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Cadenas-Jiménez I, Saiz-Escobedo L, Carrera-Salinas A, Camprubí-Márquez X, Calvo-Silveria S, Camps-Massa P, Berbel D, Tubau F, Santos S, Domínguez MA, González-Díaz A, Ardanuy C, Martí S. Molecular characterization of macrolide resistance in Haemophilus influenzae and Haemophilus parainfluenzae strains (2018-21). J Antimicrob Chemother 2024; 79:2194-2203. [PMID: 38946313 DOI: 10.1093/jac/dkae214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 06/07/2024] [Indexed: 07/02/2024] Open
Abstract
OBJECTIVES This study aimed to explore the prevalence of macrolide resistance and the underlying resistance mechanisms in Haemophilus influenzae (n = 2556) and Haemophilus parainfluenzae (n = 510) collected between 2018 and 2021 from Bellvitge University Hospital, Spain. METHODS Antimicrobial susceptibility was tested by microdilution. Whole-genome sequencing was performed using Illumina MiSeq and Oxford Nanopore technologies, and sequences were examined for macrolide resistance determinants and mobile genetic structures. RESULTS Macrolide resistance was detected in 67 H. influenzae (2.6%) and 52 (10.2%) H. parainfluenzae strains and associated with resistance to other antimicrobials (co-trimoxazole, chloramphenicol, tetracycline). Differences in macrolide resistance existed between the two species. Acquired resistance genes were more prevalent in H. parainfluenzae (35/52; 67.3%) than in H. influenzae (12/67; 17.9%). Gene mutations and amino acid substitutions were more common in H. influenzae (57/67; 85%) than in H. parainfluenzae (16/52; 30.8%). Substitutions in L22 and in 23S rRNA were only detected in H. influenzae (34.3% and 29.0%, respectively), while substitutions in L4 and AcrAB/AcrR were observed in both species. The MEGA element was identified in 35 (67.3%) H. parainfluenzae strains, five located in an integrative and conjugative element (ICE); by contrast, 11 (16.4%) H. influenzae strains contained the MEGA element (all in an ICE). A new ICEHpaHUB8 was described in H. parainfluenzae. CONCLUSIONS Macrolide resistance was higher in H. parainfluenzae than in H. influenzae, with differences in the underlying mechanisms. H. parainfluenzae exhibits co-resistance to other antimicrobials, often leading to an extensively drug-resistant phenotype. This highlights the importance of conducting antimicrobial resistance surveillance.
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Affiliation(s)
- Irene Cadenas-Jiménez
- Microbiology Department, Hospital Universitari Bellvitge, IDIBELL-UB, Feixa Llarga s/n, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
| | - Lucía Saiz-Escobedo
- Microbiology Department, Hospital Universitari Bellvitge, IDIBELL-UB, Feixa Llarga s/n, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Anna Carrera-Salinas
- Microbiology Department, Hospital Universitari Bellvitge, IDIBELL-UB, Feixa Llarga s/n, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Xenia Camprubí-Márquez
- Microbiology Department, Hospital Universitari Bellvitge, IDIBELL-UB, Feixa Llarga s/n, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Sara Calvo-Silveria
- Microbiology Department, Hospital Universitari Bellvitge, IDIBELL-UB, Feixa Llarga s/n, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
| | - Paula Camps-Massa
- Microbiology Department, Hospital Universitari Bellvitge, IDIBELL-UB, Feixa Llarga s/n, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
- Respiratory Medicine Department, Hospital Universitari Bellvitge, IDIBELL-UB, Barcelona, Spain
| | - Dàmaris Berbel
- Microbiology Department, Hospital Universitari Bellvitge, IDIBELL-UB, Feixa Llarga s/n, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
| | - Fe Tubau
- Microbiology Department, Hospital Universitari Bellvitge, IDIBELL-UB, Feixa Llarga s/n, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
| | - Salud Santos
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
- Respiratory Medicine Department, Hospital Universitari Bellvitge, IDIBELL-UB, Barcelona, Spain
| | - M Angeles Domínguez
- Microbiology Department, Hospital Universitari Bellvitge, IDIBELL-UB, Feixa Llarga s/n, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
- Research Network for Infectious Diseases, CIBERINFEC, ISCIII, Madrid, Spain
| | - Aida González-Díaz
- Microbiology Department, Hospital Universitari Bellvitge, IDIBELL-UB, Feixa Llarga s/n, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
| | - Carmen Ardanuy
- Microbiology Department, Hospital Universitari Bellvitge, IDIBELL-UB, Feixa Llarga s/n, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
| | - Sara Martí
- Microbiology Department, Hospital Universitari Bellvitge, IDIBELL-UB, Feixa Llarga s/n, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
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Caméléna F, Merimèche M, Liberge M, Maubaret C, Donay JL, Taha MK, Fouéré S, Berçot B. Detection of CTX-M-15 ESBL in XDR Haemophilus parainfluenzae from a urethral swab. J Antimicrob Chemother 2024; 79:539-545. [PMID: 38197448 DOI: 10.1093/jac/dkad408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/07/2023] [Indexed: 01/11/2024] Open
Abstract
OBJECTIVES Haemophilus parainfluenzae is an opportunistic pathogen causing respiratory tract infection and sexually transmitted diseases. The emergence of multidrug resistance in this species is particularly worrisome, especially since the recent description of CTX-M-15 ESBL-producing isolates in Spain. The aim of this study was to characterize a CTX-M-15-producing H. parainfluenzae clinical isolate, HP01, obtained from a urethral swab. METHODS MICs were determined with gradient strips for this isolate. Hydrolysis assays were performed with the β LACTA test. Genomic DNA from HP01 was subjected to Illumina and Oxford Nanopore sequencing to investigate the genetic environment of blaCTX-M-15. Phylogenetic analysis was performed with available H. parainfluenzae genomes from the NCBI database, including CTX-M-15 producers. RESULTS HP01, an XDR isolate, was resistant to penicillin, third-generation cephalosporins, fluoroquinolones, macrolides, cyclines and co-trimoxazole and susceptible only to carbapenems and rifampicin. HP01 carried blaTEM-1, blaCTX-M-15, tet(M), catS and mef(E)/mel and harboured amino acid substitutions in PBP3, PBP5, GyrA, ParC and FolA implicated in resistance. Genomic analysis revealed that blaCTX-M-15 was carried by a Tn3-like transposon inserted into a novel integrative and conjugative element (ICE), ICEHpaSLS, present on the chromosome and belonging to the ICEHin1056 family described in Haemophilus influenzae. The tet(M)-MEGA element was also detected on the chromosome. No plasmid was found. The phylogenetic analysis showed that four H. parainfluenzae producing CTX-M-15 clustered in the same clade. CONCLUSIONS Here we report the description of an XDR H. parainfluenzae producing blaCTX-M-15 isolated from a urethral swab. The blaCTX-M-15 gene was inserted into an ICE structure similar to those recently described in CTX-M-15 producers in Spain. The emergence of XDR H. parainfluenzae producing blaCTX-M-15 is a matter of great concern. Careful surveillance is required to prevent its spread.
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Affiliation(s)
- François Caméléna
- Université de Paris Cité, INSERM, IAME, Paris F-75018, France
- Department of Bacteriology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris F-75010, France
- French National Reference Centre for Bacterial STIs, Associated Laboratory for Gonococci, Paris F-75010, France
| | - Manel Merimèche
- Université de Paris Cité, INSERM, IAME, Paris F-75018, France
- Department of Bacteriology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris F-75010, France
- French National Reference Centre for Bacterial STIs, Associated Laboratory for Gonococci, Paris F-75010, France
| | - Mathilde Liberge
- Université de Paris Cité, INSERM, IAME, Paris F-75018, France
- Department of Bacteriology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris F-75010, France
| | - Clara Maubaret
- Université de Paris Cité, INSERM, IAME, Paris F-75018, France
- Department of Bacteriology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris F-75010, France
| | - Jean-Luc Donay
- Department of Bacteriology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris F-75010, France
| | - Muhamed-Kheir Taha
- Invasive Bacterial Infections Unit and National Reference Centre for Haemophilus influenzae, Institut Pasteur, Paris F-75015, France
| | - Sébastien Fouéré
- SFD/GRIDIST and Centre for Genital and Sexually Transmitted Diseases, Assistance Publique-Hôpitaux de Paris, Paris F-75010, France
| | - Béatrice Berçot
- Université de Paris Cité, INSERM, IAME, Paris F-75018, France
- Department of Bacteriology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris F-75010, France
- French National Reference Centre for Bacterial STIs, Associated Laboratory for Gonococci, Paris F-75010, France
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Troth TD, McInnes RS, Dunn SJ, Mirza J, Whittaker AH, Goodchild SA, Loman NJ, Harding SV, van Schaik W. Differences in the gut microbiota between Gurkhas and soldiers of British origin. PLoS One 2023; 18:e0292645. [PMID: 38113233 PMCID: PMC10729956 DOI: 10.1371/journal.pone.0292645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/26/2023] [Indexed: 12/21/2023] Open
Abstract
Previous work indicated that the incidence of travellers' diarrhoea (TD) is higher in soldiers of British origin, when compared to soldiers of Nepalese descent (Gurkhas). We hypothesise that the composition of the gut microbiota may be a contributing factor in the risk of developing TD in soldiers of British origin. This study aimed to characterise the gut microbial composition of Gurkha and non-Gurkha soldiers of the British Army. Recruitment of 38 soldiers (n = 22 Gurkhas, n = 16 non-Gurkhas) and subsequent stool collection, enabled shotgun metagenomic sequencing-based analysis of the gut microbiota. The microbiota of Gurkhas had significantly (P < 0.05) lower diversity, for both Shannon and Simpson diversity indices, using species level markers than the gut microbiota of non-Gurkha soldiers. Non-metric Multidimensional Scaling (NMDS) of the Bray-Curtis distance matrix revealed a significant difference in the composition of the gut microbiota between Gurkhas and non-Gurkha soldiers, at both the species level (P = 0.0178) and the genus level (P = 0.0483). We found three genera and eight species that were significantly enriched in the non-Gurkha group and one genus (Haemophilus) and one species (Haemophilus parainfluenzae) which were enriched in the Gurkha group. The difference in the microbiota composition between Gurkha soldiers and soldiers of British origin may contribute to higher colonization resistance against diarrhoeal pathogens in the former group. Our findings may enable further studies into interventions that modulate the gut microbiota of soldiers to prevent TD during deployment.
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Affiliation(s)
- Thomas D. Troth
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Ross S. McInnes
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Steven J. Dunn
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Jeremy Mirza
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Annalise H. Whittaker
- CBR Division, Defence and Science Technology Laboratory, Salisbury, Wiltshire, United Kingdom
| | - Sarah A. Goodchild
- CBR Division, Defence and Science Technology Laboratory, Salisbury, Wiltshire, United Kingdom
| | - Nicholas J. Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Sarah V. Harding
- CBR Division, Defence and Science Technology Laboratory, Salisbury, Wiltshire, United Kingdom
- School of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| | - Willem van Schaik
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
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Saiz-Escobedo L, Cadenas-Jiménez I, Olmos R, Carrera-Salinas A, Berbel D, Càmara J, Tubau F, Domínguez MA, Ardanuy C, González-Díaz A, Marti S. Detection of bla CTX-M-15 in an integrative and conjugative element in four extensively drug-resistant Haemophilus parainfluenzae strains causing urethritis. Int J Antimicrob Agents 2023; 62:106991. [PMID: 37774891 DOI: 10.1016/j.ijantimicag.2023.106991] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/12/2023] [Accepted: 09/21/2023] [Indexed: 10/01/2023]
Abstract
Haemophilus parainfluenzae is a commensal organism with rising numbers of multidrug-resistant (MDR) strains. This pathogen is of increasing clinical relevance in urogenital infection. The aim of this work was to identify and characterise the molecular mechanisms of resistance associated with four cephalosporin-resistant H. parainfluenzae strains collected from patients with urethritis. Antimicrobial resistance was determined by microdilution following European Committee on Antimicrobial Susceptibility Testing criteria. Strains were then analysed by whole-genome sequencing to determine clonal relationship and the molecular basis of antimicrobial resistance. Finally, a phylogenetic analysis was performed on all urogenital MDR strains of H. parainfluenzae previously isolated in our hospital. All strains were resistant to β-lactams, macrolides, tetracycline, fluoroquinolones, chloramphenicol, cotrimoxazole, and aminoglycosides. The resistance profile was compatible with the presence of an extended-spectrum β-lactamase (ESBL). Whole-genome sequencing detected blaCTX-M-15 that conferred high minimum inhibitory concentrations to cephalosporins in two novel integrative and conjugative elements (ICEHpaHUB6 and ICEHpaHUB7) that also harboured a blaTEM-1 β-lactamase. This study shows a novel blaCTX-M-15 ESBL carried in an integrative conjugative element in four extensively drug-resistant H. parainfluenzae strains. This resistance determinant could be transmitted to other sexually transmitted pathogens and this is a cause for concern.
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Affiliation(s)
- L Saiz-Escobedo
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain
| | - I Cadenas-Jiménez
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain; Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
| | - R Olmos
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain
| | - A Carrera-Salinas
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain
| | - D Berbel
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain; Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
| | - J Càmara
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain; Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
| | - F Tubau
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain; Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
| | - M A Domínguez
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain; Research Network for Infectious Diseases (CIBERINFEC), ISCIII, Madrid, Spain; Department of Pathology and Experimental Therapeutics, School of Medicine, University of Barcelona, Barcelona, Spain
| | - C Ardanuy
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain; Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain; Department of Pathology and Experimental Therapeutics, School of Medicine, University of Barcelona, Barcelona, Spain
| | - A González-Díaz
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain; Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain.
| | - S Marti
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain; Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain; Department of Medicine, School of Medicine, University of Barcelona, Barcelona, Spain.
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Bakó C, Balázs VL, Kerekes E, Kocsis B, Nagy DU, Szabó P, Micalizzi G, Mondello L, Krisch J, Pethő D, Horváth G. Flowering phenophases influence the antibacterial and anti-biofilm effects of Thymus vulgaris L. essential oil. BMC Complement Med Ther 2023; 23:168. [PMID: 37226152 DOI: 10.1186/s12906-023-03966-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/19/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND Essential oils are becoming increasingly popular in medicinal applications because of their antimicrobial effect. Thymus vulgaris L. (Lamiaceae) is a well-known and widely cultivated medicinal plant, which is used as a remedy for cold, cough and gastrointestinal symptoms. Essential oil content of thyme is responsible for its antimicrobial activity, however, it has been reported that the chemical composition of essential oils influences its biological activity. In order to explore flowering phenophases influence on the chemical composition of thyme essential oil and its antibacterial and anti-biofilm activity, plant materials were collected at the beginning of flowering, in full bloom and at the end of flowering periods in 2019. METHODS Essential oils from fresh and dried plant materials were distilled and analyzed with gas chromatography-mass spectrometry (GC-MS) and gas chromatography-flame ionization detection (GC-FID). The antibacterial activity was performed by broth microdilution and thin layer chromatography-direct bioautography (TLC-DB) assays and the anti-biofilm effect by crystal violet assay, respectively. Scanning electron microscopy was applied to illustrate the cellular changes of bacterial cells after essential oil treatment. RESULTS Thymol (52.33-62.46%) was the main component in the thyme essential oils. Thyme oil distilled from fresh plant material and collected at the beginning of flowering period exerted the highest antibacterial and anti-biofilm activity against Haemophilus influenzae, H. parainfluenzae and Pseudomonas aeruginosa. CONCLUSION The different flowering periods of Thymus vulgaris influence the antibacterial and anti-biofilm activity of its essential oils, therefore, the collection time has to be taken into consideration and not only the full bloom, but the beginning of flowering period may provide biological active thyme essential oil.
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Affiliation(s)
- Csongor Bakó
- Department of Pharmacognosy, Faculty of Pharmacy, University of Pécs, Pécs, H-7624, Hungary
| | - Viktória Lilla Balázs
- Department of Pharmacognosy, Faculty of Pharmacy, University of Pécs, Pécs, H-7624, Hungary
| | - Erika Kerekes
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, H-6726, Hungary
| | - Béla Kocsis
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, H-7624, Hungary
| | - Dávid U Nagy
- Institute of Geobotany and Plant Ecology, Martin-Luther University, D-06108, Halle, Germany
| | - Péter Szabó
- Institute of Geography and Earth Sciences, Faculty of Sciences, University of Pécs, Pécs, H-7624, Hungary
| | - Giuseppe Micalizzi
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, 98168, Italy
| | - Luigi Mondello
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, 98168, Italy
- Chromaleont s.r.l., c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, 98168, Italy
- Unit of Food Science and Nutrition, Department of Medicine, University Campus Bio-Medico of Rome, Rome, 00128, Italy
| | - Judit Krisch
- Department of Food Engineering, Faculty of Engineering, University of Szeged, Szeged, H-6724, Hungary
| | - Dóra Pethő
- Department of MOL Hydrocarbon and Coal Processing, University of Pannonia, Veszprém, H-8200, Hungary
| | - Györgyi Horváth
- Department of Pharmacognosy, Faculty of Pharmacy, University of Pécs, Pécs, H-7624, Hungary.
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Carrera-Salinas A, González-Díaz A, Ehrlich RL, Berbel D, Tubau F, Pomares X, Garmendia J, Domínguez MÁ, Ardanuy C, Huertas D, Marín A, Montón C, Mell JC, Santos S, Marti S. Genetic Adaptation and Acquisition of Macrolide Resistance in Haemophilus spp. during Persistent Respiratory Tract Colonization in Chronic Obstructive Pulmonary Disease (COPD) Patients Receiving Long-Term Azithromycin Treatment. Microbiol Spectr 2023; 11:e0386022. [PMID: 36475849 PMCID: PMC9927455 DOI: 10.1128/spectrum.03860-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Patients with chronic obstructive pulmonary disease (COPD) benefit from the immunomodulatory effect of azithromycin, but long-term administration may alter colonizing bacteria. Our goal was to identify changes in Haemophilus influenzae and Haemophilus parainfluenzae during azithromycin treatment. Fifteen patients were followed while receiving prolonged azithromycin treatment (Hospital Universitari de Bellvitge, Spain). Four patients (P02, P08, P11, and P13) were persistently colonized by H. influenzae for at least 3 months and two (P04 and P11) by H. parainfluenzae. Isolates from these patients (53 H. influenzae and 18 H. parainfluenzae) were included to identify, by whole-genome sequencing, antimicrobial resistance changes and genetic variation accumulated during persistent colonization. All persistent lineages isolated before treatment were azithromycin-susceptible but developed resistance within the first months, apart from those belonging to P02, who discontinued the treatment. H. influenzae isolates from P08-ST107 acquired mutations in 23S rRNA, and those from P11-ST2480 and P13-ST165 had changes in L4 and L22. In H. parainfluenzae, P04 persistent isolates acquired changes in rlmC, and P11 carried genes encoding MefE/MsrD efflux pumps in an integrative conjugative element, which was also identified in H. influenzae P11-ST147. Other genetic variation occurred in genes associated with cell wall and inorganic ion metabolism. Persistent H. influenzae strains all showed changes in licA and hgpB genes. Other genes (lex1, lic3A, hgpC, and fadL) had variation in multiple lineages. Furthermore, persistent strains showed loss, acquisition, or genetic changes in prophage-associated regions. Long-term azithromycin therapy results in macrolide resistance, as well as genetic changes that likely favor bacterial adaptation during persistent respiratory colonization. IMPORTANCE The immunomodulatory properties of azithromycin reduce the frequency of exacerbations and improve the quality of life of COPD patients. However, long-term administration may alter the respiratory microbiota, such as Haemophilus influenzae, an opportunistic respiratory colonizing bacteria that play an important role in exacerbations. This study contributes to a better understanding of COPD progression by characterizing the clinical evolution of H. influenzae in a cohort of patients with prolonged azithromycin treatment. The emergence of macrolide resistance during the first months, combined with the role of Haemophilus parainfluenzae as a reservoir and source of resistance dissemination, is a cause for concern that may lead to therapeutic failure. Furthermore, genetic variations in cell wall and inorganic ion metabolism coding genes likely favor bacterial adaptation to host selective pressures. Therefore, the bacterial pathoadaptive evolution in these severe COPD patients raise our awareness of the possible spread of macrolide resistance and selection of host-adapted clones.
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Affiliation(s)
- Anna Carrera-Salinas
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain
| | - Aida González-Díaz
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
| | - Rachel L. Ehrlich
- Department of Microbiology and Immunology, Center for Genomic Sciences, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Dàmaris Berbel
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
| | - Fe Tubau
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
| | - Xavier Pomares
- Department of Respiratory Medicine, Hospital de Sabadell, Hospital Universitari Parc Taulí, Institut d’Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Junkal Garmendia
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
- Instituto de Agrobiotecnología, CSIC-Gobierno de Navarra, Mutilva, Spain
| | - M. Ángeles Domínguez
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain
- Research Network for Infectious Diseases (CIBERINFEC), ISCIII, Madrid, Spain
- Department of Pathology and Experimental Therapeutics, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Carmen Ardanuy
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
- Department of Pathology and Experimental Therapeutics, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Daniel Huertas
- Department of Respiratory Medicine, Hospital Residència Sant Camil, Consorci Sanitari Alt Penedès-Garraf, Barcelona, Spain
| | - Alicia Marín
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
- Department of Respiratory Medicine, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - Conchita Montón
- Department of Respiratory Medicine, Hospital de Sabadell, Hospital Universitari Parc Taulí, Institut d’Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Joshua Chang Mell
- Department of Microbiology and Immunology, Center for Genomic Sciences, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Salud Santos
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
- Department of Respiratory Medicine, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain
- Department of Medicine, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Sara Marti
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
- Department of Medicine, School of Medicine, University of Barcelona, Barcelona, Spain
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Arregui Garcia I, Portillo Bordonabe ME, Gil Setas A, Ezpeleta Baquedano C. Emergence of multidrug-resistant Haemophilus parainfluenzae in genital specimens: Importance of culture and antimicrobial susceptibility surveillance. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2022; 41:255-256. [PMID: 36588028 DOI: 10.1016/j.eimce.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/27/2022] [Accepted: 07/19/2022] [Indexed: 12/31/2022]
Affiliation(s)
- Irati Arregui Garcia
- Servicio de Microbiología Clínica, Hospital Universitario de Navarra, Pamplona, Spain.
| | - M Eugenia Portillo Bordonabe
- Servicio de Microbiología Clínica, Hospital Universitario de Navarra, Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdisNA), Pamplona, Spain
| | - Alberto Gil Setas
- Servicio de Microbiología Clínica, Hospital Universitario de Navarra, Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdisNA), Pamplona, Spain
| | - Carmen Ezpeleta Baquedano
- Servicio de Microbiología Clínica, Hospital Universitario de Navarra, Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdisNA), Pamplona, Spain
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Emergencia de Haemophilus parainfluenzae multirresistente en muestras genitales: importancia del cultivo y vigilancia de sensibilidad antimicrobiana. Enferm Infecc Microbiol Clin 2022. [DOI: 10.1016/j.eimc.2022.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Johannessen H, Anthonisen IL, Zecic N, Hegstad K, Ranheim TE, Skaare D. Characterization and Fitness Cost of Tn7100, a Novel Integrative and Conjugative Element Conferring Multidrug Resistance in Haemophilus influenzae. Front Microbiol 2022; 13:945411. [PMID: 35935209 PMCID: PMC9355037 DOI: 10.3389/fmicb.2022.945411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/16/2022] [Indexed: 12/15/2022] Open
Abstract
A multidrug-resistant (MDR) strain of Haemophilus influenzae, Hi-228, with phenotypic resistance toward ampicillin, cefotaxime, chloramphenicol, gentamicin, and azithromycin, was isolated in Oslo, Norway. The strain was part of a clonal outbreak (2016–2017) comprising five ST143 strains with identical resistotypes. Hi-228 carries a novel integrative and conjugative element (ICE), Tn7100, contributing to this remarkable and previously unreported MDR profile. Tn7100 contains the following resistance genes: blaTEM−1B, catA2, aac(6′)-Im, aph(2″)-Ib, mef (E), and mel. The latter four are previously unreported or rarely reported in H. influenzae. In this study, we investigated the genetic environment, mechanisms of transfer, impact on phenotypic susceptibility, and fitness cost of this ICE. We found that Tn7100 has an overall structure similar to the previously described ICE Tn6686, with blaTEM−1B and catA2 carried by Tn3 and Tn10, respectively. The major difference between Tn7100 and Tn6686 is that Tn7100 lacks tet(B) but carries the resistance gene pairs aac(6′)-Im and aph(2″)-Ib and mef (E) and mel. The gene pairs are located on the novel transposable elements Tn7470 and Tn7471, which have high sequence identities to a plasmid in Enterobacterales and an ICE in streptococcal species, respectively. Tn7100 does circularize and is transferable, however, at a low frequency. Head-to-head competition experiments showed that uptake of Tn7100 reduces bacterial fitness. Our study shows that MDR strains are capable of clonal spread and that the H. influenzae supragenome comprises an increasingly wide range of transferable resistance genes, with evidence of transfer from unrelated genera. The findings offer a glimpse into the genome dynamics of H. influenzae, highlighting the importance of rational antibiotic usage to contain antimicrobial resistance and the emergence of MDR strains in this important pathogen.
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Affiliation(s)
- Helene Johannessen
- Department of Microbiology, Vestfold Hospital Trust, Tønsberg, Norway
- *Correspondence: Helene Johannessen
| | | | - Nermin Zecic
- Department of Microbiology, Vestfold Hospital Trust, Tønsberg, Norway
| | - Kristin Hegstad
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | | | - Dagfinn Skaare
- Department of Microbiology, Vestfold Hospital Trust, Tønsberg, Norway
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Diricks M, Kohl TA, Käding N, Leshchinskiy V, Hauswaldt S, Jiménez Vázquez O, Utpatel C, Niemann S, Rupp J, Merker M. Whole genome sequencing-based classification of human-related Haemophilus species and detection of antimicrobial resistance genes. Genome Med 2022; 14:13. [PMID: 35139905 PMCID: PMC8830169 DOI: 10.1186/s13073-022-01017-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 01/24/2022] [Indexed: 12/31/2022] Open
Abstract
Background Bacteria belonging to the genus Haemophilus cause a wide range of diseases in humans. Recently, H. influenzae was classified by the WHO as priority pathogen due to the wide spread of ampicillin resistant strains. However, other Haemophilus spp. are often misclassified as H. influenzae. Therefore, we established an accurate and rapid whole genome sequencing (WGS) based classification and serotyping algorithm and combined it with the detection of resistance genes. Methods A gene presence/absence-based classification algorithm was developed, which employs the open-source gene-detection tool SRST2 and a new classification database comprising 36 genes, including capsule loci for serotyping. These genes were identified using a comparative genome analysis of 215 strains belonging to ten human-related Haemophilus (sub)species (training dataset). The algorithm was evaluated on 1329 public short read datasets (evaluation dataset) and used to reclassify 262 clinical Haemophilus spp. isolates from 250 patients (German cohort). In addition, the presence of antibiotic resistance genes within the German dataset was evaluated with SRST2 and correlated with results of traditional phenotyping assays. Results The newly developed algorithm can differentiate between clinically relevant Haemophilus species including, but not limited to, H. influenzae, H. haemolyticus, and H. parainfluenzae. It can also identify putative haemin-independent H. haemolyticus strains and determine the serotype of typeable Haemophilus strains. The algorithm performed excellently in the evaluation dataset (99.6% concordance with reported species classification and 99.5% with reported serotype) and revealed several misclassifications. Additionally, 83 out of 262 (31.7%) suspected H. influenzae strains from the German cohort were in fact H. haemolyticus strains, some of which associated with mouth abscesses and lower respiratory tract infections. Resistance genes were detected in 16 out of 262 datasets from the German cohort. Prediction of ampicillin resistance, associated with blaTEM-1D, and tetracycline resistance, associated with tetB, correlated well with available phenotypic data. Conclusions Our new classification database and algorithm have the potential to improve diagnosis and surveillance of Haemophilus spp. and can easily be coupled with other public genotyping and antimicrobial resistance databases. Our data also point towards a possible pathogenic role of H. haemolyticus strains, which needs to be further investigated. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01017-x.
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Affiliation(s)
- Margo Diricks
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Nadja Käding
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany.,German Center for Infection Research (DZIF), TTU HAARBI, Lübeck, Germany
| | - Vladislav Leshchinskiy
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Susanne Hauswaldt
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Omar Jiménez Vázquez
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany.,German Center for Infection Research (DZIF), TTU HAARBI, Lübeck, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany. .,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany. .,Evolution of the Resistome, Research Center Borstel, Borstel, Germany.
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