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Morsli M, Salipante F, Magnan C, Dunyach-Remy C, Sotto A, Lavigne JP. Direct metagenomics investigation of non-surgical hard-to-heal wounds: a review. Ann Clin Microbiol Antimicrob 2024; 23:39. [PMID: 38702796 PMCID: PMC11069288 DOI: 10.1186/s12941-024-00698-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 04/22/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Non-surgical chronic wounds, including diabetes-related foot diseases (DRFD), pressure injuries (PIs) and venous leg ulcers (VLU), are common hard-to-heal wounds. Wound evolution partly depends on microbial colonisation or infection, which is often confused by clinicians, thereby hampering proper management. Current routine microbiology investigation of these wounds is based on in vitro culture, focusing only on a limited panel of the most frequently isolated bacteria, leaving a large part of the wound microbiome undocumented. METHODS A literature search was conducted on original studies published through October 2022 reporting metagenomic next generation sequencing (mNGS) of chronic wound samples. Studies were eligible for inclusion if they applied 16 S rRNA metagenomics or shotgun metagenomics for microbiome analysis or diagnosis. Case reports, prospective, or retrospective studies were included. However, review articles, animal studies, in vitro model optimisation, benchmarking, treatment optimisation studies, and non-clinical studies were excluded. Articles were identified in PubMed, Google Scholar, Web of Science, Microsoft Academic, Crossref and Semantic Scholar databases. RESULTS Of the 3,202 articles found in the initial search, 2,336 articles were removed after deduplication and 834 articles following title and abstract screening. A further 14 were removed after full text reading, with 18 articles finally included. Data were provided for 3,628 patients, including 1,535 DRFDs, 956 VLUs, and 791 PIs, with 164 microbial genera and 116 species identified using mNGS approaches. A high microbial diversity was observed depending on the geographical location and wound evolution. Clinically infected wounds were the most diverse, possibly due to a widespread colonisation by pathogenic bacteria from body and environmental microbiota. mNGS data identified the presence of virus (EBV) and fungi (Candida and Aspergillus species), as well as Staphylococcus and Pseudomonas bacteriophages. CONCLUSION This study highlighted the benefit of mNGS for time-effective pathogen genome detection. Despite the majority of the included studies investigating only 16 S rDNA, ignoring a part of viral, fungal and parasite colonisation, mNGS detected a large number of bacteria through the included studies. Such technology could be implemented in routine microbiology for hard-to-heal wound microbiota investigation and post-treatment wound colonisation surveillance.
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Affiliation(s)
- Madjid Morsli
- Department of Microbiology and Hospital Hygiene, VBIC, INSERM U1047, Univ Montpellier, Platform MICRO&BIO, CHU Nîmes, Nîmes, France
| | - Florian Salipante
- Department of Biostatistics, Clinical Epidemiology, Public Health, and Innovation in Methodology (BESPIM), CHU Nîmes, Nîmes, France
| | - Chloé Magnan
- Department of Microbiology and Hospital Hygiene, VBIC, INSERM U1047, Univ Montpellier, Platform MICRO&BIO, CHU Nîmes, Nîmes, France
| | - Catherine Dunyach-Remy
- Department of Microbiology and Hospital Hygiene, VBIC, INSERM U1047, Univ Montpellier, Platform MICRO&BIO, CHU Nîmes, Nîmes, France
| | - Albert Sotto
- Department of Infectious Diseases, VBIC, INSERM U1047, Univ Montpellier, CHU Nîmes, Nîmes, France
| | - Jean-Philippe Lavigne
- Department of Microbiology and Hospital Hygiene, VBIC, INSERM U1047, Univ Montpellier, Platform MICRO&BIO, CHU Nîmes, Nîmes, France.
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Pilliol V, Morsli M, Terlier L, Hassani Y, Malat I, Guindo CO, Davoust B, Lamglait B, Drancourt M, Aboudharam G, Grine G, Terrer E. Candidatus Methanosphaera massiliense sp. nov., a methanogenic archaeal species found in a human fecal sample and prevalent in pigs and red kangaroos. Microbiol Spectr 2024; 12:e0514122. [PMID: 38189277 PMCID: PMC10845953 DOI: 10.1128/spectrum.05141-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 11/24/2023] [Indexed: 01/09/2024] Open
Abstract
Methanosphaera stadtmanae was the sole Methanosphaera representative to be cultured and detected by molecular methods in the human gut microbiota, further associated with digestive and respiratory diseases, leaving unknown the actual diversity of human-associated Methanosphaera species. Here, a novel Methanosphaera species, Candidatus Methanosphaera massiliense (Ca. M. massiliense) sp. nov. was isolated by culture using a hydrogen- and carbon dioxide-free medium from one human feces sample. Ca. M. massiliense is a non-motile, 850 nm Gram-positive coccus autofluorescent at 420 nm. Whole-genome sequencing yielded a 29.7% GC content, gapless 1,785,773 bp genome sequence with an 84.5% coding ratio, encoding for alcohol and aldehyde dehydrogenases promoting the growth of Ca. M. massiliense without hydrogen. Screening additional mammal and human feces using a specific genome sequence-derived DNA-polymerase RT-PCR system yielded a prevalence of 22% in pigs, 12% in red kangaroos, and no detection in 149 other human samples. This study, extending the diversity of Methanosphaera in human microbiota, questions the zoonotic sources of Ca. M. massiliense and possible transfer between hosts.IMPORTANCEMethanogens are constant inhabitants in the human gut microbiota in which Methanosphaera stadtmanae was the only cultivated Methanosphaera representative. We grew Candidatus Methanosphaera massiliense sp. nov. from one human feces sample in a novel culture medium under a nitrogen atmosphere. Systematic research for methanogens in human and animal fecal samples detected Ca. M. massiliense in pig and red kangaroo feces, raising the possibility of its zoonotic acquisition. Host specificity, source of acquisition, and adaptation of methanogens should be further investigated.
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Affiliation(s)
- Virginie Pilliol
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Ecole de Médecine Dentaire, Marseille, France
| | - Madjid Morsli
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Laureline Terlier
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Yasmine Hassani
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Ihab Malat
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Cheick Oumar Guindo
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Bernard Davoust
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | | | - Michel Drancourt
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Gérard Aboudharam
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Ecole de Médecine Dentaire, Marseille, France
| | | | - Elodie Terrer
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
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Morsli M, Salipante F, Gelis A, Magnan C, Guigon G, Lavigne J, Sotto A, Dunyach‐Remy C. Evolution of the urinary microbiota in spinal cord injury patients with decubitus ulcer: A snapshot study. Int Wound J 2024; 21:e14626. [PMID: 38272816 PMCID: PMC10805533 DOI: 10.1111/iwj.14626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
Current microbiome investigations of patients with pressure ulcers (PU) are mainly based on wound swabs and/or biopsy sequencing, leaving the colonization scenario unclear. Urinary microbiota has been never studied. As a part of the prospective ESCAFLOR study, we studied urinary microbiota of spinal cord injury (SCI) patients with PU without any urinary tract infection at the inclusion, collected at two times (at admission [D0] and after 28 days [D28]) during the patient's care, investigated by 16S rDNA metagenomics next generation sequencing. Subgroup analyses were carried out between patients with wounds showing improved evolution versus stagnated/worsened wounds at D28. Analysis was done using EPISEQ® 16S and R software. Among the 12 studied patients, the urinary microbiota of patients with improved wound evolution at D28 (n = 6) presented a significant decrease of microbial diversity. This modification was associated with the presence of Proteobacteria phylum and an increase of Escherichia-Shigella (p = 0.005), as well as the presence of probiotic anaerobic bacteria Lactobacillus and Bifidobacterium. In contrast, Proteus abundance was significantly increased in urine of patients with stagnated/worsened wound evolution (n = 6) (p = 0.003). This study proposes urinary microbiota as a complementary factor indirectly associated with the wound evolution and patient cure. It opens new perspectives for further investigations based on multiple body microbiome comparison to describe the complete scenario of the transmission dynamics of wound-colonizing microorganisms.
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Affiliation(s)
- Madjid Morsli
- Department of Microbiology and Hospital HygieneCHU Nîmes, Univ MontpellierNîmesFrance
| | - Florian Salipante
- Department of Biostatistics, Epidemiology, Public Health, and Innovation in Methodology (BESPIM)CHU Nîmes, Univ MontpellierNîmesFrance
| | - Anthony Gelis
- Centre Mutualiste Neurologique ProparaMontpellierFrance
| | - Chloé Magnan
- VBIC, INSERM U1047, Department of Microbiology and Hospital HygieneCHU Nîmes, Univ MontpellierNîmesFrance
| | | | - Jean‐Philippe Lavigne
- VBIC, INSERM U1047, Department of Microbiology and Hospital HygieneCHU Nîmes, Univ MontpellierNîmesFrance
| | - Albert Sotto
- VBIC, INSERM U1047, Department of Infectious and Tropical DiseasesCHU Nîmes, Univ MontpellierNîmesFrance
| | - Catherine Dunyach‐Remy
- VBIC, INSERM U1047, Department of Microbiology and Hospital HygieneCHU Nîmes, Univ MontpellierNîmesFrance
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Plumet L, Morsli M, Ahmad-Mansour N, Clavijo-Coppens F, Berry L, Sotto A, Lavigne JP, Costechareyre D, Molle V. Isolation and Characterization of New Bacteriophages against Staphylococcal Clinical Isolates from Diabetic Foot Ulcers. Viruses 2023; 15:2287. [PMID: 38140529 PMCID: PMC10747802 DOI: 10.3390/v15122287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/09/2023] [Accepted: 11/19/2023] [Indexed: 12/24/2023] Open
Abstract
Staphylococcus sp. is the most common bacterial genus in infections related to diabetic foot ulcers (DFUs). The emergence of multidrug-resistant bacteria places a serious burden on public health systems. Phage therapy is an alternative treatment to antibiotics, overcoming the issue of antibiotic resistance. In this study, six phages (SAVM01 to SAVM06) were isolated from effluents and were used against a panel of staphylococcal clinical samples isolated from DFUs. A genomic analysis revealed that the phages belonged to the Herelleviridae family, with sequences similar to those of the Kayvirus genus. No lysogeny-associated genes, known virulence or drug resistance genes were identified in the phage genomes. The phages displayed a strong lytic and antibiofilm activity against DFU clinical isolates, as well as against opportunistic pathogenic coagulase-negative staphylococci. The results presented here suggest that these phages could be effective biocontrol agents against staphylococcal clinical isolates from DFUs.
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Affiliation(s)
- Lucile Plumet
- VBIC, INSERM U1047, University of Montpellier, 34095 Montpellier, France; (L.P.); (N.A.-M.)
| | - Madjid Morsli
- VBIC, INSERM U1047, Department of Microbiology and Hospital Hygiene, University of Montpellier, CHU Nîmes, 30908 Nîmes, France; (M.M.); (J.-P.L.)
| | - Nour Ahmad-Mansour
- VBIC, INSERM U1047, University of Montpellier, 34095 Montpellier, France; (L.P.); (N.A.-M.)
| | | | - Laurence Berry
- Laboratory of Pathogen and Host Immunity, CNRS UMR5294, University of Montpellier, 34095 Montpellier, France;
| | - Albert Sotto
- VBIC, INSERM U1047, Department of Infectious Diseases, University of de Montpellier, CHU Nîmes, 30908 Nîmes, France;
| | - Jean-Philippe Lavigne
- VBIC, INSERM U1047, Department of Microbiology and Hospital Hygiene, University of Montpellier, CHU Nîmes, 30908 Nîmes, France; (M.M.); (J.-P.L.)
| | | | - Virginie Molle
- VBIC, INSERM U1047, University of Montpellier, 34095 Montpellier, France; (L.P.); (N.A.-M.)
- VBIC, INSERM U1047, Department of Microbiology and Hospital Hygiene, University of Montpellier, CHU Nîmes, 30908 Nîmes, France; (M.M.); (J.-P.L.)
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Keita ML, Morsli M, Levy M, Basse G, Verrier C, Drancourt M. Detection of Mycobacterium angelicum in Human Urinary Tract, French Polynesia. Emerg Infect Dis 2023; 29:1490-1492. [PMID: 37347937 PMCID: PMC10310377 DOI: 10.3201/eid2907.221864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2023] Open
Abstract
We definitively characterized Mycobacterium angelicum, an aquatic zoonotic opportunistic pathogen of the M. szulgai complex, using a polyphasic approach that included whole-genome sequencing. The sequence was obtained on the island of Tahiti, French Polynesia, from a urine specimen collected from a patient experiencing a urinary tract infection.
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Morsli M, Salipante F, Kerharo Q, Boudet A, Stephan R, Dunyach-Remy C, Zandotti C, Lavigne JP, Drancourt M. Dynamics of community-acquired meningitis syndrome outbreaks in southern France. Front Microbiol 2023; 13:1102130. [PMID: 36777029 PMCID: PMC9909019 DOI: 10.3389/fmicb.2022.1102130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/30/2022] [Indexed: 01/27/2023] Open
Abstract
In southern France, cases of community-acquired meningitis syndrome (CAM) are typically clustered as outbreaks with determinants which remain unknown. This 61-month retrospective investigation in Nîmes and Marseille university hospital laboratories, yielded 2,209/20,779 (10.63%) documented CAM cases caused by 62 different micro-organisms, represented by seasonal viral etiologies (78.8%), including Enterovirus, Herpes Simplex Virus (HSV), and Varicella-Zoster Virus (VZV; 1,620/2,209 = 73.4%). Multi correspondence analysis revealed an association of infection with age and sex, with the risk of infection being relatively higher in young men, as confirmed by Fisher's exact test (p < 10-3). Bacterial meningitis accounted for 20% of cases, mostly caused by Streptococcus pneumoniae (27.4% of cases), Neisseria meningitidis (12.5%), and Haemophilus influenzae (9.5%) with bacteria/virus coinfection (0.9%), and only six cases of documented fungal meningitis. In total, 62.6% of cases, of which 88.7% were undocumented, arose from 10 outbreaks. 33.2% of undocumented cases were aged >60 years compared to 19.2% of documented cases (p < 0.001), and viral infection was more common in the summer (87.5%) compared to other seasons (72.3%; p < 0.001). Outbreaks most often started in Nîmes and moved eastward toward Marseille at a speed of ~9 km/day, and these dynamics significantly correlated with atmospheric temperature, especially during summer outbreaks. In particular, the incidence of Enterovirus-driven outbreaks correlated with temperature, revealing correlation coefficients of 0.64 in Nîmes and 0.72 in Marseille, and its occurrence in Marseille lagged that in Nîmes by 1-2 weeks. Tracing the dynamics of CAM outbreak during this retrospective investigation in southern France yielded a speed of displacement that correlated with the variation in temperature between both cities, and these results provide clues for the next occurrence of undocumented outbreaks.
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Affiliation(s)
- Madjid Morsli
- IHU Méditerranée Infection, Marseille, France,Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Florian Salipante
- Laboratoire de biostatistique, Épidémiologie Clinique, Santé Publique, Innovation et Méthodologie, CHU de Nîmes, Université de Montpellier, Nîmes, France
| | - Quentin Kerharo
- Laboratoire de Microbiologie, Assistance Publique-Hôpitaux de Marseille, IHU Méditerranée Infection, Marseille, France
| | - Agathe Boudet
- VBIC, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Robin Stephan
- VBIC, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Catherine Dunyach-Remy
- VBIC, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Christine Zandotti
- IHU Méditerranée Infection, Marseille, France,Laboratoire de Microbiologie, Assistance Publique-Hôpitaux de Marseille, IHU Méditerranée Infection, Marseille, France
| | - Jean-Philippe Lavigne
- VBIC, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Michel Drancourt
- IHU Méditerranée Infection, Marseille, France,Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France,Laboratoire de Microbiologie, Assistance Publique-Hôpitaux de Marseille, IHU Méditerranée Infection, Marseille, France,*Correspondence: Michel Drancourt, ✉
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Morsli M, Boudet A, Kerharo Q, Stephan R, Salipante F, Dunyach-Remy C, Houhamdi L, Fournier PE, Lavigne JP, Drancourt M. Real-time metagenomics-based diagnosis of community-acquired meningitis: A prospective series, southern France. EBioMedicine 2022; 84:104247. [PMID: 36087524 PMCID: PMC9463524 DOI: 10.1016/j.ebiom.2022.104247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 08/16/2022] [Accepted: 08/16/2022] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Point-Of-Care (POC) diagnosis of life-threatening community-acquired meningitis currently relies on multiplexed RT-PCR assays, that lack genotyping and antibiotic susceptibility profiling. We assessed the usefulness of real-time metagenomics (RTM) directly applied to the cerebrospinal fluid (CSF) for the identification, typing and susceptibility profiling of pathogens responsible for community-acquired meningitis. METHODS A series of 52 CSF samples from patients suspected of having community-acquired meningitis, were investigated at POC by direct RTM in parallel to routine real-time multiplex PCR (RT-PCR) and bacterial culture, for the detection of pathogens. RTM-generated sequences were blasted in real-time against an in-house database incorporating the panel of 12 most prevalent pathogens and against NCBI using EPI2ME online software, for pathogen identification. In-silico antibiogram and genotype prediction were determined using the ResFinder bio-tool and MLST online software. FINDINGS Over eight months, routine multiplex RT-PCR yielded 49/52 positive CSFs, including 21 Streptococcus pneumoniae, nine Neisseria meningitidis, eight Haemophilus influenzae, three Streptococcus agalactiae, three Herpesvirus-1, two Listeria monocytogenes, and one each of Escherichia coli, Staphylococcus aureus and Varicella-Zoster Virus. Parallel RTM agreed with the results of 47/52 CSFs and revealed two discordant multiplex RT-PCR false positives, one H. influenzae and one S. pneumoniae. Both multiplex RT-PCR and RTM agreed on the negativity of three CSFs. While multiplex RT-PCR routinely took 90 min, RTM took 120 min, although the pipeline analysis detected the pathogen genome after 20 min of sequencing in 33 CSF samples; and after two hours in 14 additional CSFs; yielding > 50% genome coverage in 19 CSFs. RTM identified 14 pathogen genotypes, including a majority of H. influenzae b, N. meningitidis B and S. pneumoniae 11A and 3A. In all 16 susceptible cultured bacteria, the in-silico antibiogram agreed with the in-vitro antibiogram in 10 cases, available within 48 h in routine bacteriology. INTERPRETATION In addition to pathogen detection, RTM applied to CSF samples offered supplementary information on bacterial profiling and genotyping. These data provide the proof-of-concept that RTM could be implemented in a POC laboratory for one-shot diagnostic and genomic surveillance of pathogens responsible for life-threatening meningitis. FUNDING This work was supported by the French Government under the Investments in the Future programme managed by the National Agency for Research reference: Méditerranée Infection 10-IAHU-03.
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Affiliation(s)
- Madjid Morsli
- IHU Méditerranée Infection, Marseille, France; IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Université, France
| | - Agathe Boudet
- VBIC, INSERM U 1047, Université de Montpellier, France; Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Quentin Kerharo
- IHU Méditerranée Infection, Marseille, France; Laboratoire de Microbiologie, Assistance Publique-Hôpitaux de Marseille, IHU, Méditerranée Infection, Marseille, France
| | - Robin Stephan
- Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Florian Salipante
- Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France; Service de Biostatistique, Epidémiologie, Santé Publique, Innovation en Méthodologie, CHU Nîmes, Nîmes, France
| | - Catherine Dunyach-Remy
- VBIC, INSERM U 1047, Université de Montpellier, France; Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | | | - Pierre-Edouard Fournier
- IHU Méditerranée Infection, Marseille, France; VITROME, IHU Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | - Jean Philippe Lavigne
- VBIC, INSERM U 1047, Université de Montpellier, France; Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Michel Drancourt
- IHU Méditerranée Infection, Marseille, France; IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Université, France; Laboratoire de Microbiologie, Assistance Publique-Hôpitaux de Marseille, IHU, Méditerranée Infection, Marseille, France.
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Morsli M, Lavigne JP, Drancourt M. Direct Metagenomic Diagnosis of Community-Acquired Meningitis: State of the Art. Front Microbiol 2022; 13:926240. [PMID: 35865915 PMCID: PMC9294516 DOI: 10.3389/fmicb.2022.926240] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Current routine diagnosis of community-acquired meningitis (CAM) by multiplex real-time polymerase chain reaction (RT-PCR) is limited in the number of tested pathogens and their full characterisation, requiring additional in vitro investigations to disclose genotype and antimicrobial susceptibility. We reviewed 51 studies published through December 2021 reporting metagenomic next generation sequencing (mNGS) directly applied to the cerebrospinal fluid (CSF). This approach, potentially circumventing the above-mentioned limitations, indicated 1,248 investigated patients, and 617 patients dually investigated by routine diagnosis and mNGS, in whom 116 microbes were detected, including 50 by mNGS only, nine by routine methods only, and 57 by both routine methods and mNGS. Of 217 discordant CSF findings, 103 CSF samples were documented by mNGS only, 87 CSF samples by routine methods only, and 27 CSF samples in which the pathogen identified by mNGS was different than that found using routine methods. Overall, mNGS allowed for diagnosis and genomic surveillance of CAM causative pathogens in real-time, with a cost which is competitive with current routine multiplex RT-PCR. mNGS could be implemented at point-of-care (POC) laboratories as a part of routine investigations to improve the diagnosis and molecular epidemiology of CAM, particularly in the event of failure of routine assays.
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Affiliation(s)
- Madjid Morsli
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Jean Philippe Lavigne
- VBIC, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Michel Drancourt
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Laboratoire de Microbiologie, Assistance Publique-Hôpitaux de Marseille, IHU Méditerranée Infection, Marseille, France
- *Correspondence: Michel Drancourt,
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Harouna Hamidou Z, Morsli M, Mamadou S, Drancourt M, Saad J. Emergence of multi-drug-resistant Mycobacterium tuberculosis in Niger: A snapshot based on whole-genome sequencing. PLoS Negl Trop Dis 2022; 16:e0010443. [PMID: 35613072 PMCID: PMC9132302 DOI: 10.1371/journal.pntd.0010443] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 04/22/2022] [Indexed: 11/27/2022] Open
Abstract
Background Among other West African countries experiencing the high endemicity of deadly tuberculosis, the situation in Niger is poorly evidenced by microbiological investigations. Methodology/Principal findings The study of 42 isolates of Mycobacterium tuberculosis from Niger by whole genome sequencing using Illumina iSeq technology yielded four M. tuberculosis lineages: Indo-Oceanic L1 (n = 1) (2.3%), East-Asian (n = 1) (2.3%), East-African Indian L3 (n = 2) (4.7%) and Euro-American L4 (n = 38) (90.4%). The sub-lineage L4.1.3 comprising 18 isolates (47.3%) was predominant, followed by the L4.6.2.2 sub-lineage (Cameroon genotype, n = 13 isolates) (34.2%). Investigating drug resistance profile for 12 antibiotics found 8/42 (19%) pan-susceptible isolates and 34/42 (81%) resistant isolates; with 40/42 (95.2%) isolates being susceptible to clofazimine-bedaquiline. Conclusions/Significance These unprecedented data from Niger highlight the dynamics of tuberculosis transmission and drug resistance in Niger and may assist tuberculosis control in this country which continues to support a high burden of tuberculosis. Tuberculosis is a major public health problem in Niger, in West Africa. Niger has an emerging problem with multidrug-resistant tuberculosis (MDR-TB). Whole genome sequencing was used to understand the epidemiology of tuberculosis and genetics of multi-drug resistance among patients from the regions in Niger. In this study, most isolates of M. tuberculosis from this dataset belonged to the L4.6.2.2 sub-lineage and L4.1.3 sub-lineage within the Euro-American lineage. Thirty-four out of 42 (81%) isolates were detected as resistant isolates. Our study highlights the need for epidemiological surveillance and more concerted efforts to ensure that patients are put through treatment.
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Affiliation(s)
- Zelika Harouna Hamidou
- Aix-Marseille-Univ, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Laboratoire National de Référence des IST/VIH et de la Tuberculose, Niamey, Niger
| | - Madjid Morsli
- Aix-Marseille-Univ, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Saidou Mamadou
- Laboratoire National de Référence des IST/VIH et de la Tuberculose, Niamey, Niger
- Université Abdou Moumouni, Niamey, Niger
| | - Michel Drancourt
- Aix-Marseille-Univ, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Jamal Saad
- Aix-Marseille-Univ, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- * E-mail:
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Robinne S, Saad J, Morsli M, Hamidou ZH, Tazerart F, Drancourt M, Baron SA. Rapid Identification of Mycobacterium tuberculosis Complex Using Mass Spectrometry: A Proof of Concept. Front Microbiol 2022; 13:753969. [PMID: 35432257 PMCID: PMC9008353 DOI: 10.3389/fmicb.2022.753969] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Mycobacteria that form the Mycobacterium tuberculosis complex are responsible for deadly tuberculosis in animals and patients. Identification of these pathogens at the species level is of primary importance for treatment and source tracing and currently relies on DNA analysis, including whole genome sequencing (WGS), which requires a whole day. In this study, we report the unprecedented discrimination of M. tuberculosis complex species using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS), with WGS as the comparative reference standard. In the first step, optimized peptide extraction applied to 36 isolates otherwise identified in five of the 11 M. tuberculosis complex variants by WGS yielded 139 MALDI-TOF spectra, which were used to identify biomarkers of interest that facilitate differentiation between variants. In a second step, 70/80 (88%) other isolates were correctly classified by an algorithm based on specific peaks. This study is the first to report a MALDI-TOF-MS method for discriminating M. tuberculosis complex mycobacteria that is easily implemented in clinical microbiology laboratories.
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Affiliation(s)
- Simon Robinne
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Jamal Saad
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Madjid Morsli
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Zelika Harouna Hamidou
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Laboratoire National de Référence des IST/VIH et de la Tuberculose, Niamey, Niger
| | - Fatah Tazerart
- IHU Méditerranée Infection, Marseille, France
- Institut des Sciences Vétérinaires, Université de Blida 1, Blida, Algeria
| | - Michel Drancourt
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Sophie Alexandra Baron
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- *Correspondence: Sophie Alexandra Baron,
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Guindo CO, Morsli M, Bellali S, Drancourt M, Grine G. A Tetragenococcus halophilus human gut isolate. Current Research in Microbial Sciences 2022; 3:100112. [PMID: 35243447 PMCID: PMC8866149 DOI: 10.1016/j.crmicr.2022.100112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/02/2022] [Accepted: 02/07/2022] [Indexed: 10/28/2022] Open
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Morsli M, Faltot M, Astier H, Le Dault E, Chaudier B, Garnotel E, Baron SA, Drancourt M. Real-time next-generation sequencing on shell-vial culture to contribute to diagnosis of lymphatic tuberculosis: a case report. Diagn Microbiol Infect Dis 2021; 101:115492. [PMID: 34343856 DOI: 10.1016/j.diagmicrobio.2021.115492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 10/20/2022]
Abstract
Lymph node tuberculosis is a of limited clinical suspicion form of Mycobacterium tuberculosis infection. After 15 days incubation in a cellular culture and directly from the supernatant, 11 minutes of Oxford Nanopore MinION sequencing provided a preliminary result of an antibiotic-susceptible M. tuberculosis Indo-Oceanic lineage strain. Oxford Nanopore MinION sequencing is a promising tool for optimising the laboratory diagnosis of lymph node tuberculosis.
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Affiliation(s)
- Madjid Morsli
- IHU Mediterranee Infection, Marseille, France; Aix-Marseille Universite, IRD, APHM, MEPHI, Marseille, France
| | - Marc Faltot
- Aix-Marseille Universite, IRD, APHM, MEPHI, Marseille, France
| | - Hélène Astier
- Hôpital d'Instruction des Armées Laveran, Laveran, Marseille, France
| | - Erwan Le Dault
- Hôpital d'Instruction des Armées Laveran, Laveran, Marseille, France
| | - Bernard Chaudier
- Hôpital d'Instruction des Armées Laveran, Laveran, Marseille, France
| | - Eric Garnotel
- Hôpital d'Instruction des Armées Laveran, Laveran, Marseille, France
| | - Sophie Alexandra Baron
- IHU Mediterranee Infection, Marseille, France; Aix-Marseille Universite, IRD, APHM, MEPHI, Marseille, France
| | - Michel Drancourt
- IHU Mediterranee Infection, Marseille, France; Aix-Marseille Universite, IRD, APHM, MEPHI, Marseille, France.
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Morsli M, Anani H, Bréchard L, Delerce J, Bedotto M, Fournier PE, Drancourt M. LamPORE SARS-CoV-2 diagnosis and genotyping: A preliminary report. J Clin Virol 2021; 138:104815. [PMID: 33838620 PMCID: PMC8011304 DOI: 10.1016/j.jcv.2021.104815] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/16/2021] [Accepted: 03/25/2021] [Indexed: 12/23/2022]
Affiliation(s)
- M Morsli
- Aix-Marseille-Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - H Anani
- IHU Méditerranée Infection, Marseille, France
| | - L Bréchard
- IHU Méditerranée Infection, Marseille, France
| | - J Delerce
- IHU Méditerranée Infection, Marseille, France
| | - M Bedotto
- Aix Marseille Univ., IRD, AP-HM, SSA, VITROME, Marseille, France
| | - P-E Fournier
- IHU Méditerranée Infection, Marseille, France; Aix Marseille Univ., IRD, AP-HM, SSA, VITROME, Marseille, France
| | - M Drancourt
- Aix-Marseille-Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France; IHU Méditerranée Infection, Marseille, France.
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Morsli M, Vincent JJ, Milliere L, Colson P, Drancourt M. Direct next-generation sequencing diagnosis of echovirus 9 meningitis, France. Eur J Clin Microbiol Infect Dis 2021; 40:2037-2039. [PMID: 33694039 DOI: 10.1007/s10096-021-04205-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 02/17/2021] [Indexed: 12/15/2022]
Abstract
The prognosis of central nervous system infections caused by enteroviruses partially depends on the viral genotype, which is not provided by current point-of-care diagnostic methods. In this study, next-generation sequencing identified an echovirus 9 directly from the cerebrospinal fluid of a patient presenting with meningitis.
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Affiliation(s)
- Madjid Morsli
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, IHU Méditerranée Infection, Marseille, France
| | - Jean-Jacques Vincent
- IHU Méditerranée Infection, Marseille, France
- Laboratoire de Microbiologie, Assistance Publique-Hôpitaux de Marseille, IHU Méditerranée Infection, Marseille, France
| | - Laurine Milliere
- IHU Méditerranée Infection, Marseille, France
- Laboratoire de Microbiologie, Assistance Publique-Hôpitaux de Marseille, IHU Méditerranée Infection, Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, IHU Méditerranée Infection, Marseille, France
| | - Michel Drancourt
- IHU Méditerranée Infection, Marseille, France.
- Aix-Marseille Université, IRD, IHU Méditerranée Infection, Marseille, France.
- Laboratoire de Microbiologie, Assistance Publique-Hôpitaux de Marseille, IHU Méditerranée Infection, Marseille, France.
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Bouali D, Dahmouche B, Morsli M, Meliani A, Bouaita K. Oncocytome fusiforme de l’adénome hypophysaire–à propos d’un cas et revue de la littérature. Neurochirurgie 2018. [DOI: 10.1016/j.neuchi.2018.05.078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Makhlouki M, Morsli M, Bonnet A, Conan A, Bernede JC, Lefrant S. Propriétés de transport de composites de polymères conducteurs : polyvinyl alcool-polypyrrole. ACTA ACUST UNITED AC 2017. [DOI: 10.1051/jcp/1992891155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Bernède J, Cattin L, Morsli M, Kanth S, Patil S, Stephant N. Improvement of the Efficiency of Organic Solar Cells Using the Terthiophene-Pyran-Malononitrile (T3PM) as Electron Donor, through the use of a MoO3/CuI Anode Buffer Layer. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.egypro.2012.11.168] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Mouchaal Y, Lakhdar Toumi A, Yapi A, Lare Y, Soto G, Cattin L, Toubal K, Reguig A, Khelil A, Djafri A, Morsli M, Del Valle M, Bernède J. Optical and electronic proprieties of thin films based on (Z)-5-(4-chlorobenzylidene)-3-(2-ethoxyphenyl)-2 thioxothiazolidin-4-one, (CBBTZ) and possible application as exciton-blocking layer in heterojunction organic solar cells. EPJ Web of Conferences 2012. [DOI: 10.1051/epjconf/20122900030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Morsli M, Bernède J, Cattin L, Dahou F, Khelil A. On the Exciton Blocking Layer at the Interface Organic/Cathode in Multiheterojunction Organic Solar Cells. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.egypro.2012.11.167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Hakem D, Médaoud S, Lafer A, Abada-Bendib M, Morsli M, Kessaci F, Berrah A. Hypertension intra crânienne aiguë compliquant une sarcoïdose. Rev Med Interne 2011. [DOI: 10.1016/j.revmed.2011.03.272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Taoudi H, Bernede JC, Del Valle MA, Bonnet A, Molinie P, Morsli M, Diaz F, Tregouet Y, Bareau A. Polycarbazole obtained by electrochemical polymerization of monomers either in solution or in thin film form. J Appl Polym Sci 2000. [DOI: 10.1002/(sici)1097-4628(20000328)75:13<1561::aid-app1>3.0.co;2-c] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Ouadah A, Bernède JC, Pouzet J, Morsli M. MoTe2 Thin Films Synthesized by Solid State Reactions between Mo and Te Thin Films. ACTA ACUST UNITED AC 1992. [DOI: 10.1002/pssa.2211340215] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Morsli M, Bonnet A, Conan A, Ganne M, Jouanneaux A. Transport properties of polycrystalline Tl0.33MoO3 compounds. Phys Rev B Condens Matter 1989; 39:3735-3740. [PMID: 9948695 DOI: 10.1103/physrevb.39.3735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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