[The French Armed Forces Biomedical Research Institute (IRBA) and wastewater-based epidemiology: Applicability and relevance in armed forces]. / L'Institut de recherche biomédicale des armées (IRBA) et l'épidémiologie des eaux usées : intérêt pour les forces armées.

The French Armed Forces Biomedical Research Institute (IRBA) deeply involved in research on SARS-COV-2, participated in the creation of the Obépine sentinel network in charge of detecting, qualifying and quantifying the virus genome in wastewater in France. During this pandemic, wastewater-based epidemiology has proven to be a first class public health tool for assessing viral dynamics in populations and environment. Obépine has also conducted research demonstrating the low infectivity of faeces and wastewater and allowed for early detection of epidemic waves linked to new variants. The IRBA has adapted this powerful tool to the monitoring of viral infections on board the aircraft carrier Charles-de-Gaulle in order to get an operational system for anticipation after the first local outbreak in 2020. The presence of this surveillance and anticipation tool has allowed a better management of SARS-CoV-2 contingent introductions on board during stopovers or crewmembers entries. The combination of a mandatory vaccination protocol and the surveillance of viral circulation in black waters has made it possible to identify and locate cases, and thus to continue the operational mission in the COVID-19 environment while limiting the spread and preserving the health of the crew. This innovative tool can easily be redirected to the search for any other pathogens in blackwater or even, in the long term, to ensure health surveillance of any military establishment, at sea or on land, in France or on overseas bases.

Evaluation of lockdown effect on SARS-CoV-2 dynamics through viral genome quantification in waste water, Greater Paris, France, 5 March to 23 April 2020.

IntroductionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of coronavirus disease (COVID-19). People infected with SARS-CoV-2 may exhibit no or mild non-specific symptoms; thus, they may contribute to silent circulation of the virus among humans. Since SARS-CoV-2 RNA can be detected in stool samples, monitoring SARS-CoV-2 RNA in waste water (WW) has been proposed as a complementary tool to investigate virus circulation in human populations.AimTo test if the quantification of SARS-CoV-2 genomes in WW correlates with the number of symptomatic or non-symptomatic carriers.MethodWe performed a time-course quantitative analysis of SARS-CoV-2 by RT-qPCR in raw WW samples collected from several major WW treatment plants in Greater Paris. The study period was 5 March to 23 April 2020, including the lockdown period in France (from 17 March).ResultsWe showed that the increase of genome units in raw WW accurately followed the increase of human COVID-19 cases observed at the regional level. Of note, the viral genome could be detected before the epidemic grew massively (around 8 March). Equally importantly, a marked decrease in the quantities of genome units was observed concomitantly with the reduction in the number of new COVID-19 cases, 29 days following the lockdown.ConclusionThis work suggests that a quantitative monitoring of SARS-CoV-2 genomes in WW could generate important additional information for improved monitoring of SARS-CoV-2 circulation at local or regional levels and emphasises the role of WW-based epidemiology.

[Dengue fever: from disease to vaccination]. / La dengue: de la maladie à la vaccination.

Dengue is a tropical disease affecting 110 countries throughout the world and placing over 3 billion people at risk of infection. According the World Health Organization 70 to 500 million persons are infected every year including 2 million who develop hemorrhagic form and 20,000 who die. Children are at highest risk for death. Due to the absence of specialized laboratories in most endemic regions and to the lack of specifici clinical presentation, the incidence of dengue and its economic costs are certainly underestimated. Dengue iscaused by an arbovirus belonging to the Flavivirus genus of the family Flaviviridae. There are four dengue virus serotypes and no cross protection between them. The disease is transmitted through the bites of mosquitoes belonging to the Aedes genus, mainly Aedes aegypti. However A. albopictus has played an important role in the spread of the disease and other species may be involved in specific locations (e.g., A. polynesiensis in the South Pacific). There is no specific treatment for dengue. Management of severe forms depends on symptomatic treatment of hemorrhagic complications and hypovolemic shock. Prevention requires control of vector mosquitoes that is difficult to implement and maintain. Dengue is a major emerging infectious disease with a heavy impact on public health. The high human and economic costs as well as the absence of specific preventive measures underscore the need to develop a vaccine. However finding and distributing such a vaccine to populations at risk is hampered by numerous obstacles. The most notable challenges standing in the way of development of a candidate vaccine are as follows: absence of an animal model, which has important implications for the preclinical development strategy; need to develop a live attenuated vaccine; existence of 4 antigenically distinct serotypes with the resulting risk of competition between vaccine strains; immunologic risks related to antibody-dependent enhancement that has been hypothesized to be the cause of severe forms of the illness; absence of a well defined correlate of protection and preexisting vaccine, which will require the organization of large-scale pre-clinical trials to demonstrate the efficacy of the virus; complexity associated with industrial production of a tetravalent vaccine. Development and production of a safe and reliable vaccine are only the first steps to ensuring protection of the populations at risk, It twill also be necessary to identify and take into account a variety of geographic, economic, regulatory, and logistic factors: The epidemiological profile of dengue is variable. For example the age at which the likelihood of developing the disease is highest is not the same in Asia and Latin America. Vaccination programs must be tailored to regional and national epidemiological specificities. Introduction of dengue vaccination in the national immunization programs must take into account the special features of each country without jeopardizing the existing vaccines already in use. The need for an additional visit can represent a hardship both economically and logistically. Alternative funding will be needed to finance vaccination programs in some countries located in endemic zones, Long-term phase 4 effectiveness and tolerance field studies must be planned in collaboration with national authorities. All these challenges and obstacles have been taken into account in the development of Sanofi Pasteur's live attenuated tetravalent vaccine. Research for development of a dengue vaccine began during the 1990s. Clinical studies with the most promising tetravalent vaccine were started in the 2000s. A trial carried out in adults in the United States has shown that administration of three doses of the tetravalent candidate vaccine was 100% successful in inducing an antibody response capable of neutralizing all four dengue virus serotypes. Phase II clinical trials are now under way in children and adults in Mexico, Peru, and the Philippines. The first efficacy trial in children began in Thailand in February 2009. The purpose is to evaluate the efficacy of the tetravalent dengue vaccine in children. The study is being conducted in the Ratchaburi province in collaboration with the University of Mahidol and the Thai Ministry of Health as well as the Pediatric Dengue Vaccine Initiative (PDVI). This efficacy trial will be an important step for successful development of a live attenuated tetravalent vaccine.

[From genomics to surveillance, prevention and control: new challenges for the African meningitis belt]. / Ceinture africaine de la méningite: de la génomique aux stratégies de surveillance, de lutte et de prévention.

An international conference was held in Niamey, Niger, in November 2005. It aimed at reviewing the current situation in the meningitis belt. This region stretches from Senegal to Ethiopia and is characterized by high levels of seasonal endemicity with large epidemics of meningococcal meningitis occurring cyclically, generally caused by N. meningiditis serogroup A. WHO currently recommends a reactive strategy based on rapid detection of epidemics, intervention with antibiotics to treat cases and mass vaccination with a meningococcal polysaccharide vaccine to halt the outbreak. Epidemiological patterns of the disease in Africa have been changing with the occurrence of outbreaks outside the meningitis belt and with the emergence of serogroup W135, which first caused an epidemic among Hajj pilgrims in 2000 and then a large-scale meningitis outbreak in Burkina Faso in 2002. Consequently enhanced laboratory surveillance and confirmation of the strain responsible for the outbreak are required. New rapid dipstick tests have been developed through a collaboration between Institut Pasteur and CERMES. They are designed for bedside diagnosis and detect meningococcal antigens present in CSF using immunochromatography. The treatment of meningococcal meningitis during epidemics is based on short-course, long-acting oily chloramphenicol. An alternative is the use of ceftriaxone, which is equally effective and can be used in pregnant women and infants. A low-cost, monovalent serogroup A meningococcal conjugate vaccine for large-scale use in Africa is under development. In spite of the emergence of W135 strains in the meningitis belt, N. meningiditis A continues to be the principal strain isolated during the epidemic seasons and elimination of outbreaks of N. meningiditis serogroup A can still be considered as the primary objective of a preventive vaccination strategy.

Surveillance network for herpes simplex virus resistance to antiviral drugs: 3-year follow-up.

Herpes simplex virus (HSV) infections are very common in the general population and among immunocompromised patients. Acyclovir (ACV) is an effective treatment which is widely used. We deemed it essential to conduct a wide and coordinated survey of the emergence of ACV-resistant HSV strains. We have formed a network of 15 virology laboratories which have isolated and identified, between May 1999 and April 2002, HSV type 1 (HSV-1) and HSV-2 strains among hospitalized subjects. The sensitivity of each isolate to ACV was evaluated by a colorimetric test (C. Danve, F. Morfin, D. Thouvenot, and M. Aymard, J. Virol. Methods 105:207-217, 2002). During this study, 3900 isolated strains among 3357 patients were collected; 55% of the patients were immunocompetent. Only six immunocompetent patients excreted ACV-resistant HSV strains (0.32%), including one female patient not treated with ACV who was infected primary by an ACV-resistant strain. Among the 54 immunocompromised patients from whom ACV-resistant HSV strains were isolated (3.5%), the bone marrow transplantation patients showed the highest prevalence of resistance (10.9%), whereas among patients infected by human immunodeficiency virus, the prevalence was 4.2%. In 38% of the cases, the patients who excreted the ACV-resistant strains were treated with foscarnet (PFA), and 61% of them developed resistance to PFA. The collection of a large number of isolates enabled an evaluation of the prevalence of resistance of HSV strains to antiviral drugs to be made. This prevalence has remained stable over the last 10 years, as much among immunocompetent patients as among immunocompromised patients.

Use of equivocal zone in interpretation of results of the amplified mycobacterium tuberculosis direct test for diagnosis of tuberculosis.

The sensitivity and specificity of the Amplified Mycobacterium Tuberculosis Direct (AMTD) test, evaluated with 1,363 respiratory samples (128 from tuberculous patients), were 92.97 and 98.7%, respectively. When an equivocal zone (30,000 to 1,000,000 relative light units [RLU]) was used instead of a 30,000-RLU cutoff, the sensitivity and specificity of the AMTD test were 92.97 and 100%, respectively.

[Antibiotic sensitivity of Salmonella isolated in army hospitals between 1998-1999]. / Sensibilité aux antibiotiques des salmonelles isolées dans les hôpitaux des armées en 1998-1999.

OBJECTIVES: Monitor the evolution in France of antibiotic sensitivity of non-typhoid salmonella isolated in fecal cultures conducted in army hospital laboratories. METHODS: A prospective study was performed from January 1998 to December 1999 in all the biology departments of the 11 army hospitals in France. All the non-repetitive strains were sent to an official center for serotyping and determination of the minimum inhibiting concentrations, by dilution in Mueller Hinton's gelose. The antibiotics currently used in treatment were tested and interpretation endpoints followed the recent recommendations of the Antibiogram committee of the French society of microbiology. Identification of beta-lactamase was conducted by iso-electric focalization and polymerization by chain reaction (PCR). For Salmonella Typhimurium, research for the specific resistance locus of the DT104 clone was made using PCR. RESULTS: Two hundred and twenty-two non-repetitive salmonella strains were isolated. The principle serotypes found were: Salmonella Enterididis (23.9%), S. Typhimurium (21.2%) and S. Hadar (10.8%). All the strains were sensitive to ciprofloxacin and cefotaxim, whereas one third exhibited reduced sensitivity to aminopenicillin. Depending on the serotype, Typhimurium and Hadar serotypes exhibited significantly lesser sensitivity to aminopenicillin, nalidixic acid and tetracycline. For S. Typhimurium, resistance is related to the diffusion of the multiresistant DT104 clone, which involves half of the strains of this serotype. For S. Hadar, 18 out of 24 strains (75%) were resistance to nalidixic acid, and 5 of them exhibited reduced resistance to ciprofloxacin. There was no difference in sensitivity to antibiotics between the strains responsible for diarrhea and those isolated in systematic examinations for capacity to work in the food trade (respectively 54 and 46% of strains). CONCLUSION: Non-typhoid salmonella are frequently isolated in diarrhea of infectious origin. The increasing resistance to antibiotics is primarily related to the diffusion of the DT104 clone, regarding S. Typhimurium and to the increase in resistance to quinolone, regarding S. Hadar.

[Epidemiology of resistance to antituberculosis drugs in Mycobacterium tuberculosis complex strains isolated from adenopathies in Djibouti. Prospective study carried out in 1999]. / Epidemiologie de la resistance aux antituberculeux des souches du complexe Mycobacterium tuberculosis isolees d'adenopathies a Djibouti. Etude prospective realisee en 1999.

Tuberculosis is a major cause of death in the Republic of Djibouti. Tuberculous lymphadenitis represents about 25% of the clinical forms of tuberculosis in this country. Between January 1999 and April 1999, 196 lymph node specimens were consecutively collected from 153 patients living in Djibouti. Testing of susceptibility to the major anti-tuberculosis drugs was performed by the proportion method. Growth of Mycobacterium tuberculosis complex strains was obtained from specimens of 85 patients including 9 with prior treatment. Strains were identified as Mycobacterium tuberculosis in 78 cases, Mycobacterium canetti in 3, Mycobacterium africanum in 3, and Mycobacterium bovis in 1. Prevalence of HIV infection was 15%. Assessment of primary resistance demonstrated that the overall resistance rate, i.e., resistance to 1 or more drugs, was 18 (21.2%). Results showed resistance to isoniazid (H) in 6 cases (7.1%), rifampicin (R) in 3 (3.5%), ethambutol (E) in 1 (1.2%), streptomycin (S) in 13 (15.3%) and pyrazinamide (Z) in 1 (1.2%). Multidrug resistance (MDR) was found in 2 cases (2.4%). Assessment of acquired resistance demonstrated resistance to H in 4 cases (44%), R in 2 (22%), S in 2 (22%), E in 0, Z in 0 and MDR in 1 (11%). These findings were not significantly different from data obtained from sputum samples analysed between 1997 and 2000 or from those described in a study conducted in 1985.

[Status of resistance of HIV-1 strains in Africa: what is the role of viral surveillance networks?]. / Etat de la resistance des souches de VIH-1 en Afrique: quelle place pour les reseaux de surveillance virologique?

The human immunodeficiency virus (HIV-1) epidemic has spread dramatically in sub-Saharan African countries. Implementation of active antiretroviral (ARV) therapy programs is urgently needed. However this emergency situation must not extenuate the importance of preliminary studies on ARV resistance of African HIV-1 isolates. Findings show that genetic mutations underlying the resistance of African strains are generally identical to those observed in HIV-1 subtype B in industrialized countries. However the incidence of some mutations associated with mild resistance to protease inhibitors (PI) appears higher in African isolates. The potential impact of these mutations for development of frank resistance to PI is still unclear. The incidence of high-grade resistance markers in untreated subjects is low. While these results do not compromise use of ARV therapy in Africa, they underline the need to set up local networks for patient follow-up and to carry out epidemiological surveillance of HIV-1 resistance. Success of ARV therapies in Africa will also depend on economic and social programs.

[Sero-epidemiological study of the hepatitis epidemic in Mitrovica in the aftermath of the war in Kosovo (1999)]. / Etude séro-épidémiologique des hépatites épidémiques à Mitrovica dans les suites de la guerre du Kosovo (1999).

In July 1999, after the return of the Kosovar refugees to their country, an outbreak of acute hepatitis A (HAV) and E (HEV) occurred. Epidemic hepatitis and diarrhoea are closely monitored communicable diseases which had been singled out as priorities by the health authorities of the former Republic of Yougoslavia. Several field surveys were undertaken: description of reported cases, serological study of clinical patients, study of anti-HAV seroprevalence in a school and a case control study to assess risk factors. The analysis of the reports indicates an epidemic peak at the end of September, 2 or 3 weeks after the start of the new school year, with an increase of cases relative to the age of the children in school. In a serologic study of 104 samples, we found an anti-HAV IgM positivity in 88% of the cases. Children were more likely to be positive when compared to teenagers and adults; likewise, consumers of well-water as versus those drinking network water (p = 0.03). The study of seroprevalence showed that transmission had taken place within the school. The case control study, in spite of its imperfections, indicated that consumption of water melon, the only fruit cultivated locally, is a factor which facilitates the HAV transmission. Circulation of the hepatitis E virus was confirmed for 4 sick persons (including 2 co-infected HAV-HEV) and in 4 persons without clinical symptoms. These results show the permanent risk of faeco-oral infections in this area and the need to develop a relevant prevention policy.

[Sensitivity to antibiotics of bacteria from nosocomial infections. Evolution in resuscitation services of military hospitals]. / Sensibilité aux antibiotiques des bactéries d'infections nosocomiales. Evolution dans les services de réanimation des hôpitaux des armées.

OBJECTIVE: The aim of this study, conducted in the French Military hospitals, was to monitor the course of the antimicrobial sensibility of bacteria isolated from nosocomial infection in intensive care units. PATIENTS AND METHODS: A prospective study has been conducted from January to December 1998 in all the intensive care units of the French Army. All the non-repetitive strains isolated from nosocomial infection were collected and sent to a reference centre. Antimicrobial susceptibility was determined by the agar dilution method. Beta-lactamase were identified by iso-electro-focalisation. Antibiotics choice and interpretative criteria were those of the "Comité Français de l'Antibiogramme de la Société Française de Microbiologie". RESULTS: A total of 849 strains are included in this study. Pseudomonas aeruginosa was the most frequently isolated bacterium (20%) followed by Escherichia coli (19%) Staphylococcus aureus (15%), coagulase-negative Staphylococci (CoNS) (11%) and Enterococci (7%). Imipenem was the most effective antibiotic against enterobacteriaceae (336 isolates; 100% susceptibility). Gentamicin (92%), amikacin (92%) third generation cephalosporins (83%), aztreonam (83%) and ciprofloxacin (78%) were also very effective. Resistance to III generation cephalosporins was correlated with an extended spectrum beta-lactamase (BLSE) in 36% of cases. This BLSE could be associated with an over production of the constitutive cephalosporinase. The most frequent species producing BLSE were Enterobacter aerogenes (75% of BLSE) and Klebsiella pneumoniae (17%). Among the 172 P. aeruginosa isolated, antimicrobial susceptibility were respectively: 71% for imipenem, 62%: tobramycin, 60%: amikacin 59%: ciprofloxacin 59% piperacillin + tazobactam, 55% piperacillin, 53%: ceftazidime and 44% for ticarcillin. Seventy per cent of the 96 CoNS and 50.2% of the 126 S. aureus isolated were resistant to methicillin. A strain of S. aureus and 2 CoNS strains had intermediate resistance to teicoplanin. Twenty per cent of the 59 Enterococci strains isolated were resistant to aminopenicillins (10/11 strains of E. faecium), and 9% presented a high level of resistance to gentamicine. One strain of E. faecium was resistant to vancomycin. CONCLUSION: The evolution of the susceptibility to antibiotics in intensive care units reflects the antibiotic pressure and level of cross-transmission. High rates of meticillin-resistance among staphylococci, of resistance to beta-lactams antibiotics among P. aeruginosa and of ciprofloxacin among Enterobacteriaceae are shown in this study. The implementation of appropriate strategies for surveillance and prevention is necessary.

Identification of a novel hepatitis E virus in Nigeria.

Sporadic cases of acute hepatitis E among ten native Nigerian adults were reported in Port-Harcourt (Nigeria). Hepatitis E virus (HEV) was detected in serum and/or faecal samples of seven patients by RT-PCR of the open reading frame (ORF)-1 polymerase region and the 3'-end of ORF2. Restriction analysis widely used to distinguish genotypes I and III showed that all Nigerian strains have a pattern similar to the Mexican strain (NotI, nt 286; SmaI, nt 397; no KpnI restriction site) but displayed a BsmI restriction site at nt 213 as do most African HEV strains sequenced so far. Sequence analysis performed from internal ORF1 and ORF2 PCR products displayed strong homogeneity between the HEV isolates, determining a regional cluster. Phylogenetic analysis of nucleotide sequences revealed that these strains were more related to the Mexican prototype genotype III (87% homology in ORF1, 80% homology in ORF2) than to either the African strain genotype I (74% homology in ORF1, 77% homology in ORF2) or the USA strain genotype II (75% homology in ORF1, 77% homology in ORF2). Genetic divergence up to 15% in ORF2 with the Mexican genotype clearly defined a new subgenotype within genotype III. At the amino acid level, Nigerian strains showed more homology with genotype III (96%) than with genotype I (92%). This study clearly determined the co-existence of genotypes I and III in Africa. These Nigerian HEV strains belonging to genotype III, but sharing some properties with genotype I, could be one of the missing links between African and Latin American HEV and could help us to determine the phylogenetic evolution of HEV from the ancestral virus.

[First confirmed case of laryngeal diphtheria in Djibouti]. / Premier cas confirmé d'angine diphtérique à Djibouti.

The first bacteriologically confirmed case of laryngeal diphtheria in Djibouti was reported in 1998. It involved a three-year-old native-born infant who had been vaccinated during the first year of life with three doses of a combined vaccine against diphtheria, tetanus, poliomyelitis, and pertussis. A rapid clinical improvement was observed under erythromycin treatment. Other cases of laryngeal diphtheria have been observed. It is important to reverse decreasing vaccinal coverage in Djibouti and to warn incoming travelers of the need to be adequate immunized against diphtheria. Enhanced epidemiologic surveillance of this disease is also needed.

[Fall in the seroprevalence of hepatitis A in French youth]. / Effondrement de la séroprévalence de l'hépatite virale A chez les jeunes français.

OBJECTIVE: An anti-hepatitis A virus seroprevalence survey was performed in 1997 in 1052 French army recruits (mean age: 21.2 years). To describe epidemiological trends, the current pattern was compared to previous results obtained by similar methods in 1985, 1990 and 1993. RESULTS: In 1997, overall anti-hepatitis A virus seroprevalence was 11.5%. The greatest risk factor of hepatitis A infection was related to travel in intermediate or highly endemic areas for hepatitis A virus: 46% of overseas residents (odds ratio = 10.3), 28% of recruits who had travelled in developing countries (odds ratio = 3.7) and 7.65% of French living in industrialised countries are anti-hepatitis A virus antibody positive. Moreover, seroprevalence was higher in subjects with a history of icteria (adjusted odds ratio = 3.5) and families with at least 3 children (adjusted odds ratio = 3). No association was found with drinking water, socioeconomic status such as baccalaureat degree, or parents profession. The seroepidemiological shift of hepatitis A, as assessed in three previous studies, shows a marked decrease of 20% in 12 years from 30.4% in 1985, to 21.3% in 1990, to 16.3% in 1993, and to 11.5% in 1997. The decrease in the prevalence of anti-hepatitis A virus was more marked in young adults who had never travelled in endemic countries (decrease of 20%) than those who had visited or lived in developing countries (decrease of 10%). CONCLUSION: Although France is not highly endemic for hepatitis A thanks to improved hygiene and housing conditions over the past 20 years, a pattern of intermediate endemicity was seen in French overseas areas in which the risk of outbreaks of hepatitis A was higher. The decrease in anti-hepatitis A virus seroprevalence in French youth can be used to draft a public health policy for hepatitis A control.