[Reforming Biosciences and Health Research: Part I, Funding]. / Rapport 21-06. Réformer la recherche en sciences biologiques et en santé : partie I, le financement.

The COVID-19 pandemic occurred in the context of a dramatic decline in support for biological and health research in France. An analysis of resources allocated to this sector shows that the credits in 2020 correspond to only 17.2 % of the total credits allocated to research, the lowest ratio inat least 15 years. Another weakness in the system of support for hospital research is the way funds from the health insurance system are allocated. To bring it into line with international best practices, the task of allocating these funds should be entrusted to a "Hospital Research Orientation Council", which should also be involved in the implementation of national research programming. Another article deals with the organization of research. Recommendations are also made to improve the functioning of the research system at the local level, particularly in university hospitals, and at the national level.

The death of Henry II, King of France (1519-1559). From myth to medical and historical fact.

On 30 June 1559, Henry II, King of France, was mortally wounded in the head by a lance during a jousting match. Despite the best efforts of his physicians, Ambroise Paré and Andreas Vesalius, King Henry died 11 days later. This article, based on previously unpublished evidence, aims at examining the historical account of his death against modern medical practice to establish the probable cause of the king's death. We also discuss what treatments the doctors in the sixteenth century may have had to offer. Historical accounts of the joust provide details of the incident including the position of the visor of the king's helmet. Descriptions of the wood fragments removed from the right orbit by Italian observers and a new translation of the autopsy by Andreas Vesalius allow an accurate description of the actual injury. Our research counters previous theories and concludes that Henry II was the victim of craniofacial trauma involving the right eye and that he died from periorbital cellulitis caused by a retained foreign body in the wound, complicated by a left interhemispheric empyema preceded by a traumatic interhemispheric haematoma. It would appear that the royal court doctors advocated a wait-and-see strategy, with little actual input from Ambroise Paré or Andreas Vesalius, with a clearly regrettable outcome.

[In the wake of Alphonse Laveran]. / Dans le sillage d'Alphonse Laveran.

Alphonse Laveran (Nobel Prize 1907) played a pioneering role in discovering the causative agent of malaria, a disease that has existed since time immemorial, and long emblematic of the miasma theory until the end of the 19th century. In 1880, this unknown military doctor discovered the role of a hematazoan in malaria, designated Plasmodium. This was the first protozoan to be discovered in an infectious disease, at a time when bacteria were mainly suspected. This major discovery led to the identification of the role of mosquitoes in the spread of malaria by Ronald Ross (Nobel Prize 1902) and Battista Grassi. The recurrence of malaria attacks over many years was for a long time an enigma only solved after the Second World War by the discovery of the exo-erythrocytic cycle of Plasmodium. Progress was then made in treatment, from cinchona bark, quinine and chloroquine, to the recent discovery of artemisinin in 1972 by the Chinese researcher Tu Youyou (Nobel Prize 2015).

Gain-of-function and origin of Covid19.

In nature, wild viruses adapted for transmission circulate in many animal species (bats, birds, primates…). Contamination of other animals, including humans, may occur by crossing of the species barrier. Genetic manipulations have been carried out on wild viruses to favor the species jumping and to increase of viral virulence. The aim was to identify the critical genes for pathogenicity. This has been mainly performed on potentially epidemic pathogens, as Myxovirus influenzae of avian flu and coronaviruses of SARS and MERS epidemics. These dangerous experiments were subject to a moratorium in the United States (2014-2017). Three years after the emergence of Covid-19, the origin of du SARS-CoV2 remains a mystery. Covid19 appeared in Wuhan, officially in December 2019, but probably during the autumn 2019. The virus was identified in January 2020. It belongs to the genus Betacoronavirus (subgenus Sarbecovirus). It was at once highly contagious. In addition, the primary isolates were genetically very homogeneous, differing only by two nucleotides without evidence for adaptive mutations. In addition, the Spike protein, a major virulence factor, has a furin site, not found in any other known sarbecovirus. Unlike the SARS and MERS epidemics, no intermediate host has been detected so far. Finally, no other outbreaks were reported at the beginning of the pandemic outside of Wuhan, contrary to what happened with the emergence of SARS (2002) and H7N9 avian influenza (2013). Today, there are two scenarios to explain the emergence of SARS-CoV2. Proponents of the natural origin argue that the bat virus might have directly infected humans, spreading silently at a low level in humans for years, without eliminating the existence of undetected intermediate hosts. This does not explain the origin in Wuhan, far away from the natural virus reservoirs. The furin site would have arisen spontaneously from other coronaviruses. The alternative scenario is that of a laboratory accident after gain-of-function manipulations from a SARS-like virus, or even the occurrence of a human contamination by a natural CoV virus grown on cells in Wuhan. This article is an update to the Quarterly Medical Review (QMR) devoted to the history of modern pandemics. To access this QMR contents, please go here: https://www.sciencedirect.com/journal/la-presse-medicale/vol/51/issue/3.

The Spanish flu.

The Spanish flu occurred at the end of the First world war, in disastrous epidemiological conditions on populations exhausted by four years of war. At that time, there were no vaccines, no antibiotics, no oxygen and no resuscitation. It was even thought that the infectious agent was a bacterium. Humanity was poorly equipped to fight against a pandemic that caused 50-100 million deaths. The first palpable signs of the outbreak were the rapidly spreading multiple epidemics among young recruits in the American military training camps in March 1918. The flu then spread to the civilian populations and circled the globe twice, sparing no country, even the most remote islands, in tropical as well as polar climates, evolving in successive waves up until April 1919. The first was mild (lethality 0.21%), the second was lethal (lethality 2-4%), and during the third wave, lethality declined (1%), after which the flu became seasonal, with low lethality (0.1%). Between 20 and 40 years of age, patients often died within a few days of pneumonia, with respiratory distress leading to cyanosis, frequently associated with bacterial superinfection. The influenza virus, Myxovirus influenzae, was first discovered in 1931 by Richard Shope in pigs, and then in 1933 by Wilson Smith, Patrick Laidlaw and Christopher Andrews in humans during a seasonal influenza epidemic in London. In 1943, it was first observed under the electron microscope. Hemagglutinin and neuraminidase, the two main virulence factors, were discovered in the 1940s by George Hirst and Alfred Gottschalk. An RNA virus composed of 13,500 nucleotides in eight segments, it was initially sequenced in the 1980s, when Jeffrey Taubenberger determined the complete nucleotide sequence of the 1918 virus from lung tissue samples from patients who died of influenza. The 1918 H1N1 virus was found to have originated in birds. In 2005, it was successfully resuscitated in cell culture. It is 40,000 times more virulent in primates than the seasonal H1N1 virus. The lethality of the second wave could have been due to mutations in the hemagglutinin H1 gene, which would have resulted in a stronger affinity for α,2-6 galactose sialic acids, the virus' receptors on human epithelial cells. That said, the origin of the Spanish flu virus remains controversial. It probably emerged and circulated in the population before March 1918 in America, although European origin has also been evoked. The high mortality in the 20-40 age group remains an enigma. Some experts point to reduced immune response in patients previously exposed to related viral hemagglutinins during the 1889 pandemic. In any event, even though it concerns a markedly different virus, the history of the Spanish flu sheds light on the difficulties of management during today's pandemic.

Life and death of smallpox.

Smallpox is an ancient scourge known since the Antiquity. It is caused by a highly contagious airborne poxvirus. This strictly human disease exists in two forms: variola major (Asian smallpox) with mortality of 20-45%, and an attenuated form called variola minor or alatrim with mortality of 1-2%, which only recently appeared in Europe and America towards the end of the 19th century. The first smallpox pandemic was the "Antonine plague", which swept through the Roman Empire in the 2nd century AD, after which smallpox became endemic in the Old World, causing seasonal and regional epidemics in Europe, affecting mostly young children until the 19th century. The discovery of the New World in 1492 and the opening of the African slave trade favored in 1518 the contamination by smallpox of the native Amerindian populations, who were massively decimated during the following centuries. In the absence of any effective treatment, preventive methods were developed from the 18th century. First, variolation was used, a dangerous procedure that consists in inoculating intradermally a small quantity of virus from convalescent patients. In the early 19th century, Edward Jenner popularized the practice of inoculating cowpox, a mild cow disease. This procedure proved to be very effective and relatively safe, leading to the decline of smallpox during the 19th century. In the 20th century, a ten-year WHO vaccination campaign led to the total eradication of smallpox in 1977. During that century, smallpox caused an estimated 300-500 million deaths worldwide. Using molecular approach, it has been discovered that the smallpox virus emerged 3000-4000 years ago in East Africa and is closely related to the taterapox virus from African gerbils and to the camelpox virus, which causes variola in camelids. Today, smallpox virus strains are stored in freezers at the CDC in Atlanta and at the Vector Center in Koltsovo, Siberia. That is why smallpox remains a potential threat to the highly susceptible human species, as a result of an accident or malicious use of the virus as a biological weapon.

The enigma of the 1889 Russian flu pandemic: A coronavirus?

The "Russian flu", which raged from 1889 to 1894, is considered as the first pandemic of the industrial era for which statistics have been collected. This planetary event started in Turkestan and hit the Russian Empire, before reaching all European countries, the United States of America, and the whole world. Contemporaries were surprised by its high contagiousness as evidenced by attack rates averaging 60% in urban populations, its rapid spread in successive waves circling the globe in a few months by rail and sea, and the tendency of the disease to relapse. Despite its low case-fatality rate (0.10%-0.28%), it is estimated to have caused one million deaths worldwide. On serological grounds, it is generally accepted that the causative agent of Russian influenza was Myxovirus influenzae, the virus identified for all influenza pandemics since the "Spanish flu" of 1918. In light of the Covid-19 pandemic, which has underscored the extraordinary epidemic potential of coronaviruses, this assumption has recently been questioned. Coronaviruses come from wild reservoirs (bats, rodents, birds, …). They induce respiratory symptoms mimicking influenza, possibly leading to respiratory distress with pneumonia. In addition to the Covid-19 pandemic, recent deadly and limited epidemics, such as SARS in 2002 and MERS in 2012, have occurred. Russian influenza presented as an influenza-like syndrome with clinical peculiarities (multivisceral and neurological involvement, skin rash, early iterative relapses), evoking some particularities of Covid-19. Four other coronaviruses circulating in the human population for decades (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1) have been found to be responsible for 15 to 30% of seasonal colds. All of these viruses are of animal origin. Recently, phylogenetic studies have revealed the genetic proximity between a bovine coronavirus BCoV and the human virus HCoV-OC43, indicating that the latter emerged around 1890, at the time of the Russian flu, when an epizootic was raging among cattle throughout Europe. Could the current human virus be the attenuated remnant that appeared after the Russian flu in 1894? Was there a coronavirus pandemic before Covid-19 ?

History of measles.

Measles is a highly contagious viral disease transmitted by aerosols through human-to-human contact. It is often considered as a benign disease, although mortality remains high in developing countries (>5%). Frequent complications (diarrhea, otitis, pneumonia, encephalitis) can be observed. The disease mainly affects young children from 5 to 6 months of age with a mortality peak in the first three years of life. The Persian physician Rhazes gave the first clinical description of the disease in the 10th century, clearly differentiating it from smallpox. Measles spread worldwide from the Renaissance. Its epidemiology was remarkably studied in 1846 by a Danish physician, Peter Panum, during an epidemic in the Faroe Islands. The viral nature of this disease was demonstrated in 1911 and the virus was identified in 1954 by Thomas Peebles and John Enders. It is a morbillivirus (family Paramyxoviridae), also responsible for rinderpest (ovine, bovine), distemper (canine, feline), and epidemic diseases of dolphins, porpoises and seals. The current measles virus appeared recently from the rinderpest virus around the 6th century BCE. It has adapted perfectly to the human species, becoming strictly human, without animal reservoirs. A live attenuated vaccine was developed in 1958 by Enders' team after numerous passages in cell cultures. The vaccine was licensed in the United States in 1963 and is used on a large scale by the WHO throughout the world. This highly effective and well-tolerated vaccine has greatly reduced the number of measles cases and saved millions of lives. Measles remains a major public health concern, causing over 100,000 deaths per year worldwide. Today, the most affected continents remain Africa, South America and Asia.

Diagnosis of Listeria monocytogenes meningoencephalitis by real-time PCR for the hly gene.

Listeria monocytogenes is a bacterial pathogen that can invade the central nervous system (CNS), causing meningoencephalitis and brain abscesses. The diagnosis of CNS listeriosis, based on the isolation of the bacteria in the cerebrospinal fluid (CSF), can be difficult because of previous antibiotic treatment and a low number of bacteria in the CSF. To improve the sensitivity of microbiological diagnosis, we have developed a real-time PCR assay for detecting and quantifying L. monocytogenes DNA in the CSF. The designed primers specifically amplify the L. monocytogenes hly gene, which encodes listeriolysin O, a pore-forming cytolysin. The PCR assay for the hly gene (PCR-hly) provides reproducible quantitative results over a wide dynamic range of concentrations and was highly sensitive while detecting a single gene copy/ml. By assaying a large panel of bacterial species, including species secreting pore-forming cytolysin, we determined the specificity of the PCR-hly, which exclusively detects the L. monocytogenes DNA. We then analyzed 214 CSF samples from patients suspected of having CNS listeriosis. PCR-hly was positive in all cases in which L. monocytogenes was isolated by culture. Positive PCR-hly of the CSF was also obtained for five additional, clinically confirmed cases of CNS listeriosis for which bacterial cultures were negative presumably due to previous treatment with antibiotics. As a complement to classical bacteriological CSF culture, our designed real-time PCR-hly assay proved to be valuable by enhancing the rapidity and the accuracy of the diagnosis of CNS infection by L. monocytogenes. In addition, the quantitative results provided may, in some instances, be useful for the follow-up of patients under treatment.

Listeria monocytogenes: a rare complication of ventriculoperitoneal shunt in children.

We report a case of ventriculoperitoneal (VP) shunt infection in a 3-year-old boy caused by the food-borne pathogen Listeria monocytogenes, subsequent to acute peritonitis. This unusual presentation of central nervous system (CNS) listeriosis underlines the ability of the bacteria to form and survive within biofilms on indwelling medical devices. Bacterial persistence may lead to treatment failure and spreading. We highlight the helpfulness of specific quantitative real-time PCR for the hly gene (PCR-hly) for the diagnosis and follow-up of such infections in detecting bacterial persistence within medical devices despite effective antibiotic treatment. Only the surgical replacement of the VP shunt will resolve the infection.

Efficacy of rifampin-moxifloxacin-metronidazole combination therapy in hidradenitis suppurativa.

BACKGROUND: Antibiotics have been shown to improve hidradenitis suppurativa (HS) patients but complete remission is rare using these treatments. OBJECTIVE: To assess the efficacy and safety of a combination of oral rifampin, moxifloxacin and metronidazole in long-lasting refractory HS. METHODS: We retrospectively studied 28 consecutive HS patients including 6, 10 and 12 Hurley stage 1, 2 and 3 patients, respectively. Complete remission, defined as a clearance of all inflammatory lesions including hypertrophic scars, was the main outcome criterion of the study. RESULTS: Complete remission was obtained in 16 patients, including 6/6, 8/10 and 2/12 patients with Hurley stage 1, 2 and 3, respectively (p=0.0004). The median duration of treatment to obtain complete remission was 2.4 (range 0.9-6.5) and 3.8 months (range 1.6-7.4) in stage 1 and 2 patients, respectively, and 6.2 and 12 months in the 2 stage 3 patients. Main adverse events of the treatments were gastrointestinal disorders (64% of patients) and vaginal candidiasis (35% of females). Reversible tendinopathy and hepatitis occurred in 4 and 1 patient, respectively. CONCLUSIONS: Complete remission of refractory HS can be obtained using broad-spectrum antibiotics and Hurley staging is a prognostic factor of response to the treatment.

COVID-19: individual and herd immunity.

Immunity to the SARS-CoV-2 virus ensures protection against reinfection by this virus thanks to the combined action of neutralizing antibodies and T lymphocytes specific to viral proteins, in particular the Spike protein. It must be distinguished from the immune response that ensures healing of the infection following contamination that involves innate immunity, particularly type 1 interferons, and which is followed by adaptive cellular and humoral immunity. The importance of the effect of interferons is highlighted by the occurrence of severe forms of the disease in genetically deficient subjects or in patients with antibodies neutralizing type 1 interferon. Herd immunity is not an individual biological property. It is a mathematical property that qualifies the fact that when the proportion of subjects with individual immunity is high enough, there is little chance that an epidemic can occur. The level of that proportion-the herd immunity of the population can be computed under theoretical, often unrealistic, hypotheses, and is difficult to assess in natural conditions.

L'immunité individuelle contre le virus SARS-CoV-2 assure la protection contre la réinfection par ce virus grâce à l'action conjuguée des anticorps neutralisants et des lymphocytes T spécifiques des protéines virales, notamment la protéine Spike (spicule). Il faut la distinguer de la réponse immunitaire qui assure la guérison de l'infection dans les jours suivant la contamination. Celle-ci fait intervenir l'immunité innée et tout particulièrement les interférons de type 1 puis l'immunité adaptative cellulaire et humorale. L'importance de l'effet des interférons est soulignée par la survenue de formes graves chez des sujets génétiquement déficients dans leur synthèse ou encore des patients présentant des anticorps neutralisant l'interféron de type 1. L'immunité collective caractérise la faible probabilité de développement d'une épidémie dans une population ayant un pourcentage élevé de sujets présentant une immunité individuelle. Le taux d'immunité collective nécessaire pour faire disparaître l'épidémie a été calculé dans des modèles mathématiques supposant la panmixie ; il est difficile à évaluer dans les populations réelles.

Human listeriosis caused by Listeria ivanovii.

Two species of Listeria are pathogenic; L. monocytogenes infects humans and animals, and L. ivanovii has been considered to infect ruminants only. We report L. ivanovii-associated gastroenteritis and bacteremia in a man. This isolate was indistinguishable from prototypic ruminant strains. L. ivanovii is thus an enteric opportunistic human pathogen.

Real-time identification of bacteria and Candida species in positive blood culture broths by matrix-assisted laser desorption ionization-time of flight mass spectrometry.

Delays in the identification of microorganisms are a barrier to the establishment of adequate empirical antibiotic therapy of bacteremia. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) allows the identification of microorganisms directly from colonies within minutes. In this study, we have adapted and tested this technology for use with blood culture broths, thus allowing identification in less than 30 min once the blood culture is detected as positive. Our method is based on the selective recovery of bacteria by adding a detergent that solubilizes blood cells but not microbial membranes. Microorganisms are then extracted by centrifugation and analyzed by MALDI-TOF-MS. This strategy was first tested by inoculating various bacterial and fungal species into negative blood culture bottles. We then tested positive patient blood or fluid samples grown in blood culture bottles, and the results obtained by MALDI-TOF-MS were compared with those obtained using conventional strategies. Three hundred twelve spiked bottles and 434 positive cultures from patients were analyzed. Among monomicrobial fluids, MALDI-TOF-MS allowed a reliable identification at the species, group, and genus/family level in 91%, 5%, and 2% of cases, respectively, in 20 min. In only 2% of these samples, MALDI-TOF MS did not yield any result. When blood cultures were multibacterial, identification was improved by using specific databases based on the Gram staining results. MALDI-TOF-MS is currently the fastest technique to accurately identify microorganisms grown in positive blood culture broths.

Rapid identification of mycobacterial whole cells in solid and liquid culture media by matrix-assisted laser desorption ionization-time of flight mass spectrometry.

Mycobacterial identification is based on several methods: conventional biochemical tests that require several weeks for accurate identification, and molecular tools that are now routinely used. However, these techniques are expensive and time-consuming. In this study, an alternative method was developed using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). This approach allows a characteristic mass spectral fingerprint to be obtained from whole inactivated mycobacterial cells. We engineered a strategy based on specific profiles in order to identify the most clinically relevant species of mycobacteria. To validate the mycobacterial database, a total of 311 strains belonging to 31 distinct species and 4 species complexes grown in Löwenstein-Jensen (LJ) and liquid (mycobacterium growth indicator tube [MGIT]) media were analyzed. No extraction step was required. Correct identifications were obtained for 97% of strains from LJ and 77% from MGIT media. No misidentification was noted. Our results, based on a very simple protocol, suggest that this system may represent a serious alternative for clinical laboratories to identify mycobacterial species.

[A virologist visits the Papuan anthropophagists]. / Un virologue chez les anthropophages papous.

In the 1950's, the American Carleton Gajdusek (1923-2008) was able to find the cause for kuru, a systematically fatal neurological disease, observed mainly on the Western Highlands of New Guinea. While living for a long period with the local indigenous population and studying their customs, he evidenced the infectious origin of this pathology and its transmission mechanism, cannibalism. He also demonstrated the transmissible nature of the agent of Creutzfeldt-Jakob. His works opened an important prospective field of research in neuroscience. A Nobel prize rewarded this outstanding scientific and human adventure.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of nonfermenting gram-negative bacilli isolated from cystic fibrosis patients.

The identification of nonfermenting gram-negative bacilli isolated from cystic fibrosis (CF) patients is usually achieved by using phenotype-based techniques and eventually molecular tools. These techniques remain time-consuming, expensive, and technically demanding. We used a method based on matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) for the identification of these bacteria. A set of reference strains belonging to 58 species of clinically relevant nonfermenting gram-negative bacilli was used. To identify peaks discriminating between these various species, the profile of 10 isolated colonies obtained from 10 different passages was analyzed for each referenced strain. Conserved peaks with a relative intensity greater than 0.1 were retained. The spectra of 559 clinical isolates were then compared to that of each of the 58 reference strains as follows: 400 Pseudomonas aeruginosa, 54 Achromobacter xylosoxidans, 32 Stenotrophomonas maltophilia, 52 Burkholderia cepacia complex (BCC), 1 Burkholderia gladioli, 14 Ralstonia mannitolilytica, 2 Ralstonia pickettii, 1 Bordetella hinzii, 1 Inquilinus limosus, 1 Cupriavidus respiraculi, and 1 Burkholderia thailandensis. Using this database, 549 strains were correctly identified. Nine BCC strains and one R. mannnitolilytica strain were identified as belonging to the appropriate genus but not the correct species. We subsequently engineered BCC- and Ralstonia-specific databases using additional reference strains. Using these databases, correct identification for these species increased from 83 to 98% and from 94 to 100% of cases, respectively. Altogether, these data demonstrate that, in CF patients, MALDI-TOF-MS is a powerful tool for rapid identification of nonfermenting gram-negative bacilli.

Fusobacterium necrophorum middle ear infections in children and related complications: report of 25 cases and literature review.

BACKGROUND: Fusobacterium necrophorum is associated with Lemierre syndrome (pharyngitis with septic thrombosis of the internal jugular veins) but it can also be involved in other head and neck infections, including sinusitis, parotitis, dental infections, and otitis media. METHODS: This retrospective study analyzes a series of 25 pediatric cases of acute otitis media caused by F. necrophorum and treated in our institution between 1995 and 2006. RESULTS: We observed 3 clinical presentations: (1) uncomplicated otitis media (44%; n = 11); (2) acute mastoiditis (40%; n = 10); and (3) otogenic variant of Lemierre syndrome (16%; n = 4) associating acute mastoiditis, suppurative thrombophlebitis of the lateral and/or cavernous sinuses, meningitis syndrome, and sometimes distant septic metastasis or extensive osteolysis of the temporal bone. Sixty percent of these cases were diagnosed during the last 4 years of the study. Children less than 1 year of age were at increased risk for Lemierre syndrome. Broad range 16S rDNA polymerase chain reaction and sequencing were used to confirm the identification of F. necrophroum and to detect secondary sites of infection. All patients had favorable clinical outcome, but complicated cases (mastoiditis and otogenic variant of Lemierre syndrome) required prolonged hospital stays and duration of treatment. CONCLUSIONS: Based on bacteriologic investigation, we recommend systematic culture for anaerobes and that antibiotic treatment of F. necrophorum middle ear infections and subsequent complications includes coverage for anaerobic bacteria.