Long-Read Sequencing and De Novo Genome Assembly Pipeline of Two Plasmodium falciparum Clones (Pf3D7, PfW2) Using Only the PromethION Sequencer from Oxford Nanopore Technologies without Whole-Genome Amplification.

Antimalarial drug resistance has become a real public health problem despite WHO measures. New sequencing technologies make it possible to investigate genomic variations associated with resistant phenotypes at the genome-wide scale. Based on the use of hemisynthetic nanopores, the PromethION technology from Oxford Nanopore Technologies can produce long-read sequences, in contrast to previous short-read technologies used as the gold standard to sequence Plasmodium. Two clones of P. falciparum (Pf3D7 and PfW2) were sequenced in long-read using the PromethION sequencer from Oxford Nanopore Technologies without genomic amplification. This made it possible to create a processing analysis pipeline for human Plasmodium with ONT Fastq only. De novo assembly revealed N50 lengths of 18,488 kb and 17,502 kb for the Pf3D7 and PfW2, respectively. The genome size was estimated at 23,235,407 base pairs for the Pf3D7 clone and 21,712,038 base pairs for the PfW2 clone. The average genome coverage depth was estimated at 787X and 653X for the Pf3D7 and PfW2 clones, respectively. This study proposes an assembly processing pipeline for the human Plasmodium genome using software adapted to large ONT data and the high AT percentage of Plasmodium. This search provides all the parameters which were optimized for use with the software selected in the pipeline.

Chronic chikungunya disease (CCD): clinical insights, immunopathogenesis, and therapeutic perspectives.

Chikungunya virus, an arthropod-borne pathogen is recognised by the World Health Organization as a top priority Emerging Infectious Disease and is ranked fourth in public health needs according to the Coalition for Epidemic Preparedness Innovations (CEPI). Despite its substantial impact, as evidenced by an annual estimate of 120,274 disability-adjusted life years, our understanding of the chronic aspects of chikungunya disease remains limited. This review focuses on Chronic Chikungunya Disease (CCD), emphasising its clinical manifestations, immunopathogenesis, therapeutic options, and disease burden.

Chikungunya infection in returned travellers: results from the geosentinel network, 2005-2020.

BACKGROUND: Chikungunya is an important travel-related disease because of its rapid geographical expansion and potential for prolonged morbidity. Improved understanding of the epidemiology of travel-related chikungunya infections may influence prevention strategies including education and vaccination. METHODS: We analysed data from travellers with confirmed or probable chikungunya reported to GeoSentinel sites from 2005 to 2020. Confirmed chikungunya was defined as a compatible clinical history plus either virus isolation, positive nucleic acid test or seroconversion/rising titre in paired sera. Probable chikungunya was defined as a compatible clinical history with a single positive serology result. RESULTS: 1202 travellers (896 confirmed and 306 probable) with chikungunya were included. The median age was 43 years (range 0-91; interquartile range [IQR]: 31-55); 707 (58.8%) travellers were female. Most infections were acquired in the Caribbean (28.8%), Southeast Asia (22.8%), South Central Asia (14.2%) and South America (14.2%). The highest numbers of chikungunya cases reported to GeoSentinel were in 2014 (28.3%), 2015 (14.3%) and 2019 (11.9%). The most frequent reasons for travel were tourism (n = 592; 49.3%) and visiting friends or relatives (n = 334; 27.7%). The median time to presentation to a GeoSentinel site was 23 days (IQR: 7-52) after symptom onset. In travellers with confirmed chikungunya and no other reported illnesses, the most frequently reported symptoms included musculoskeletal symptoms (98.8%), fever/chills/sweats (68.7%) and dermatologic symptoms (35.5%). Among 917 travellers with information available, 296 (32.3%) had a pretravel consultation. CONCLUSIONS: Chikungunya was acquired by international travellers in almost 100 destinations globally. Vector precautions and vaccination where recommended should be integrated into pretravel visits for travellers going to areas with chikungunya or areas with the potential for transmission. Continued surveillance of travel-related chikungunya may help public health officials and clinicians limit the transmission of this potentially debilitating disease by defining regions where protective measures (e.g. pretravel vaccination) should be strongly considered.

Impact, healthcare utilization and costs of travel-associated mosquito-borne diseases in international travellers: a prospective study.

BACKGROUND: International travellers frequently acquire infectious diseases whilst travelling, yet relatively little is known about the impact and economic burden of these illnesses on travellers. We conducted a prospective exploratory costing study on adult returning travellers with falciparum malaria, dengue, chikungunya or Zika virus. METHODS: Patients were recruited in eight Travel and Tropical Medicine clinics between June 2016 and March 2020 upon travellers' first contact with the health system in their country of residence. The patients were presented with a structured 52-question self-administered questionnaire after full recovery to collect information on patients' healthcare utilization and out-of-pocket costs both in the destination and home country, and about income and other financial losses due to the illness. RESULTS: A total of 134 patients participated in the study (malaria, 66; dengue, 51; chikungunya, 8; Zika virus, 9; all fully recovered; median age 40; range 18-72 years). Prior to travelling, 42% of patients reported procuring medical evacuation insurance. Across the four illnesses, only 7% of patients were hospitalized abroad compared with 61% at home. Similarly, 15% sought ambulatory services whilst abroad compared with 61% at home. The average direct out-of-pocket hospitalization cost in the destination country (USD $2236; range: $108-$5160) was higher than the direct out-of-pocket ambulatory cost in the destination country (USD $327; range: $0-$1560), the direct out-of-pocket hospitalization cost at home (USD $35; range: $0-$120) and the direct out-of-pocket ambulatory costs at home (US$45; range: $0-$192). Respondents with dengue or malaria lost a median of USD $570 (Interquartile range [IQR] 240-1140) and USD $240 (IQR 0-600), respectively, due to their illness, whilst those with chikungunya and Zika virus lost a median of USD $2400 (IQR 1200-3600) and USD $1500 (IQR 510-2625), respectively. CONCLUSION: Travellers often incur significant costs due to travel-acquired diseases. Further research into the economic impact of these diseases on travellers should be conducted.

Chikungunya Outbreak in Country with Multiple Vectorborne Diseases, Djibouti, 2019-2020.

During 2019-2020, a chikungunya outbreak occurred in Djibouti City, Djibouti, while dengue virus and malaria parasites were cocirculating. We used blotting paper to detect arbovirus emergence and confirm that it is a robust method for detecting and monitoring arbovirus outbreaks remotely.

Monkeypox clinical disease: Literature review and a tool proposal for the monitoring of cases and contacts.

The human monkeypox disease has mainly been described in Western and Central Africa. Since May 2022, the monkeypox virus has been spreading worldwide in a new epidemiological pattern, where cases result from person-to-person transmission, and develop clinically milder or less typical illness than during previous outbreaks in endemic areas. The newly-emerging monkeypox disease needs to be described over the long term, to improve cases definitions, to implement prompt control measures against epidemics, and to provide supportive care. Hence, we first conducted a review of historical and recent outbreaks to define the full clinical spectrum of the monkeypox disease and its course known so far. Then, we built a self-administrated questionnaire collecting daily symptoms of the monkeypox infection to follow cases and their contacts, even remotely. This tool will assist in the management of cases, the surveillance of contacts, and the conduct of clinical studies.

Clinical and Epidemiological Changes in French Soldiers After Deployment: Impact of Doxycycline Malaria Prophylaxis on Body Weight.

BACKGROUND: Antibiotics are growth promotors used in animal farming. Doxycycline (DOXY) is a tetracycline antibiotic taken daily and continued 1 month after return to protect against malaria during travel and deployment in endemic areas. We evaluated DOXY impact on body weight in military international travelers. MATERIEL AND METHODS: A prospective cohort analysis was conducted in 2016-2018, recruiting 170 French soldiers before a 4-month assignment overseas. Many clinical data including anthropometric measures by an investigator were collected before and after deployment. Weight gain was defined by an increase of 2% from baseline. The study protocol was supported by the French Armed Forces Health Services and approved by the French ethics committee (IRB no. 2015-A01961-48, ref promoter 2015RC0). Written, informed consent was obtained with signature from each volunteer before inclusion. RESULTS: After deployment, 84 soldiers were followed up. Overall, 38/84 (45%) were deployed to Mali with DOXY malaria prophylaxis, and others were deployed to Iraq or Lebanon without malaria prophylaxis according to international recommendations. Body weight increased in 24/84 (30%), of whom 14/24 (58%) were exposed to DOXY. In bivariate analysis, DOXY had a positive but not significant effect on weight gain (P-value = .4). In the final logistic regression model (Fig. 3), weight gain after deployment positively correlated with an increase in waist circumference (odds ratio [OR] 1.23 with 95% CI [1.06-1.47]) suggesting fat gain; with sedentary work (OR 5.34; 95% CI [1.07-31.90]); and with probiotic intake (OR 5.27; 95% CI [1.51-20.40]). Weight impact of probiotics was more important when associated with DOXY intake (OR 6.86; 95% CI [1.52-38.1]; P-value = .016). CONCLUSIONS: Doxycycline (DOXY) malaria prophylaxis during several months did not cause significant weight gain in soldiers. Further studies are required in older and less sportive traveling populations, and to investigate a cumulative effect over time and recurrent DOXY exposure. Doxycycline (DOXY) may enhance other growth-promoting factors including fatty food, sedentariness, and strain-specific probiotics contained in fermented dairy products which are also used as growth promotors.

Dengue outbreak amongst travellers returning from Cuba-GeoSentinel surveillance network, January-September 2022.

Increasing numbers of travellers returning from Cuba with dengue virus infection were reported to the GeoSentinel Network from June to September 2022, reflecting an ongoing local outbreak. This report demonstrates the importance of travellers as sentinels of arboviral outbreaks and highlights the need for early identification of travel-related dengue.

Origin of COVID-19: Dismissing the Mojiang mine theory and the laboratory accident narrative.

The origin of SARS-CoV-2 is still the subject of a controversial debate. The natural origin theory is confronted to the laboratory leak theory. The latter is composite and comprises contradictory theories, one being the leak of a naturally occurring virus and the other the leak of a genetically engineered virus. The laboratory leak theory is essentially based on a publication by Rahalkar and Bahulikar in 2020 linking SARS-CoV-2 to the Mojiang mine incident in 2012 during which six miners fell sick and three died. We analyzed the clinical reports. The diagnosis is not that of COVID-19 or SARS. SARS-CoV-2 was not present in the Mojiang mine. We also bring arguments against the laboratory leak narrative.

Gut Microbiota in Military International Travelers with Doxycycline Malaria Prophylaxis: Towards the Risk of a Simpson Paradox in the Human Microbiome Field.

Dysbiosis, developed upon antibiotic administration, results in loss of diversity and shifts in the abundance of gut microbes. Doxycycline is a tetracycline antibiotic widely used for malaria prophylaxis in travelers. We prospectively studied changes in the fecal microbiota of 15 French soldiers after a 4-month mission to Mali with doxycycline malaria prophylaxis, compared to changes in the microbiota of 28 soldiers deployed to Iraq and Lebanon without doxycycline. Stool samples were collected with clinical data before and after missions, and 16S rRNA sequenced on MiSeq targeting the V3-V4 region. Doxycycline exposure resulted in increased alpha-biodiversity and no significant beta-dissimilarities. It led to expansion in Bacteroides, with a reduction in Bifidobacterium and Lactobacillus, as in the group deployed without doxycycline. Doxycycline did not alter the community structure and was specifically associated with a reduction in Escherichia and expression of Rothia. Differences in the microbiota existed at baseline between military units but not within the studied groups. This group-effect highlighted the risk of a Simpson paradox in microbiome studies.

Lessons learned from the investigation of a COVID-19 cluster in Creil, France: effectiveness of targeting symptomatic cases and conducting contact tracing around them.

BACKGROUND: This study presents the methods and results of the investigation into a SARS-CoV-2 outbreak in a professional community. Due to the limited testing capacity available in France at the time, we elaborated a testing strategy according to pre-test probability. METHODS: The investigation design combined active case finding and contact tracing around each confirmed case with testing of at-risk contact persons who had any evocative symptoms (n = 88). One month later, we performed serology testing to test and screen symptomatic and asymptomatic cases again (n = 79). RESULTS: Twenty-four patients were confirmed (14 with RT-PCR and 10 with serology). The attack rate was 29% (24/83). Median age was 40 (24 to 59), and the sex ratio was 15/12. Only three cases were asymptomatic (= no symptoms at all, 13%, 95% CI, 3-32). Nineteen symptomatic cases (79%, 95% CI, 63-95) presented a respiratory infection, two of which were severe. All the RT-PCR confirmed cases acquired protective antibodies. Median incubation was 4 days (from 1 to 13 days), and the median serial interval was 3 days (0 to 15). We identified pre-symptomatic transmission in 40% of this cluster, but no transmission from asymptomatic to symptomatic cases. CONCLUSION: We report the effective use of targeted testing according to pre-test probability, specifically prioritizing symptomatic COVID-19 diagnosis and contact tracing. The asymptomatic rate raises questions about the real role of asymptomatic infected people in transmission. Conversely, pre-symptomatic contamination occurred frequently in this cluster, highlighting the need to identify, test, and quarantine asymptomatic at-risk contact persons (= contact tracing). The local lockdown imposed helped reduce transmission during the investigation period.

Infections Due to Carbapenem-Resistant Bacteria in Patients With Hematologic Malignancies.

In developed countries, hematological malignancies (HM) account for 8 to 10% of cancers diagnosed annually and one-third of patients with HM (HMP) are expected to die from their disease. The former wide spectrum "magic bullet," imipenem, has been ousted by the emergence of carbapenem resistant (CR) pathogens. In endemic areas, infections with CR-bacteria occur in vulnerable patients, notably in HMP, who suffer from high mortality related to infectious complications. In this work, we reviewed epidemiologic and clinical factors associated with CR-infections in adult HMP and data on CR-related mortality and antibiotic treatments in this population. We found that resistance profile of strains involved in HMP infections, mainly bacteremia, reflect local epidemiology. Significant risk factors for infections with CR-bacteria include sex male, age around 50 years old, acute leukemia, selvage chemotherapy, neutropenia, and digestive colonization by CR-bacteria. Mortality rate is high in HMP infected with CR-Enterobacteriaceae, more particularly in case of acute myeloid leukemia and unresolved neutropenia, due to inappropriate empiric management and delayed administration of targeted antibiotics, such as tigecycline, colistin, or new associations of active drugs. Thus, we developed an algorithm for clinicians, assessing the incremental risk for CR-bacterial infection occurrence and mortality in febrile HMP, to guide decisions related to empirical therapeutic strategies.

Chikungunya resurgence in the Maldives and risk for importation via tourists to Europe in 2019-2020: A GeoSentinel case series.

BACKGROUND: Chikungunya virus (CHIKV) is an arthropod-borne virus mainly transmitted in tropical areas by Aedes spp. mosquitoes. It has been responsible for small-to-large outbreaks in temperate areas including southern Europe and North America. Past outbreaks in 2006 on the islands of Maldives, as well as on other islands in the Indian Ocean and in Southeast Asia, demonstrated for the first time the capacity of CHIKV to disseminate through travel and transcontinental commerce, and revealed the major socio-economic impact of CHIKV epidemics. Recently, CHIKV has been circulating in highly touristic areas including the Maldives, where 1736 cases were notified by the Health Protection Agency during 2019. CASE SERIES: Among EuroTravNet/GeoSentinel patient records, eight CHIKV-confirmed cases imported the Maldives to France, Germany, Denmark, Italy and Spain were identified between February 2019 and February 2020; exceeding the total number of CHIKV infections travel-acquired in Maldives reported to this surveillance network during the previous 10 years. CONCLUSIONS: The prevention and control of CHIKV introduction into naïve areas colonised by competent vectors is crucial. CHIKV outbreaks must be detected and reported in a timely manner. This must lead to adapted health information for international travellers and to prompt management of suspected imported cases. Conversely, travellers make for excellent sentinels and increased reports of imported cases might reflect a change in the level of endemicity or even herald an outbreak. Feedback to the local health authorities and matching this with local epidemiological surveillance data may lead to health benefits for the local population.