiology, Department of Medical and Surgical Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Valeria Gaspari
- Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Sara Morselli
- Section of Microbiology, Department of Medical and Surgical Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Luca Rapparini
- Section of Dermatology, Department of Medical and Surgical Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Claudio Foschi
- Section of Microbiology, Department of Medical and Surgical Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
- Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Simone Ambretti
- Section of Microbiology, Department of Medical and Surgical Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
- Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Tiziana Lazzarotto
- Section of Microbiology, Department of Medical and Surgical Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
- Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Bianca Maria Piraccini
- Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Section of Dermatology, Department of Medical and Surgical Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Antonella Marangoni
- Section of Microbiology, Department of Medical and Surgical Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
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de Block T, De Baetselier I, Van den Bossche D, Abdellati S, Gestels Z, Laumen JGE, Van Dijck C, Vanbaelen T, Claes N, Vandelannoote K, Kenyon C, Harrison O, Santhini Manoharan-Basil S. Genomic oropharyngeal Neisseria surveillance detects MALDI-TOF MS species misidentifications and reveals a novel Neisseria cinerea clade. J Med Microbiol 2024; 73. [PMID: 39212029 DOI: 10.1099/jmm.0.001871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
Introduction. Commensal Neisseria spp. are highly prevalent in the oropharynx as part of the healthy microbiome. N. meningitidis can colonise the oropharynx too from where it can cause invasive meningococcal disease. To identify N. meningitidis, clinical microbiology laboratories often rely on Matrix Assisted Laser Desorption/Ionisation Time of Flight Mass Spectrometry (MALDI-TOF MS).Hypothesis/Gap statement. N. meningitidis may be misidentified by MALDI-TOF MS.Aim. To conduct genomic surveillance of oropharyngeal Neisseria spp. in order to: (i) verify MALDI-TOF MS species identification, and (ii) characterize commensal Neisseria spp. genomes.Methodology. We analysed whole genome sequence (WGS) data from 119 Neisseria spp. isolates from a surveillance programme for oropharyngeal Neisseria spp. in Belgium. Different species identification methods were compared: (i) MALDI-TOF MS, (ii) Ribosomal Multilocus Sequence Typing (rMLST) and (iii) rplF gene species identification. WGS data were used to further characterize Neisseria species found with supplementary analyses of Neisseria cinerea genomes.Results. Based on genomic species identification, isolates from the oropharyngeal Neisseria surveilence study were composed of the following species: N. meningitidis (n=23), N. subflava (n=61), N. mucosa (n=15), N. oralis (n=8), N. cinerea (n=5), N. elongata (n=3), N. lactamica (n=2), N. bacilliformis (n=1) and N. polysaccharea (n=1). Of these 119 isolates, four isolates identified as N. meningitidis (n=3) and N. subflava (n=1) by MALDI-TOF MS, were determined to be N. polysaccharea (n=1), N. cinerea (n=2) and N. mucosa (n=1) by rMLST. Phylogenetic analyses revealed that N. cinerea isolates from the general population (n=3, cluster one) were distinct from those obtained from men who have sex with men (MSM, n=2, cluster two). The latter contained genomes misidentified as N. meningitidis using MALDI-TOF MS. These two N. cinerea clusters persisted after the inclusion of published N. cinerea WGS (n=42). Both N. cinerea clusters were further defined through pangenome and Average Nucleotide Identity (ANI) analyses.Conclusion. This study provides insights into the importance of genomic genus-wide Neisseria surveillance studies to improve the characterization and identification of the Neisseria genus.
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Affiliation(s)
- Tessa de Block
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Irith De Baetselier
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | | | - Saïd Abdellati
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Zina Gestels
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | | | - Christophe Van Dijck
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Thibaut Vanbaelen
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Nathalie Claes
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Koen Vandelannoote
- Bacterial Phylogenomics group, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Chris Kenyon
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Odile Harrison
- Nuffield Department of Population Health, Infectious Diseases Epidemiology Unit, University of Oxford, Oxford, UK
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He Z, Yang H, Chen Q, Chen YPP, Qin H, He W, Chen Z. Role of TAP1 in the identification of immune-hot tumor microenvironment and its prognostic significance for immunotherapeutic efficacy in gastric carcinoma. J Gastrointest Oncol 2024; 15:890-907. [PMID: 38989426 PMCID: PMC11231864 DOI: 10.21037/jgo-24-28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/19/2024] [Indexed: 07/12/2024] Open
Abstract
Background Gastric cancer (GC), a multifaceted gastrointestinal malignancy, is the fourth most prevalent contributor to cancer-related fatalities globally. As a member of the ATP-binding cassette (ABC) family, transporter associated with antigen processing 1 (TAP1) is crucial for conveying antigen peptides from the cytoplasm to the lumen of the endoplasmic reticulum and subsequently loading them onto the major histocompatibility complex (MHC) class I molecules. Recent studies have established the biological significance of TAP1 in upholding tumor survival and facilitating immune evasion by remodeling the tumor microenvironment (TME) and orchestrating immune infiltration. The study was conducted to elucidate the association of TAP1 expression with immunological characteristics, and sought to exploit the value of TAP1 as a biomarker reflecting the inflamed TME and immunotherapeutic response. Methods RNA-sequencing profiles and clinical annotations were obtained from The Cancer Genome Atlas-stomach adenocarcinoma (TCGA-STAD) cohort and Gene Expression Omnibus (GEO) portal. Preprocessing was conducting using the limma package. Weighted gene co-expression network analysis (WGCNA) was used to identify gene modules and TAP1 co-expressed genes (CEGs) based on correlation patterns. Consensus clustering and silhouette analysis determined the optimal number of TAP1-related groups. Gene expression profiles were integrated and classified using the pamr package. The Estimation of STromal and Immune cells in MAlignant Tumors using Expression data (ESTIMATE) algorithm and single-sample gene set enrichment analysis (ssGSEA) were used to evaluate immunological characteristics. Differential expression analysis was conducted using the limma package. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed. Single-cell RNA sequencing (scRNA-seq) datasets were analyzed using the Seurat toolkit to characterize cell types. Results Within this investigation, no significant differences in TAP1 expression were observed among patients exhibiting various clinicopathological features, indicating that TAP1 expression was not specific to molecular subtypes. Subsequent analysis revealed a positive correlation between TAP1 and diverse immunological traits, encompassing immunomodulators, tumor-infiltrating immune cells, as well as immune checkpoints across multiple datasets. Besides, within a GC immunotherapy cohort, individuals displaying high TAP1 expression demonstrated an increased likelihood of achieving complete remission (CR) post-treatment, suggesting heightened sensitivity to immunotherapy. In the clinical cohort, TAP1 overexpression in GC patients was positively correlated with CD8. Conclusions TAP1 appears linked to an inflamed TME and serves as a prospective biomarker for discerning immunological attributes and gauging immunotherapeutic responses in GC, particularly in identifying immune-reactive tumors.
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Affiliation(s)
- Zehua He
- Department of General Surgery, Guangxi Hospital Division of The First Affiliated Hospital, Sun Yat-sen University, Nanning, China
| | - Hong Yang
- Department of Anesthesia Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qingfeng Chen
- School of Computer, Electronic and Information, Guangxi University, Nanning, China
| | - Yi-Ping Phoebe Chen
- Department of Computer Science and Information Technology, La Trobe University, Melbourne, Australia
| | - Huabo Qin
- Department of General Surgery, Guangxi Hospital Division of The First Affiliated Hospital, Sun Yat-sen University, Nanning, China
| | - Wanrong He
- Department of Computer Science and Information Technology, La Trobe University, Melbourne, Australia
| | - Zhihui Chen
- Department of General Surgery, Guangxi Hospital Division of The First Affiliated Hospital, Sun Yat-sen University, Nanning, China
- Department of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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Abdellati S, Laumen JGE, de Block T, De Baetselier I, Van Den Bossche D, Van Dijck C, Manoharan-Basil SS, Kenyon C. Gonococcal resistance to zoliflodacin could emerge via transformation from commensal Neisseria species. An in-vitro transformation study. Sci Rep 2024; 14:1179. [PMID: 38216602 PMCID: PMC10786824 DOI: 10.1038/s41598-023-49943-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024] Open
Abstract
One of the most promising new treatments for gonorrhoea currently in phase 3 clinical trials is zoliflodacin. Studies have found very little resistance to zoliflodacin in currently circulating N. gonorrhoeae strains, and in-vitro experiments demonstrated that it is difficult to induce resistance. However, zoliflodacin resistance may emerge in commensal Neisseria spp., which could then be transferred to N. gonorrhoeae via transformation. In this study, we investigated this commensal-resistance-pathway hypothesis for zoliflodacin. To induce zoliflodacin resistance, ten wild-type susceptible isolates belonging to 5 Neisseria species were serially passaged for up to 48 h on gonococcal agar plates containing increasing zoliflodacin concentrations. Within 7 to 10 days, all strains except N. lactamica, exhibited MICs of ≥ 4 µg/mL, resulting in MIC increase ranging from 8- to 64-fold. The last passaged strains and their baseline were sequenced. We detected mutations previously reported to cause zoliflodacin resistance in GyrB (D429N and S467N), novel mutations in the quinolone resistance determining region (QRDR) (M464R and T472P) and mutations outside the QRDR at amino acid positions 28 and 29 associated with low level resistance (MIC 2 µg/mL). Genomic DNA from the laboratory evolved zoliflodacin-resistant strains was transformed into the respective baseline wild-type strain, resulting in MICs of ≥ 8 µg/mL in most cases. WGS of transformants with decreased zoliflodacin susceptibility revealed presence of the same zoliflodacin resistance determinants as observed in the donor strains. Two inter-species transformation experiments were conducted to investigate whether zoliflodacin resistance determinants of commensal Neisseria spp. could be acquired by N. gonorrhoeae. N. gonorrhoeae strain WHO P was exposed to (i) pooled genomic DNA from the two resistant N. mucosa strains and (ii) a gyrB amplicon of the resistant N. subflava strain 45/1_8. Transformants of both experiments exhibited an MIC of 2 µg/mL and whole genome analysis revealed uptake of the mutations detected in the donor strains. This is the first in-vitro study to report that zoliflodacin resistance can be induced in commensal Neisseria spp. and subsequently transformed into N. gonorrhoeae.
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Affiliation(s)
- Saïd Abdellati
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Jolein Gyonne Elise Laumen
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Laboratory of Medical Microbiology, University of Antwerp, Wilrijk, Belgium
| | - Tessa de Block
- Clinical Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Irith De Baetselier
- Clinical Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Dorien Van Den Bossche
- Clinical Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Christophe Van Dijck
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Laboratory of Medical Microbiology, University of Antwerp, Wilrijk, Belgium
| | | | - Chris Kenyon
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Division of Infectious Diseases and HIV Medicine, University of Cape Town, Cape Town, South Africa
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Abdellati S, Gestels Z, Laumen JGE, Van Dijck C, De Baetselier I, de Block T, Van den Bossche D, Vanbaelen T, Kanesaka I, Manoharan-Basil SS, Kenyon C. Antimicrobial susceptibility of commensal Neisseria spp. in parents and their children in Belgium: a cross-sectional survey. FEMS Microbiol Lett 2024; 371:fnae069. [PMID: 39210455 DOI: 10.1093/femsle/fnae069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/11/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND commensal Neisseria species are part of the oropharyngeal microbiome and play an important role in nitrate reduction and protecting against colonization by pathogenic bacteria. They do, however, also serve as a reservoir of antimicrobial resistance. Little is known about the prevalence of these species in the general population, how this varies by age and how antimicrobial susceptibility varies between species. METHODS we assessed the prevalence and antimicrobial susceptibility of commensal Neisseria species in the parents (n = 38) and children (n = 50) of 35 families in Belgium. RESULTS various commensal Neisseria (n = 5) could be isolated from the participants. Most abundant were N. subflava and N. mucosa. Neisseria subflava was detected in 77 of 88 (87.5%) individuals and N. mucosa in 64 of 88 (72.7%). Neisseria mucosa was more prevalent in children [41/50 (82%)] than parents [23/38 (60.5%); P < .05], while N. bacilliformis was more prevalent in parents [7/36 (19.4%)] than children [2/50 (4%); P < .05]. Neisseria bacilliformis had high ceftriaxone minimum inhibitory concentrations (MICs; median MIC 0.5 mg/l; IQR 0.38-0.75). The ceftriaxone MICs of all Neisseria isolates were higher in the parents than in the children. This could be explained by a higher prevalence of N. bacilliformis in the parents. INTERPRETATION the N. bacilliformis isolates had uniformly high ceftriaxone MICs which warrant further investigation.
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Affiliation(s)
- Saïd Abdellati
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium
| | - Zina Gestels
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium
| | | | - Christophe Van Dijck
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium
| | - Irith De Baetselier
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium
| | - Tessa de Block
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium
| | - Dorien Van den Bossche
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium
| | - Thibaut Vanbaelen
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium
| | - Izumo Kanesaka
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium
- Department of Infection Control and Prevention, Faculty of Nursing, Toho University, 3219, Japan
| | | | - Chris Kenyon
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium
- University of Cape Town, Cape Town, 42145, South Africa
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Gaspari V, Djusse ME, Morselli S, Rapparini L, Foschi C, Ambretti S, Lazzarotto T, Piraccini BM, Marangoni A. Non-pathogenic Neisseria species of the oropharynx as a reservoir of antimicrobial resistance: a cross-sectional study. Front Cell Infect Microbiol 2023; 13:1308550. [PMID: 38076458 PMCID: PMC10703147 DOI: 10.3389/fcimb.2023.1308550] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/02/2023] [Indexed: 12/18/2023] Open
Abstract
Commensal Neisseria species of the oropharynx represent a significant reservoir of antimicrobial resistance determinants that can be transferred to Neisseria gonorrhoeae. This aspect is particularly crucial in 'men having sex with men' (MSM), a key population in which pharyngeal co-colonization by N. gonorrhoeae and non-pathogenic Neisseria species is frequent and associated with the emergence of antimicrobial resistance. Here, we explored the antimicrobial susceptibility of a large panel of non-pathogenic Neisseria species isolated from the oropharynx of two populations: a group of MSM attending a 'sexually transmitted infection' clinic in Bologna (Italy) (n=108) and a group of males representing a 'general population' (n=119). We collected 246 strains, mainly belonging to N. subflava (60%) and N. flavescens (28%) species. Their antimicrobial susceptibility was evaluated assessing the minimum inhibitory concentrations (MICs) for azithromycin, ciprofloxacin, cefotaxime, and ceftriaxone using E-test strips. Overall, commensal Neisseria spp. showed high rates of resistance to azithromycin (90%; median MICs: 4.0 mg/L), and ciprofloxacin (58%; median MICs: 0.12 mg/L), whereas resistance to cephalosporins was far less common (<15%). Neisseria strains from MSM were found to have significantly higher MICs for azithromycin (p=0.0001) and ciprofloxacin (p<0.0001) compared to those from the general population. However, there was no significant difference in cephalosporin MICs between the two groups. The surveillance of the antimicrobial resistance of non-pathogenic Neisseria spp. could be instrumental in predicting the risk of the spread of multi-drug resistant gonorrhea. This information could be an early predictor of an excessive use of antimicrobials, paving the way to innovative screening and prevention policies.
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Affiliation(s)
- Valeria Gaspari
- Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Marielle Ezekielle Djusse
- Section of Microbiology, Department of Medical and Surgical Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Sara Morselli
- Section of Microbiology, Department of Medical and Surgical Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Luca Rapparini
- Section of Dermatology, Department of Medical and Surgical Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Claudio Foschi
- Section of Microbiology, Department of Medical and Surgical Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
- Microbiology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Simone Ambretti
- Section of Microbiology, Department of Medical and Surgical Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
- Microbiology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Tiziana Lazzarotto
- Section of Microbiology, Department of Medical and Surgical Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
- Microbiology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Bianca Maria Piraccini
- Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Section of Dermatology, Department of Medical and Surgical Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Antonella Marangoni
- Section of Microbiology, Department of Medical and Surgical Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
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Kenyon C, Herrmann B, Hughes G, de Vries HJ. Management of asymptomatic sexually transmitted infections in Europe: towards a differentiated, evidence-based approach. THE LANCET REGIONAL HEALTH. EUROPE 2023; 34:100743. [PMID: 37927435 PMCID: PMC10624996 DOI: 10.1016/j.lanepe.2023.100743] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/05/2023] [Accepted: 09/18/2023] [Indexed: 11/07/2023]
Abstract
Most sexually transmitted infections (STIs) can be accurately diagnosed and treated during asymptomatic carriage. Widespread screening for these STIs is therefore assumed to be an effective way to reduce their prevalence and associated disease. In this review, we provide evidence that this is the case for HIV and syphilis. However, for other STIs such as Neisseria gonorrhoeae and Chlamydia trachomatis, our review reveals that the evidence that screening reduces infection prevalence and associated disease is weak. There is also growing evidence of harms from screening that might outweigh any benefits. The harms include the increased consumption of antimicrobials that follows frequent screening and increased detection of asymptomatic STIs in key populations, such as men who have sex with men taking HIV pre-exposure prophylaxis, and associated risk of antimicrobial resistance in target and non-target organisms. There may also be psycho-social harm associated with an STI diagnosis. We conclude that in the absence of symptoms, in high STI prevalence populations frequent STI screening should be limited to HIV and syphilis.
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Affiliation(s)
- Chris Kenyon
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Björn Herrmann
- Section of Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Gwenda Hughes
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, UK
| | - Henry J.C. de Vries
- Department of Dermatology, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
- Center for Sexual Health, Department of Infectious Diseases, Public Health Service Amsterdam, the Netherlands
- Amsterdam Institute for Global Health and Development, Amsterdam, the Netherlands
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8
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Fostier CR, Ousalem F, Leroy EC, Ngo S, Soufari H, Innis CA, Hashem Y, Boël G. Regulation of the macrolide resistance ABC-F translation factor MsrD. Nat Commun 2023; 14:3891. [PMID: 37393329 PMCID: PMC10314930 DOI: 10.1038/s41467-023-39553-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 06/19/2023] [Indexed: 07/03/2023] Open
Abstract
Antibiotic resistance ABC-Fs (ARE ABC-Fs) are translation factors that provide resistance against clinically important ribosome-targeting antibiotics which are proliferating among pathogens. Here, we combine genetic and structural approaches to determine the regulation of streptococcal ARE ABC-F gene msrD in response to macrolide exposure. We show that binding of cladinose-containing macrolides to the ribosome prompts insertion of the leader peptide MsrDL into a crevice of the ribosomal exit tunnel, which is conserved throughout bacteria and eukaryotes. This leads to a local rearrangement of the 23 S rRNA that prevents peptide bond formation and accommodation of release factors. The stalled ribosome obstructs the formation of a Rho-independent terminator structure that prevents msrD transcriptional attenuation. Erythromycin induction of msrD expression via MsrDL, is suppressed by ectopic expression of mrsD, but not by mutants which do not provide antibiotic resistance, showing correlation between MsrD function in antibiotic resistance and its action on this stalled complex.
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Affiliation(s)
- Corentin R Fostier
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005, Paris, France
| | - Farès Ousalem
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005, Paris, France
| | - Elodie C Leroy
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 33607, Pessac, France
| | - Saravuth Ngo
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005, Paris, France
| | - Heddy Soufari
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 33607, Pessac, France
- SPT Labtech Ltd., SG8 6HB, Melbourn, United Kingdom
| | - C Axel Innis
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 33607, Pessac, France
| | - Yaser Hashem
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 33607, Pessac, France.
| | - Grégory Boël
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005, Paris, France.
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Van Dijck C, Laumen JGE, de Block T, Abdellati S, De Baetselier I, Tsoumanis A, Malhotra-Kumar S, Manoharan-Basil SS, Kenyon C, Xavier BB. The oropharynx of men using HIV pre-exposure prophylaxis is enriched with antibiotic resistance genes: A cross-sectional observational metagenomic study. J Infect 2023; 86:329-337. [PMID: 36764395 DOI: 10.1016/j.jinf.2023.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 02/01/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023]
Abstract
BACKGROUND Phenotypic studies have found high levels of antimicrobial resistance to cephalosporins, macrolides and fluoroquinolones in commensal Neisseria species in the oropharynx of men who have sex with men (MSM) using HIV pre-exposure prophylaxis (PrEP). These species include Neisseria subflava and Neisseria mucosa. This may represent a risk to pathogens like Neisseria gonorrhoeae which tend to take up antibiotic resistance genes (ARGs) from other bacteria. We aimed to explore to what extent the oropharyngeal resistome of MSM using PrEP differed from the general population. METHODS We collected oropharyngeal swabs from 32 individuals of the general population and from 64 MSM using PrEP. Thirty-two MSM had consumed antibiotics in the previous six months, whereas none of the other participants had. Samples underwent shotgun metagenomic sequencing. Sequencing reads were mapped against MEGARes 2.0 to estimate ARG abundance. ARG abundance was compared between groups by zero-inflated negative binomial regression. FINDINGS ARG abundance was significantly lower in the general population than in MSM (ratio 0.41, 95% CI 0.26-0.65). More specifically, this was the case for fluoroquinolones (0.33, 95% CI 0.15-0.69), macrolides (0.37, 95% CI 0.25-0.56), tetracyclines (0.41, 95% CI 0.25-0.69), and multidrug efflux pumps (0.11, 95% CI 0.03-0.33), but not for beta-lactams (1.38, 95% CI 0.73-2.61). There were no significant differences in ARG abundance between MSM who had used antibiotics and those that had not. INTERPRETATION The resistome of MSM using PrEP is enriched with ARGs, independent of recent antibiotic use. Stewardship campaigns should aim to reduce antibiotic consumption in populations at high risk for STIs.
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Affiliation(s)
- Christophe Van Dijck
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000 Antwerp, Belgium; Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium.
| | - Jolein Gyonne Elise Laumen
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000 Antwerp, Belgium; Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium.
| | - Tessa de Block
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000 Antwerp, Belgium.
| | - Saïd Abdellati
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000 Antwerp, Belgium.
| | - Irith De Baetselier
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000 Antwerp, Belgium.
| | - Achilleas Tsoumanis
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000 Antwerp, Belgium.
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium.
| | | | - Chris Kenyon
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000 Antwerp, Belgium; University of Cape Town, Rondebosch, Cape Town 7700, South Africa.
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium.
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10
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The Discovery of Oropharyngeal Microbiota with Inhibitory Activity against Pathogenic Neisseria gonorrhoeae and Neisseria meningitidis: An In Vitro Study of Clinical Isolates. Microorganisms 2022; 10:microorganisms10122497. [PMID: 36557750 PMCID: PMC9787740 DOI: 10.3390/microorganisms10122497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/02/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
With increasing incidence of pathogenic Neisseria infections coupled with emerging resistance to antimicrobials, alternative approaches to limit the spread are sought. We investigated the inhibitory effect of oropharyngeal microbiota on the growth of N. gonorrhoeae and N. meningitidis and the impact of the essential oil-based mouthwash Listerine Cool Mint® (Listerine). Oropharyngeal swabs from 64 men who have sex with men (n = 118) from a previous study (PReGo study) were analysed (ClinicalTrials.gov, NCT03881007). These included 64 baseline and 54 samples following three months of daily use of Listerine. Inhibition was confirmed by agar overlay assay, and inhibitory bacteria isolated using replica plating and identified using MALDI-TOF. The number of inhibitory isolates were compared before and after Listerine use. Thirty-one pharyngeal samples (26%) showed inhibitory activity against N. gonorrhoeae and/or N. meningitidis, and 62 inhibitory isolates were characterised. Fourteen species belonging to the genera Streptococci and Rothia were identified. More inhibitory isolates were observed following Listerine use compared to baseline, although this effect was not statistically significant (p = 0.073). This study isolated and identified inhibitory bacteria against pathogenic Neisseria spp. and established that daily Listerine use did not decrease their prevalence. These findings could provide a new approach for the prevention and treatment of pharyngeal Neisseria infections.
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11
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Khoder M, Osman M, Kassem II, Rafei R, Shahin A, Fournier PE, Rolain JM, Hamze M. Whole Genome Analyses Accurately Identify Neisseria spp. and Limit Taxonomic Ambiguity. Int J Mol Sci 2022; 23:13456. [PMID: 36362240 PMCID: PMC9657967 DOI: 10.3390/ijms232113456] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 10/27/2023] Open
Abstract
Genome sequencing facilitates the study of bacterial taxonomy and allows the re-evaluation of the taxonomic relationships between species. Here, we aimed to analyze the draft genomes of four commensal Neisseria clinical isolates from the semen of infertile Lebanese men. To determine the phylogenetic relationships among these strains and other Neisseria spp. and to confirm their identity at the genomic level, we compared the genomes of these four isolates with the complete genome sequences of Neisseria gonorrhoeae and Neisseria meningitidis and the draft genomes of Neisseria flavescens, Neisseria perflava, Neisseria mucosa, and Neisseria macacae that are available in the NCBI Genbank database. Our findings revealed that the WGS analysis accurately identified and corroborated the matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) species identities of the Neisseria isolates. The combination of three well-established genome-based taxonomic tools (in silico DNA-DNA Hybridization, Ortho Average Nucleotide identity, and pangenomic studies) proved to be relatively the best identification approach. Notably, we also discovered that some Neisseria strains that are deposited in databases contain many taxonomical errors. The latter is very important and must be addressed to prevent misdiagnosis and missing emerging etiologies. We also highlight the need for robust cut-offs to delineate the species using genomic tools.
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Affiliation(s)
- May Khoder
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon
- Institut de Recherche pour le Développement (IRD), Microbes, Evolution, Phylogénie et Infection (MEPHI), Faculté de Médecine et de Pharmacie, Aix Marseille Université, 13005 Marseille, France
| | - Marwan Osman
- Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, NY 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Issmat I Kassem
- Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, GA 30223-1797, USA
| | - Rayane Rafei
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon
| | - Ahmad Shahin
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon
| | - Pierre Edouard Fournier
- Institut de Recherche pour le Développement (IRD), Microbes, Evolution, Phylogénie et Infection (MEPHI), Faculté de Médecine et de Pharmacie, Aix Marseille Université, 13005 Marseille, France
| | - Jean-Marc Rolain
- Institut de Recherche pour le Développement (IRD), Microbes, Evolution, Phylogénie et Infection (MEPHI), Faculté de Médecine et de Pharmacie, Aix Marseille Université, 13005 Marseille, France
| | - Monzer Hamze
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon
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12
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Ciprofloxacin Concentrations 1/1000th the MIC Can Select for Antimicrobial Resistance in N. gonorrhoeae—Important Implications for Maximum Residue Limits in Food. Antibiotics (Basel) 2022; 11:antibiotics11101430. [PMID: 36290088 PMCID: PMC9598464 DOI: 10.3390/antibiotics11101430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/08/2022] [Accepted: 10/15/2022] [Indexed: 11/25/2022] Open
Abstract
Background: Concentrations of fluoroquinolones up to 200-fold lower than the minimal inhibitory concentration (MIC) have been shown to be able to select for antimicrobial resistance in E. coli and Salmonella spp. (the minimum selection concentration—MSC). We hypothesized that the low concentrations of quinolones found in meat may play a role in the genesis of quinolone resistance in Neisseria gonorrhoeae. We aimed to (i) establish the ciprofloxacin MSC for N. gonorrhoeae and (ii) assess if, at the ecological level, the prevalence of gonococcal ciprofloxacin resistance is associated with the concentration of quinolones used in food animal production, which is an important determinant of long-term low-dose exposure to ciprofloxacin in humans. Methods: (i) To assess if subinhibitory ciprofloxacin concentrations could select for de novo generated resistant mutants, a susceptible WHO-P N. gonorrhoeae isolate was serially passaged at 1, 1:10, 1:100 and 1:1000 of the ciprofloxacin MIC of WHO-P (0.004 mg/L) on GC agar plates. (ii) Spearman’s correlation was used to assess the association between the prevalence of ciprofloxacin resistance in N. gonorrhoeae and quinolone use for animals and quinolone consumption by humans. Results: Ciprofloxacin concentrations as low as 0.004 µg/L (1/1000 of the MIC of WHO-P) were able to select for ciprofloxacin resistance. The prevalence of ciprofloxacin resistance in N. gonorrhoeae was positively associated with quinolone use for food animals (ρ = 0.47; p = 0.004; N = 34). Conclusion: Further individual level research is required to assess if low doses of ciprofloxacin from ingested foodstuffs are able to select for ciprofloxacin resistance in bacteria colonizing humans and other species.
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13
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Canary in the Coal Mine: How Resistance Surveillance in Commensals Could Help Curb the Spread of AMR in Pathogenic Neisseria. mBio 2022; 13:e0199122. [PMID: 36154280 DOI: 10.1128/mbio.01991-22] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial resistance (AMR) is widespread within Neisseria gonorrhoeae populations. Recent work has highlighted the importance of commensal Neisseria (cN) as a source of AMR for their pathogenic relatives through horizontal gene transfer (HGT) of AMR alleles, such as mosaic penicillin binding protein 2 (penA), multiple transferable efflux pump (mtr), and DNA gyrase subunit A (gyrA) which impact beta-lactam, azithromycin, and ciprofloxacin susceptibility, respectively. However, nonpathogenic commensal species are rarely characterized. Here, we propose that surveillance of the universally carried commensal Neisseria may play the role of the "canary in the coal mine," and reveal circulating known and novel antimicrobial resistance determinants transferable to pathogenic Neisseria. We summarize the current understanding of commensal Neisseria as an AMR reservoir, and call to increase research on commensal Neisseria species, through expanding established gonococcal surveillance programs to include the collection, isolation, antimicrobial resistance phenotyping, and whole-genome sequencing (WGS) of commensal isolates. This will help combat AMR in the pathogenic Neisseria by: (i) determining the contemporary AMR profile of commensal Neisseria, (ii) correlating AMR phenotypes with known and novel genetic determinants, (iii) qualifying and quantifying horizontal gene transfer (HGT) for AMR determinants, and (iv) expanding commensal Neisseria genomic databases, perhaps leading to the identification of new drug and vaccine targets. The proposed modification to established Neisseria collection protocols could transform our ability to address AMR N. gonorrhoeae, while requiring minor modifications to current surveillance practices. IMPORTANCE Contemporary increases in the prevalence of antimicrobial resistance (AMR) in Neisseria gonorrhoeae populations is a direct threat to global public health and the effective treatment of gonorrhea. Substantial effort and financial support are being spent on identifying resistance mechanisms circulating within the gonococcal population. However, these surveys often overlook a known source of resistance for gonococci-the commensal Neisseria. Commensal Neisseria and pathogenic Neisseria frequently share DNA through horizontal gene transfer, which has played a large role in rendering antibiotic therapies ineffective in pathogenic Neisseria populations. Here, we propose the expansion of established gonococcal surveillance programs to integrate a collection, AMR profiling, and genomic sequencing pipeline for commensal species. This proposed expansion will enhance the field's ability to identify resistance in and from nonpathogenic reservoirs and anticipate AMR trends in pathogenic Neisseria.
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14
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de Block T, González N, Abdellati S, Laumen JGE, Van Dijck C, De Baetselier I, Van den Bossche D, Manoharan-Basil SS, Kenyon C. Successful Intra- but Not Inter-species Recombination of msr(D) in Neisseria subflava. Front Microbiol 2022; 13:855482. [PMID: 35432273 PMCID: PMC9007320 DOI: 10.3389/fmicb.2022.855482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/02/2022] [Indexed: 11/23/2022] Open
Abstract
Resistance acquisition via natural transformation is a common process in the Neisseria genus. Transformation has played an important role in the emergence of resistance to many antimicrobials in Neisseria gonorrhoeae and Neisseria meningitidis. In a previous study, we found that currently circulating isolates of Neisseria subflava had acquired an msr(D) gene that has been found to result in macrolide resistance in other bacteria but never found in Neisseria species before. To determine if this resistance mechanism is transferable among Neisseria species, we assessed if we could transform the msr(D) gene into other commensal and pathogenic Neisseria under low dose azithromycin pressure. Intraspecies recombination in commensal N. subflava was confirmed with PCR and resulted in high-level macrolide resistance. Whole-genome sequencing of these transformed strains identified the complete uptake of the msr(D) integration fragment. Sequence analysis showed that a large fragment of DNA (5 and 12 kb) was transferred through a single horizontal gene transfer event. Furthermore, uptake of the msr(D) gene had no apparent fitness cost. Interspecies transformation of msr(D) from N. subflava to N. gonorrhoeae was, however, not successful.
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Affiliation(s)
- Tessa de Block
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Natalia González
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Saïd Abdellati
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Jolein Gyonne Elise Laumen
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Christophe Van Dijck
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Irith De Baetselier
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | | | - Chris Kenyon
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Department of Medicine, University of Cape Town, Cape Town, South Africa
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15
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Vanbaelen T, Van Dijck C, Laumen J, Gonzalez N, De Baetselier I, Manoharan-Basil SS, De Block T, Kenyon C. Global epidemiology of antimicrobial resistance in commensal Neisseria species: A systematic review. Int J Med Microbiol 2022; 312:151551. [DOI: 10.1016/j.ijmm.2022.151551] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 01/19/2022] [Accepted: 02/21/2022] [Indexed: 11/16/2022] Open
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16
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Neisseria mucosa Does Not Inhibit the Growth of Neisseria gonorrhoeae. SCI 2022. [DOI: 10.3390/sci4010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Antibiotic-sparing treatments are required to prevent the further emergence of antimicrobial resistance in Neisseria gonorrhoeae. Commensal Neisseria species have previously been found to inhibit the growth of pathogenic Neisseria species. For example, a previous study found that three out of five historical isolates of Neisseria mucosa could inhibit the growth of N. gonorrhoeae. In this study, we used agar overlay assays to assess if 24 circulating and historical isolates of Neisseria mucosa could inhibit the growth of 28 circulating and historical isolates of N. gonorrhoeae. Although pitting around each colony of N. mucosa created an optical illusion of decreased growth of N. gonorrhoeae, we found no evidence of inhibition (n = 24). In contrast, positive controls of Streptococcus pneumoniae and Escherichia coli demonstrated a strong inhibitory effect against the growth of N. gonorrhoeae.
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17
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Raisman JC, Fiore MA, Tomin L, Adjei JKO, Aswad VX, Chu J, Domondon CJ, Donahue BA, Masciotti CA, McGrath CG, Melita J, Podbielski PA, Schreiner MR, Trumpore LJ, Wengert PC, Wrightstone EA, Hudson AO, Wadsworth CB. Evolutionary paths to macrolide resistance in a Neisseria commensal converge on ribosomal genes through short sequence duplications. PLoS One 2022; 17:e0262370. [PMID: 35025928 PMCID: PMC8758062 DOI: 10.1371/journal.pone.0262370] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/22/2021] [Indexed: 11/19/2022] Open
Abstract
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.
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Affiliation(s)
- Jordan C. Raisman
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Michael A. Fiore
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Lucille Tomin
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Joseph K. O. Adjei
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Virginia X. Aswad
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Jonathan Chu
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Christina J. Domondon
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Ben A. Donahue
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Claudia A. Masciotti
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Connor G. McGrath
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Jo Melita
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Paul A. Podbielski
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Madelyn R. Schreiner
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Lauren J. Trumpore
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Peter C. Wengert
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Emalee A. Wrightstone
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - André O. Hudson
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Crista B. Wadsworth
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
- * E-mail:
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18
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Laumen JGE, Van Dijck C, Abdellati S, De Baetselier I, Serrano G, Manoharan-Basil SS, Bottieau E, Martiny D, Kenyon C. Antimicrobial susceptibility of commensal Neisseria in a general population and men who have sex with men in Belgium. Sci Rep 2022; 12:9. [PMID: 34997050 PMCID: PMC8741786 DOI: 10.1038/s41598-021-03995-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/08/2021] [Indexed: 12/03/2022] Open
Abstract
Non-pathogenic Neisseria are a reservoir of antimicrobial resistance genes for pathogenic Neisseria meningitidis and Neisseria gonorrhoeae. Men who have sex with men (MSM) are at risk of co-colonization with resistant non-pathogenic and pathogenic Neisseria. We assessed if the antimicrobial susceptibility of non-pathogenic Neisseria among MSM differs from a general population and if antimicrobial exposure impacts susceptibility. We recruited 96 participants at our center in Belgium: 32 employees, 32 MSM who did not use antibiotics in the previous 6 months, and 32 MSM who did. Oropharyngeal Neisseria were cultured and identified with MALDI-TOF–MS. Minimum inhibitory concentrations for azithromycin, ceftriaxone and ciprofloxacin were determined using E-tests® and compared between groups with non-parametric tests. Non-pathogenic Neisseria from employees as well as MSM were remarkably resistant. Those from MSM were significantly less susceptible than employees to azithromycin and ciprofloxacin (p < 0.0001, p < 0.001), but not ceftriaxone (p = 0.3). Susceptibility did not differ significantly according to recent antimicrobial exposure in MSM. Surveilling antimicrobial susceptibility of non-pathogenic Neisseria may be a sensitive way to assess impact of antimicrobial exposure in a population. The high levels of antimicrobial resistance in this survey indicate that novel resistance determinants may be readily available for future transfer from non-pathogenic to pathogenic Neisseria.
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Affiliation(s)
- Jolein Gyonne Elise Laumen
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000, Antwerp, Belgium.,Laboratory of Medical Microbiology, University of Antwerp, Wilrijk, Belgium
| | - Christophe Van Dijck
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000, Antwerp, Belgium.,Laboratory of Medical Microbiology, University of Antwerp, Wilrijk, Belgium
| | - Saïd Abdellati
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000, Antwerp, Belgium
| | - Irith De Baetselier
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000, Antwerp, Belgium
| | - Gabriela Serrano
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles, Pôle Hospitalier Universitaire de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Emmanuel Bottieau
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000, Antwerp, Belgium
| | - Delphine Martiny
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles, Pôle Hospitalier Universitaire de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium.,Faculté de Médecine et Pharmacie, Université de Mons, Mons, Belgium
| | - Chris Kenyon
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000, Antwerp, Belgium. .,Department of Medicine, University of Cape Town, Cape Town, South Africa.
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19
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Zhang Q, Liu X, Liu H, Zhang B, Yang H, Mi K, Guddat LW, Rao Z. Conformational Changes in a Macrolide Antibiotic Binding Protein From Mycobacterium smegmatis Upon ADP Binding. Front Microbiol 2021; 12:780954. [PMID: 34956144 PMCID: PMC8696161 DOI: 10.3389/fmicb.2021.780954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Rv3197 (MABP-1), a non-canonical ABC protein in Mycobacterium tuberculosis, has ATPase activity and confers inducible resistance to the macrolide family of antibiotics. Here we have shown that MSMEG_1954, the homolog of Rv3197 in M. smegmatis, has a similar function of conferring macrolide resistance. Crystal structures of apo-MSMEG_1954 (form1 and form 2) and MSMEG_1954 in complex with ADP have been determined. These three structures show that MSMEG_1954 has at least two different conformations we identify as closed state (MSMEG_1954-form 1) and open state (MSMEG_1954-form 2 and MSMEG_1954-ADP). Structural superimposition shows that the MSMEG_1954-form 2 and MSMEG_1954-ADP complex have similar conformation to that observed for MABP-1 and MABP-1-erythromicin complex structure. However, the antibiotic binding pocket in MSMEG_1954-form 1 is completely blocked by the N-terminal accessory domain. When bound by ADP, the N-terminal accessory domain undergoes conformational change, which results in the open of the antibiotic binding pocket. Because of the degradation of N terminal accessory domain in MSMSG_1954-form 2, it is likely to represent a transitional state between MSMEG_1954-form 1 and MSMEG_1954-ADP complex structure.
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Affiliation(s)
- Qingqing Zhang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China.,Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China
| | - Xiang Liu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Huijuan Liu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Bingjie Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China
| | - Kaixia Mi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China.,Shanghai Institute for Advanced Immunochemical Studies and School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,Laboratory of Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China
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20
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Singh R, Kusalik A, Dillon JAR. Bioinformatics tools used for whole-genome sequencing analysis of Neisseria gonorrhoeae: a literature review. Brief Funct Genomics 2021; 21:78-89. [PMID: 34170311 DOI: 10.1093/bfgp/elab028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 01/02/2023] Open
Abstract
Whole-genome sequencing (WGS) data are well established for the investigation of gonococcal transmission, antimicrobial resistance prediction, population structure determination and population dynamics. A variety of bioinformatics tools, repositories, services and platforms have been applied to manage and analyze Neisseria gonorrhoeae WGS datasets. This review provides an overview of the various bioinformatics approaches and resources used in 105 published studies (as of 30 April 2021). The challenges in the analysis of N. gonorrhoeae WGS datasets, as well as future bioinformatics requirements, are also discussed.
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Affiliation(s)
- Reema Singh
- Department of Biochemistry, Microbiology and Immunology
| | - Anthony Kusalik
- Department of Computer Science at the University of Saskatchewan
| | - Jo-Anne R Dillon
- Department of Biochemistry Microbiology and Immunology, College of Medicine, c/o Vaccine and Infectious Disease Organization, University of Saskatchewan, 120 Veterinary Road, Saskatoon, Saskatchewan S7N5E3, Canada
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21
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Kenyon C, Laumen J, Manoharan-Basil S. Choosing New Therapies for Gonorrhoea: We Need to Consider the Impact on the Pan- Neisseria Genome. A Viewpoint. Antibiotics (Basel) 2021; 10:515. [PMID: 34062856 PMCID: PMC8147325 DOI: 10.3390/antibiotics10050515] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/27/2021] [Accepted: 04/27/2021] [Indexed: 11/16/2022] Open
Abstract
The development of new gonorrhoea treatment guidelines typically considers the resistance-inducing effect of the treatment only on Neisseria gonorrhoeae. Antimicrobial resistance in N. gonorrhoeae has, however, frequently first emerged in commensal Neisseria species and then been passed on to N. gonorrhoeae via transformation. This creates the rationale for considering the effect of gonococcal therapies on resistance in commensal Neisseria. We illustrate the benefits of this pan-Neisseria strategy by evaluating three contemporary treatment options for N. gonorrhoeae-ceftriaxone plus azithromycin, monotherapy with ceftriaxone and zoliflodacin.
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Affiliation(s)
- Chris Kenyon
- HIV/STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (J.L.); (S.M.-B.)
- Division of Infectious Diseases and HIV Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town 7701, South Africa
- STI Reference Center, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Jolein Laumen
- HIV/STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (J.L.); (S.M.-B.)
| | - Sheeba Manoharan-Basil
- HIV/STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (J.L.); (S.M.-B.)
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