Biology subjects

Raoult, D.

Publications and source records attributed to Raoult, D..

At least 19 recordsLinked to original sources

bioRxiv2023

Resuscitating Sleeping Beauties: reviving a six-hundred-year-old amoeba and endosymbiont.

Coprolites are sources of ancient human gut microbiota and parasites. Paleomicrobiological investigation of a 14th-century coprolite revealed amoeba cysts that when cultured were identified as Acanthamoeba castellanii strain Namur. Genomic DNA sequencing indicated a 69-Mb, 57.9% GC content genome encoding 40,545 proteins, including 266 amoeba sequences sharing the best hit with amoeba-resisting microorganisms, including 170 with giant viruses. An endosymbiont we named Coprolita marseillensis was revealed by electron microscopy that harbored a 1-Mb genome of Rickettsiales ancestry encoding 1,738 predicted genes. Most of the amoeba genomic complement was related to biological functions giving the amoeba the capacity to survive in various ecological niches, including genes associated with anaerobic respiration and dormancy that were detected in bacteria resuscitated from permafrost, but not in controls that had not been resurrected. Investigating these 600-year-old "sleeping beauties" indicated the centuries-long survival of unicellular organisms and the mixed capability of anaerobic respiration coupled with dormancy.

microbiology↗

bioRxiv2023

Role of SARS-CoV-2 mutations in the evolution of the COVID-19 pandemic

RNA viruses, including SARS-CoV-2, evolve by mutation acquisition, or by hybridization between viral genomes. The SARS-CoV-2 pandemic provided an exceptional opportunity to analyze the mutations that appeared over a three-year period. In this study, we analysed the type of mutations and their epidemic consequences on the thousands of genomes produced in our laboratory. These were obtained by next-generation sequencing from respiratory samples performed for genomic surveillance. The frequencies of mutations were calculated using Nextclade, Microsoft Excel, and an in-house Python script. In total, 61,397 genomes matching 483 Pangolin lineages were analyzed; 22,225 nucleotide mutations were identified, and of them 220 (1.0%) were each at the root of at least 836 genomes, a frequency threshold classifying mutations as "hyperfertile". Two of these seeded the pandemic in Europe, namely a mutation in the RNA-dependent RNA polymerase associated with an increased mutation rate (P323L) and one in the spike protein (D614G), which plays a particular role in virus fitness. Most of these 220 "hyperfertile" mutations occurred in areas not predicted to be associated with increased virulence. Their number was 8{+/-}6 (0-22) per 1,000 nucleotides on average per gene. They were 3.7 times more frequent in accessory than informational genes (14 versus 4; p= 0.0037). Particularly, they were 4.1 times more frequent in ORF8 than in the gene encoding RNA polymerase. Interestingly, stop codons were present in 97 positions, almost only in six accessory genes including ORF7a (25 per 100 codons) and ORF8 (21). Furthermore, 1,661 mutations (16.3%) were associated with a lower number of "offspring" (50-835) and classified as "fertile". In conclusion, except for two initial mutations that could predict a change in the dynamics of the epidemic (mutation rate and change in the virus attachment site), most of the "hyperfertile" mutations did not predict the emergence of a new epidemic form. Significantly, some mutations were in non-coding areas and some consisted of stop codons, indicating that some genes (particularly ORF7a and ORF8) were rather "non-virulence genes" at a given stage of the epidemic, which is an unusual concept for viruses.

microbiology↗

bioRxiv2021

Adapted protocol for Saccharibacteria co-cultivation: two new members join the club of Candidate Phyla radiation

The growing application of metagenomics to different ecological and microbiome niches in recent years has enhanced our knowledge of global microbial biodiversity. Among these abundant and widespread microbes, Candidate Phyla Radiation or CPR have been recognised as representing a large proportion of the microbial kingdom (> 26%). CPR are characterised by their obligate symbiotic or exo-parasitic activity with other microbial hosts, mainly bacteria. Currently, isolating CPR is still considered challenging for microbiologists. The idea of this study was to develop an adapted protocol for the co-culture of CPR with a suitable bacterial host. Based on various sputa, we tried to purify CPR (Saccharibacteria members) and to cultivate them with pure hosts. This protocol was monitored by real-time PCR quantification using a specific system for Saccharibacteria designed in this study, as well as by electron microscopy and sequencing. We succeeded in co-culturing and sequencing a complete genome of two new Saccharibacteria species: Candidatus Minimicrobia naudis and Candidatus Minimicrobia vallesae. In addition, we noticed a decrease in the Ct number of Saccharibacteria, and a significant multiplication through their physical association with Schaalia odontolytica strains in the enriched medium that we developed. This work may help bridge gaps in the genomic database by providing new CPR members and, in the future, their currently unknown characteristics may be revealed. IMPORTANCEIn this study, the first real-time PCR system has been developed. This technique is able to quantify specifically Saccharibacteria members in any sample of interest in order to investigate their prevalence. In addition, another easy, specific and sensitive protocol has been developed to maintain the viability of Saccharibacteria cells in an enriched medium with their bacterial host. The use of this protocol subsequently facilitates studying the phenotypic characteristics of CPR and their physical interactions with bacterial species, as well as the sequencing of new genomes to improve the current database.

microbiology↗

bioRxiv2021

Unbiased lexicometry analyses illuminate plague dynamics during the second pandemic

Knowledge of the second plague pandemic that swept over Europe during the 14th-19th centuries, mainly relies on the exegesis of contemporary texts, prone to interpretive bias. Leveraging bioinformatic tools routinely used in biology, we here developed a quantitative lexicography of 32 texts describing two major plague outbreaks using contemporary plague-unrelated texts as negative controls. Nested, network and category analyses of a 207-word pan-lexicome over-represented in plague-related texts, indicated that "buboes" and "carbuncles" words were significantly associated with plague, signaling ectoparasite- borne plague. Moreover, plague-related words were associated with the words "merchandise", "movable", "tatters", "bed" and "clothes", while no association was found with rats and fleas. These results support the hypothesis that during the second plague pandemic, human ectoparasites were the major drivers of plague. Analyzing ancient texts using here reported method would certify plague-related historical records and indicate particularities of each plague outbreak, including sources of the causative Yersinia pestis.

bioinformatics↗

bioRxiv2020

Stool serology: development of a non-invasive immunological method for the detection of Enterovirus-specific antibodies in Congo gorilla feces

The incidence of poliovirus has significantly reduced by as much as 99.9% globally. Alongside this, however, vaccine-associated paralytic poliomyelitis has emerged. Recently, a new recombinant virus (Enterovirus C/Poliovirus) was identified in humans working as eco-guards and in gorillas in Democratic Republic of Congo, including one gorilla with polio-like sequelae. A strain of this recombinant virus (Ibou002) was also isolated from gorilla faeces. In order to assess the potential role of poliovirus infection, we have developed and optimised a protocol, based on the lyophilisation and solubilisation of small volumes of stool extracts, to detect specific antibodies. First, total immunoglobulins was detected in the concentrated stool extracts. Specific antibodies were then detected in 4/16 gorilla samples and 2/3 human samples by western blot using both the polio vaccine antigen and the Ibou002 antigen and by ELISA using the polio vaccine antigen. Humoral responses were greater with the Ibou002 antigen. We therefore suggest that this recombinant virus could lead to a polio-like disease in the endangered western lowland gorilla. The development of a non-invasive method to detect microorganism-specific immunoglobulins from faecal samples opens up new perspectives for the exploration of humoral responses of pathogens in animals and a greater understanding of zoonotic infectious diseases.

microbiology↗

bioRxiv2020

Tricarboxylic acid cycle and proton gradient in Pandoravirus massiliensis: Is it still a virus?

Since the discovery of Acanthamoeba polyphaga Mimivirus, the first giant virus of amoeba, the historical hallmarks defining a virus have been challenged. Giant virion sizes can reach up to 2.3 {micro}m, making them visible by optical microscopy. They have large genomes of up to 2.5 Mb that encode proteins involved in the translation apparatus. Herein, we investigated possible energy production in Pandoravirus massiliensis, the largest of our giant virus collection. MitoTracker and TMRM mitochondrial membrane markers allowed for the detection of a membrane potential in virions that could be abolished by the use of the depolarizing agent CCCP. An attempt to identify enzymes involved in energy metabolism revealed that 8 predicted proteins of P. massiliensis exhibited low sequence identities with defined proteins involved in the universal tricarboxylic acid cycle (acetyl Co-A synthase; citrate synthase; aconitase; isocitrate dehydrogenase; -ketoglutarate decarboxylase; succinate dehydrogenase; fumarase). All 8 viral predicted ORFs were transcribed together during viral replication, mainly at the end of the replication cycle. Two of these proteins were detected in mature viral particles by proteomics. The product of the ORF132, a predicted protein of P. massiliensis, cloned and expressed in Escherichia coli, provided a functional isocitrate dehydrogenase, a key enzyme of the tricarboxylic acid cycle, which converts isocitrate to -ketoglutarate. We observed that membrane potential was enhanced by low concentrations of Acetyl-CoA, a regulator of the tricarboxylic acid cycle. Our findings show for the first time that energy production can occur in viruses, namely, pandoraviruses, and the involved enzymes are related to tricarboxylic acid cycle enzymes. The presence of a proton gradient in P. massiliensis coupled with the observation of genes of the tricarboxylic acid cycle make this virus a form a life for which it is legitimate to question what is a virus?.

microbiology↗

bioRxiv2020

Monocytes and macrophages, targets of SARS-CoV-2: the clue for Covid-19 immunoparalysis

To date, the Covid-19 pandemic affected more than 18 million individuals and caused more than 690, 000 deaths. Its clinical expression is pleiomorphic and severity is related to age and comorbidities such as diabetes and hypertension. The pathophysiology of the disease relies on aberrant activation of immune system and lymphopenia that has been recognized as a prognosis marker. We wondered if the myeloid compartment was affected in Covid-19 and if monocytes and macrophages could be infected by SARS-CoV-2. We show here that SARS-CoV-2 efficiently infects monocytes and macrophages without any cytopathic effect. Infection was associated with the secretion of immunoregulatory cytokines (IL-6, IL-10, TGF-{beta}) and the induction of a macrophagic specific transcriptional program characterized by the upregulation of M2-type molecules. In addition, we found that in vitro macrophage polarization did not account for the permissivity to SARS-CoV-2, since M1-and M2-type macrophages were similarly infected. Finally, in a cohort of 76 Covid-19 patients ranging from mild to severe clinical expression, all circulating monocyte subsets were decreased, likely related to massive emigration into tissues. Monocytes from Covid-19 patients exhibited decreased expression of HLA-DR and increased expression of CD163, irrespective of the clinical status. Hence, SARS-CoV-2 drives circulating monocytes and macrophages inducing immunoparalysis of the host for the benefit of Covid-19 disease progression.

immunology↗

bioRxiv2020

Genomic diversity and evolution of coronavirus (SARS-CoV-2) in France from 309 COVID-19-infected patients

The novel coronavirus (SARS-CoV-2) causes pandemic of viral pneumonia. The evolution and mutational events of the SARS-CoV-2 genomes are critical for controlling virulence, transmissibility, infectivity, severity of symptoms and mortality associated to this infectious disease. We collected and investigated 309 SARS-CoV-2 genomes from patients infected in France. Detailed genome cartography of all mutational events (SNPs, indels) was reported and correlated to clinical features of patients. A comparative analysis between our 309 SARS-CoV-2 genomes from French patients and the reference Wuhan coronavirus genome revealed 315 substitution mutations and six deletion events: ten were in 5/3 UTR, 178 were nonsynonymous, 126 were synonymous and one generated a stop codon. Six different deleted areas were also identified in nine viral variants. In particular, 30 substitution mutations (18 nonsynonymous) and one deletion ({Delta}21765-21770) concerned the spike S glycoprotein. An average of 7.8 mutational events (+/- 1.7 SD) and a median of 8 (range, 7-9) were reported per viral isolate. Comparative analyses and clustering of specific mutational signatures in 309 genomes disclose several divisions in groups and subgroups combining their geographical and phylogenetic origin. Clinical outcomes of the 309 COVID-19-infected patients were investigated according to the mutational signatures of viral variants. These findings highlight the genome dynamics of the coronavirus 2019-20 and shed light on the mutational landscape and evolution of this virus. Inclusion of the French cohort enabled us to identify 161 novel mutations never reported in SARS-CoV-2 genomes collected worldwide. These results support a global and continuing surveillance of the emerging variants of the coronavirus SARS-CoV-2.

genomics↗

bioRxiv2020

High speed large scale automated isolation of SARS-CoV-2 from clinical samples using miniaturized co-culture coupled with high content screening

SARS-CoV-2, a novel coronavirus infecting humans, is responsible for the current COVID-19 global pandemic. If several strains could be isolated worldwide, especially for in-vitro drug susceptibility testing and vaccine development, few laboratories routinely isolate SARS-CoV-2. This is due to the fact that the current co-culture strategy is highly time consuming and requires working in a biosafety level 3 laboratory. In this work, we present a new strategy based on high content screening automated microscopy (HCS) allowing large scale isolation of SARS-CoV-2 from clinical samples in 1 week. A randomized panel of 104 samples, including 72 tested positive by RT-PCR and 32 tested negative, were processed with our HCS procedure and were compared to the classical isolation procedure. Isolation rate was 43 % with both strategies on RT-PCR positive samples, and was correlated with the initial RNA viral load in the samples, where we obtained a positivity threshold of 27 Ct. Co-culture delays were shorter with HCS strategy, where 80 % of the positive samples were recovered by the third day of co-culture, as compared to only 25 % with the classic strategy. Moreover, only the HCS strategy allowed us to recover all the positive elements after 1 week of co-culture. This system allows rapid and automated screening of clinical samples with minimal operator work load, thus reducing the risks of contamination.

microbiology↗

bioRxiv2019

High Content Screening, a reliable system for Coxiella burnetii isolation from clinical samples

Q fever, caused by Coxiella burnetii, is a worldwide zoonotic disease that may cause severe forms in humans and requires a specific and prolonged antibiotic treatment. Although the current serological and molecular detection tools enable a reliable diagnosis of the disease, culture of C. burnetii strains is mandatory to evaluate their antibiotic susceptibility and sequence their genome in order to optimize patient management and epidemiological studies. However, cultivating this fastidious microorganism is difficult and restricted to reference centers as it requires biosafety-level 3 laboratories and relies on cell culture performed by experienced technicians. In addition, the culture yield is low, which results in a small number of isolates being available. In this work, we developed a novel high content screening (HCS) isolation strategy based on optimized high-throughput cell culture and automated microscopic detection of infected cells with specifically-designed algorithms targeting cytopathic effects. This method was more efficient than the shell-vial assay when applied to both frozen specimens (7 isolates recovered by HCS only, sensitivity 91% vs 78% for shell-vial) and fresh samples (1 additional isolate using HCS, sensitivity 7% vs 5% for shell-vial). In addition, detecting positive cultures by an automated microscope reduced the need for expertise and saved 24% of technician working time. Application of HCS to antibiotic susceptibility testing of 12 strains demonstrated that it was as efficient as the standard procedure that combines shell-vial culture and quantitative PCR. Overall, this high-throughput HCS system paves the way to the development of improved cell culture isolation of human viruses.

microbiology↗

bioRxiv2019

Lactobacillus reuteri: direct passage from ingested yogurts to urine microbiota

BackgroundSerendipitously, it was observed that fecal transplantation made for Clostridium difficile may cure chronic urinary tract infections. This led us to evaluate the passage in the urine of probiotics contained in yoghurt, which have been claimed to prevent urinary infections. ResultsA commercial yogurt that contained 3 probiotics (Bifidobacterium animalis, Lactobacillus delbrueckiii and Lactobacillus reuteri) was consumed by 28 healthy subjects. We performed by culturomics, urine analysis before and after feeding these yogurts. Genome sequencing of the bacterial strains absent before yogurt consumption and present after consumption was performed. Testing more than 40,000 colonies by MALDI-TOF, we observed in two men and one woman (11% of subjects included), the urine colonization of the same Lactobacillus reuteri present in yogurts, with the same genome with 50 genes never identified in other lactobacilli. ConclusionThis confirms that, as ingested, Lactobacillus salivarius passes into the milk of lactating women, some bacteria, particularly Lactobacillus can colonize body fluids previously considered sterile after ingestion via the digestive route. Although the consequences of this passage remain unknown, we prove for the first time that there is a digestive passage in the urine after consumption of probiotics, including fermented products sold commercially.

microbiology↗

bioRxiv2019

A metallo-beta-lactamase with both beta-lactamase and ribonuclease activity is linked with traduction in giant viruses

Enzymatic proteins with a metallo-beta-lactamase (MBL) fold have been essentially studied in bacteria for their activity on beta-lactam antibiotics. However, the MBL fold is ancient and highly conserved, and these proteins are capable of cleaving a broad range of substrates. It has recently been shown that MBLs are present in a wide array of cellular organisms, including eukaryotes and archaea. We show here that Tupanvirus deep ocean, a giant virus, also encodes a protein with a MBL fold. Phylogeny showed its clustering with transfer ribonucleases (RNases) and the presence of orthologs in other giant viruses, mainly those harboring the largest sets of translation components. In addition, it suggests an ancient origin for these genes and a transfer between giant viruses and Acanthamoeba spp., a host of many giant viruses. Biologically, after its expression in Escherichia coli, the tupanvirus protein was found to hydrolyse nitrocefin, a chromogenic beta-lactam. We also observed an hydrolysis of penicillin G (10 g/mL) and detected the metabolite of penicillin G hydrolysis, benzylpenilloic acid. This was inhibited by sulbactam, a beta-lactamase inhibitor. In addition, we tested the degradation of single-stranded DNA, double-stranded DNA, and RNAs, and observed a strong activity on RNAs from seven bacteria with G+C varying from 42% to 67%, and from Acanthamoeba castellanii, the tupanvirus host. This was not inhibited by sulbactam or ceftriaxone. RNase activity was estimated to be 0.45{+/-}0.15 mU/mg using a fluorescence-based assay. Our results still broaden the range of hosts of MBL fold proteins and demonstrate that such protein can have dual beta-lactamase/nuclease activities. We suggest that they should be annotated according to this finding to avoid further confusion.

microbiology↗

bioRxiv2019

The dynamics and interactions of respiratory pathogen carriage among French pilgrims during the 2018 Hajj

Respiratory tract infections are frequent among Hajj pilgrims. We conducted this study to describe the dynamics of the acquisition of respiratory pathogens, their potential interactions and risk factors for possible lower respiratory tract infection symptoms (LRTI) among French pilgrims during the 2018 Hajj. Pilgrims from Marseille who were participating in the Hajj were recruited. Each participant underwent four successive systematic nasopharyngeal swabs before and during their stay in Saudi Arabia. Carriage of the main respiratory pathogens was assessed by PCR. 121 pilgrims were included and 93.4% reported respiratory symptoms during the study period. Polymicrobial carriage was observed in 73.8% samples. The acquisition of rhinovirus, coronaviruses and Staphylococcus aureus occurred soon after arrival in Saudi Arabia and rates decreased gradually after days 5 and 6. In contrast, Streptococcus pneumoniae and Klebsiella pneumoniae carriage increased progressively until the end of the stay in Saudi Arabia. Haemophilus influenzae and Moraxella catarrhalis carriage increased starting around days 12 and 13, following an initial clearance. Influenza viruses were rarely isolated. We observed an independent positive mutual association between S. aureus and rhinovirus carriage and between H. influenzae and M. catarrhalis carriage. Dual carriage of H. influenzae and M. catarrhalis was strongly associated with S. pneumoniae carriage (OR = 6.22, 95%CI [2.04-19.01]). Finally, our model showed that M. catarrhalis carriage was negatively associated with K. pneumoniae carriage. Chronic respiratory disease was associated with symptoms of LRTI. K. pneumoniae, M. catarrhalis-S. aureus and H. influenzae-rhinovirus dual carriage was associated with LRTI symptoms. Our data suggest that RTIs at the Hajj are a result of complex interactions between a number of respiratory viruses and bacteria.\n\nAuthor summaryDespite the recommendation to take individual preventive measures to prevent respiratory tract infections, these infections remain common among Hajj pilgrims. Respiratory pathogens acquired during the Hajj are usually studied individually, although in their natural environment they often compete or coexist with multiple microbial species. A better understanding of polymicrobial interactions in the nasopharynx among Hajj pilgrims is important. Our study describes the dynamics of the acquisition of respiratory pathogens and their potential interactions among pilgrims during the Hajj. We found that polymicrobial carriage was observed in most individuals and that some pathogens associated positively while other did not. Some pathogen associations correlated with symptoms of lower respiratory tract infections.

microbiology↗

bioRxiv2019

Transfer of CRISPR-like activity of MIMIVIRE into Bacteria

MIMIVIRE is a defence system utilized by lineage A Mimiviruses against Zamilon virophages. It is composed of a helicase, a nuclease and a gene of unknown function here named trcg (for Target Repeat-Containing gene), which contains four 15-bp repeats identical to the Zamilon sequence. Their silencing restored susceptibility to Zamilon, and the CRISPR-Cas4-like activity of the nuclease was recently characterised. We expressed these 3 genes after transformation of a modified strain of Escherichia coli made resistant to ampicillin, chloramphenicol and tetracycline. The virophage repeats were replaced with four repeats of 15 nucleotides identical to a sequence in the tetracycline resistance gene. The induction of the MIMIVIRE genes restored E. coli sensitivity to tetracycline; the tetracycline operon and its supporting plasmid harbouring the chloramphenicol resistance gene vanished. We therefore efficiently transferred the defence system MIMIVIRE from giant Mimivirus against virophage to E. coli to clear it from a plasmid.

microbiology↗

bioRxiv2019

Dramatic HIV DNA degradation associated with spontaneous HIV suppression and disease-free outcome in a young seropositive woman following her infection

Strategies to cure HIV-infected patients by virus-targeting drugs have failed to date. We identified a HIV-1-seropositive woman who spontaneously suppressed HIV replication and had normal CD4-cell counts, no HIV disease, no replication-competent virus and no cell HIV DNA detected with a routine assay. We suspected that dramatic HIV DNA degradation occurred postinfection. We performed multiple nested-PCRs followed by Sanger sequencing and applied a multiplex-PCR approach. Furthermore, we implemented a new technique based on two hybridization steps on beads prior to next-generation sequencing that removed human DNA then retrieved integrated HIV sequences with HIV-specific probes. We assembled {approx}45% of the HIV genome and further analyzed the G-to-A mutations putatively generated by cellular APOBEC3 enzymes that can change tryptophan codons into stop codons. We found more G-to-A mutations in the HIV DNA from the woman than in that of her contaminator. Moreover, 74% of the tryptophan codons were changed to stop codons (25%) or were deleted as a possible consequence of gene inactivation. Finally, we found that this womans cells remained HIV-susceptible in vitro. Our findings show that she does not exhibit innate HIV resistance but has been cured of it by extrinsic factors, a plausible candidate for which is the gut microbiota.

microbiology↗

bioRxiv2019

Paradoxical β-lactamase activity of archaeal encoding enzymes

{beta}-lactams targeting the bacterial cell wall are not active on archaea. Here, we figure out that annotation of genes as {beta}-lactamase in Archeae on the basis of homologous genes, initially annotated {beta}-lactamases, is a remnant of the identification of the original activities of this group of enzymes, which in fact, have multiple functions including nuclease, ribonuclease, {beta}-lactamase, or glyoxalase; which may specialized over time. We expressed a class B {beta}-lactamase enzyme from Methanosarcina barkeri that digest penicillin G. Moreover, while a weak glyoxalase activity was detected, a significant ribonuclease activity on bacterial and synthetic RNAs was demonstrated. The {beta}-lactamase activity was inhibited by a {beta}-lactamase inhibitor (sulbactam), but its RNAse activity was not. This gene appears to has been transferred to the Flavobacteriaceae group including Elizabethkingia genus in which the expressed gene shows a more specialized activity toward resistance to tienanmicin but no glyoxalase activity. The expressed class C-like {beta}-lactamase gene, also from Methanosarcina sp., shows also hydrolysis activity and was more closely related to DD-peptidase enzymes than known bacterial class C {beta}-lactamases. Our findings highlight the requalification needness of annotated enzymes as {beta}-lactamases and the specification overtime of multipotent enzymes in different ways in Archaea and bacteria.

microbiology↗

bioRxiv2019

Antioxidants maintain Butyrate production by Human Gut Clostridia in the presence of Oxygen

BackgroundOxygen diffused from the human gut mucosa and shape the microbiota with a radial gradient of microbes according to their oxygen tolerance, while microbial and chemical oxygen consumption maintains the lumen in a deeply anaerobic state. Uncontrolled oxidative stress and hyperoxygenation have been reported as a pathogenic mechanism in Salmonella or Citrobacter rodentium infection, in patients with HIV and in severe acute malnutrition. We recently found that antioxidants allow strict anaerobes, including methanogenic archaea, to thrive in an oxidative environment (aerobic). Here, we tested the metabolomics switching of the 3 most odorous anaerobic microbes isolated from human gut when grown in aerobiosis with antioxidants.\n\nMethodsThree human gut Clostridia, Clostridium sporogenes, Clostridium lituseburense and Clostridium subterminale, isolated by culturomics, were grown in anaerobiosis or in aerobiosis with antioxidants. Gaz and liquid chromatography-Mass spectrometry (GC/MS and LC/MS) were used for metabolomics analysis.\n\nResultsAn unexpected global dichotomic metabolomic switching from thiols, alcohols and short-chain fatty acid esters to a specific aerobic metabolic repertoire with the production of alkanes, cycloheptatriene and, paradoxically, increased butyrate production, was observed. Analysis of polar metabolites confirmed the discovery of an unexplored aerobic metabolic repertoire, including the production of specific dipeptides and several lysophospholipids, thus unraveling unsuspected human gut microbiome capacities.\n\nConclusionsAntioxidants unraveled an unexplored aerobic metabolic repertoire of human gut Clostridia. The increased production of butyrate suggests that antioxidants contribute to the maintenance and the active resilience of the human gut microbiome against oxidative aggression, as during Salmonella infection.

microbiology↗

bioRxiv2018

FilmArray Respiratory Panel Integrated in a field Point Of Care dispositive for the diagnosis of respiratory tract infections in rural areas in Senegal

The development of molecular syndrome-based kits for the diagnosis of respiratory infections offers rapid and sensitive detection of common respiratory pathogens and will have a significant impact on the care of patients. In this study, we present the results obtained after the introduction of the FilmArray respiratory panel in a field Point of care (POC) for the diagnosis of virus and bacteria responsible of respiratory tract infections in Senegal rural area. From February to August 2017, we collected nasal swabs from febrile patients that presented symptoms of respiratory tract infections in three health posts located in Niakhar. Specimens were tested on site by multiplex Polymerase Chain Reaction (PCR), using the FilmArray respiratory panel(R) that targets 20 pathogens, including 17 virus and 3 bacteria (bioMerieux). Nasal swabs were collected from 113 patients. The median age was 4 years (ranging from 4 months to 60 years) and 51 (45%) were males. The prevalence of respiratory pathogens was 37.5% (12/32) during the dry season and 54.3% (44/81) in the rainy season (p=0.16). The prevalence of respiratory pathogen carriage was higher in children under 5 years of age (38/55, 69.1%). The most prevalent micro-organisms detected were influenza B virus (16/113, 14%), human rhinovirus/enterovirus (10/113, 9%), parainfluenzae virus (9/113, 8%), respiratory syncytial virus (8/113, 7%), adenovirus (5/113, 4%), human metapneumovirus (3/113, 3%), Chlamydia pneumoniae (2/113, 2%) and Coronavirus (2/113, 2%). The study has demonstrated that the integration of the FilmArray respiratory panel into a field POC could significantly improve the management of respiratory tract infections in rural areas.\n\nAuthor summaryRespiratory tract infections are one of the leading causes of death worldwide. Populations in underdeveloped countries are the most affected, especially children under 5 years of age. Among the pathogens responsible for these infections, bacteria and viruses are the most identified. In poor countries, laboratory diagnosis can only be done in urban areas. They are generally based on bacteriological, immunological or molecular biology techniques. The concept of POC is not developed in underdeveloped countries. Its existence would have made it possible to carry out RDTs to confirm the clinicians diagnosis and allow rapid management of the patient. In the current situation, the time required to achieve results is often very long for patients. In this study, we sought to demonstrate the significant contribution of the FilmArray respiratory panel in the management of respiratory tract infections in rural areas. We also wanted to reduce the time it takes to deliver results in order to improve patient care. This dispositif was integrated in a field POC which was implemented in Niakhar since 2015, in order to improve the management of emerging diseases. The FilmArray respiratory panel gave us the opportunity to investigate the causes of respiratory tract infections in this area. For each patient, we systematically target 20 pathogens, including 17 viruses and 3 bacteria, with a single multiplex PCR. One of the main results of this study is that children under 5 years of age are the most affected by respiratory tract infections. Then we noted a lack of consultation among adults that could be explained by the banalization of respiratory problems or a preference for traditional care. The fact that children under 5 years of age are the most affected could also serve as a basis for implementing vaccination programmes directly targeting the most vulnerable age groups. It should be noted that for 51% of patients, the result of the diagnosis was negative. It would appear that some pathogens responsible for respiratory tract infections are not targeted by the multiplex PCR. Thus, it would be necessary to screen these pathogens in order to integrate them into a panel that would cover the most pathogens in circulation in this area.

molecular biology↗