Publications by authors named "Philippe Parola"

409 Publications

Virome Diversity among Mosquito Populations in a Sub-Urban Region of Marseille, France.

Viruses 2021 04 27;13(5). Epub 2021 Apr 27.

Aix Marseille Université, Intitut de Recherche pour le Développement (IRD), Assistance Publique-Hopitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI) UM 63, 13005 Marseille, France.

Some mosquito species have significant public health importance given their ability to transmit major diseases to humans and animals, making them the deadliest animals in the world. Among these, the (.) genus is a vector of several viruses such as Dengue, Chikungunya, and Zika viruses that can cause serious pathologies in humans. Since 2004, has been encountered in the South of France, and autochthonous cases of Dengue, Chikungunya, and Zika diseases have recently been reported, further highlighting the need for a comprehensive survey of the mosquitoes and their associated viruses in this area. Using high throughput sequencing (HTS) techniques, we report an analysis of the DNA and RNA viral communities of three mosquito species , (.) , and (.) vectors of human infectious diseases in a small sub-urban city in the South of France. Results revealed the presence of a significant diversity of viruses known to infect bacteria, plants, insects, and mammals. Several novel viruses were detected, including novel members of the , , , , and families. No sequence related to major zoonotic viruses transmitted by mosquitoes was detected. The use of HTS on arthropod vector populations is a promising strategy for monitoring the emergence and circulation of zoonoses and epizooties. This study is a contribution to the knowledge of the mosquito microbiome.
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http://dx.doi.org/10.3390/v13050768DOI Listing
April 2021

New records of bacteria in different species of fleas from France and Spain.

Comp Immunol Microbiol Infect Dis 2021 Jun 6;76:101648. Epub 2021 Apr 6.

IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France. Electronic address:

In this study, we assessed the presence of vector-borne microorganisms in different species of fleas collected from different hosts in diverse areas of South-Western Europe by molecular methods. A total of 319 fleas belonging to eight different species was tested for the presence of eight microorganisms. Wolbachia spp. endosymbionts were detected in Ctenocephalides felis, Pulex irritans, Archaeopsylla erinacei and Ctenophthalmus baeticus boisseauorum specimens. Rickettsia felis, an emerging pathogen, was detected in C. felis, A. erinacei and Ct. b. boisseauorum. Rickettsia typhi, the agent of murine typhus was detected for the first time in A. erinacei and Mycobacterium spp. were detected for the first time in fleas (C. felis, P. irritans and A. erinacei). Lastly, five different species of Bartonella were detected in fleas' DNA in this study, including a possible new bacterium belonging to this genus. With this study, we updated the knowledge of the flea-borne bacteria present in the South-West of Europe reinforcing the idea about the necessity to expand and increase the current knowledge on flea-borne pathogens.
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http://dx.doi.org/10.1016/j.cimid.2021.101648DOI Listing
June 2021

Tick-borne relapsing fever Borreliosis, a major public health problem overlooked in Senegal.

PLoS Negl Trop Dis 2021 Apr 22;15(4):e0009184. Epub 2021 Apr 22.

Aix Marseille Univ, IRD, APHM, SSA, VITROME, Marseille, France.

Background: Tick-borne relapsing fever (TBRF) is the most common vector-borne bacterial disease in humans in West Africa. It is frequently clinically confused with malaria. Our study aims to determine, on a micro-geographic scale, the conditions for the maintenance and spread of TBRF in the Niakhar district of Senegal.

Methodology/principal Findings: We conducted clinical, entomological and animal reservoir investigations. Field surveys were carried out in order to investigate the presence of Ornithodoros sonrai vector ticks and to detect Borrelia spp. by qPCR using the 16S rRNA and glpQ genes, respectively. Micromammal trapping series were carried out inside homes and Borrelia infection was detected using brain tissue qPCR. Capillary blood samples from febrile patients were also tested for Borrelia using qPCR. More than 97% (40/41) of the villages surveyed were infested with O. sonrai ticks. The prevalence of Borrelia spp. infections in ticks was 13% (116/910), and over 73% (85/116) were positively confirmed as being Borrelia crocidurae. Borreliosis cases accounted for 12% (94/800) of episodes of fever and all age groups were infected, with children and young people between the ages of 8-14 and 22-28 being the most infected by the disease (16% and 18.4%). TBRF cases occurred in all seasons, with a peak in August. In two species of small rodents that were found to be infected (Arvicanthis niloticus, Mus musculus), the proportion of Borrelia infection was 17.5% (10/57), and the highest prevalence of infection (40.9%, 9/22) was observed in A. niloticus.

Conclusion/significance: Our study indicates that TBRF is an endemic disease in the Niakhar district, where children and young people are the most infected. Arvicanthis niloticus and O. sonrai ticks are massively present and appear to be the main epidemiological reservoirs causing its extensive spread to humans.
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http://dx.doi.org/10.1371/journal.pntd.0009184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8096072PMC
April 2021

Imported scrub typhus in Europe: Report of three cases and a literature review.

Travel Med Infect Dis 2021 Apr 17;42:102062. Epub 2021 Apr 17.

Department of Infectious/Tropical Diseases and Microbiology (DITM), IRCCS Sacro Cuore Don Calabria Hospital, Negrar, Verona, Italy. Electronic address:

Background: Scrub typhus is a vector-borne rickettsial infection, which can cause relevant morbidity and mortality. While the number of cases is around a million per year globally, the infection is seldom diagnosed in travellers from Europe.

Methods: We herein report three cases diagnosed in Italian travellers and review the literature about imported cases in Europe in the last 60 years.

Results: Three participants to the same hiking trip to the forest of northern Laos presented fever and other symptoms, including eschars (2 individuals) and skin rash (2 individuals). Overall, they didn't report complications, and recovered soon after doxycycline treatment. Diagnosis was retrospectively confirmed with PCR in one of them. The review collected data from 40 patients. Almost all of them (95%) presented fever, more than a half had headache, skin rash, eschars, arthromyalgias. 73% of them were hospitalized, and 16.2% needed intensive care. Diagnosis was confirmed by serology in almost all cases (94.6%). Most patients (88%) were treated with doxycycline. All patients survived, although one case resulted in incomplete tetraparesis.

Conclusions: Scrub typhus should be considered in all travellers coming back from endemic areas and presenting with acute febrile illness. Laboratory diagnosis can be challenging, as specific tests are not widely available. In case of clinical suspicion, a prompt treatment with oral doxycycline could avoid severe complications.
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http://dx.doi.org/10.1016/j.tmaid.2021.102062DOI Listing
April 2021

Performance of MALDI-TOF Mass Spectrometry to Determine the Sex of Mosquitoes and Identify Specific Colonies from French Polynesia.

Am J Trop Med Hyg 2021 Mar 22. Epub 2021 Mar 22.

1Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France.

Mosquitoes are the main arthropod vectors of infectious diseases in humans. The current methods for mosquito identification include morphological and molecular methods. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), now routinely used for bacterial identification, has recently emerged in the field of entomology. The aim of this study was to use MALDI-TOF MS to identify mosquito colonies from French Polynesia. Five hundred specimens from French Polynesia belonging to three species, Aedes aegypti, Aedes polynesiensis, and Culex quinquefasciatus, were included in the study. Testing the legs of these mosquitoes by MALDI-TOF MS revealed a 100% correct identification of all specimens at the species level. The MALDI-TOF MS profiles obtained allowed differentiation of male from female mosquitoes and the specific identification of female mosquito colonies of the same species but different geographic origin.
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http://dx.doi.org/10.4269/ajtmh.20-0031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8103438PMC
March 2021

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: an emerging tool for studying the vectors of human infectious diseases.

Future Microbiol 2021 Mar 18;16:323-340. Epub 2021 Mar 18.

IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.

Arthropod vectors have historically been identified morphologically, and more recently using molecular biology methods. However, both of these methods are time-consuming and require specific expertise and equipment. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry, which has revolutionized the routine identification of microorganisms in clinical microbiology laboratories, was recently successfully applied to the identification of arthropod vectors. Since then, the robustness of this identification technique has been confirmed, extended to a large panel of arthropod vectors, and assessed for detecting blood feeding behavior and identifying the infection status in regard to certain pathogenic agents. In this study, we summarize the state-of-the-art of matrix-assisted laser desorption ionization time-of-flight mass spectrometry applied to the identification of arthropod vectors (ticks, mosquitoes, phlebotomine sand-flies, fleas, triatomines, lice and ), their trophic preferences and their ability to discriminate between infection statuses.
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http://dx.doi.org/10.2217/fmb-2020-0145DOI Listing
March 2021

Sputum proteomic analysis for distinguishing between pulmonary tuberculosis and non-tuberculosis using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS): preliminary results.

Clin Microbiol Infect 2021 Mar 9. Epub 2021 Mar 9.

Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France. Electronic address:

Objectives: The aim was to evaluate the feasibility and diagnostic contribution of protein profiling using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) applied to sputum to diagnose pulmonary tuberculosis.

Methods: Sputum samples collected from patients suspected of having pulmonary tuberculosis were analysed using MALDI-TOF MS. Using the differentially expressed protein peaks, we compared three groups of patients, including those with confirmed pulmonary tuberculosis (PTB), those without tuberculosis but with a lower respiratory tract infection (non-TB LRTI) and those without tuberculosis and without an LRTI (non-TB controls).

Results: A total of 102 patients included 35 PTB, 36 non-TB LRTI and 31 non-TB controls. The model differentiated between the PTB patients and the non-TB controls using the 25 most differentially expressed protein peaks, with a sensitivity of 97%, 95% CI 85-100%, and a specificity of 77%, 95% CI 59-90%. The model distinguished the PTB patients from the non-TB LRTI patients using the ten most differentially expressed protein peaks, with a sensitivity of 80%, 95% CI 63-92%, and a specificity of 89%, 95% CI 74-97%. We observed that the negative predictive value of MALDI-TOF MS sputum analysis was higher (96%, 95% CI 80-100%) than that of direct sputum microscopic examination and sputum culture (78%, 95% CI 62-89%) for non-TB controls. When MALDI-TOF MS sputum analysis and direct microscopic examination were combined, the negative predictive value reached 94%, 95% CI 80-99%, for non-TB LRTI patients.

Discussion: These results suggest that MALDI-TOF MS sputum analysis coupled with microscopic examination could be used as a screening tool for diagnosing pulmonary TB.
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http://dx.doi.org/10.1016/j.cmi.2021.02.031DOI Listing
March 2021

COVID-19 re-infection.

Eur J Clin Invest 2021 May 17;51(5):e13537. Epub 2021 Mar 17.

IRD, APHM, Aix-Marseille University, MEPHI, Marseille, France.

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http://dx.doi.org/10.1111/eci.13537DOI Listing
May 2021

Automated Western immunoblotting detection of anti-SARS-CoV-2 serum antibodies.

Eur J Clin Microbiol Infect Dis 2021 Mar 3. Epub 2021 Mar 3.

IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.

ELISA and chemiluminescence serological assays for COVID-19 are currently incorporating only one or two SARS-CoV-2 antigens. We developed an automated Western immunoblotting as a complementary serologic assay for COVID-19. The Jess Simple Western system, an automated capillary-based assay, was used, incorporating an inactivated SARS-CoV-2 lineage 20a strain as the source of antigen, and total immunoglobulins (IgG, IgM, IgA) detection. In total, 602 sera were tested including 223 from RT-PCR-confirmed COVID-19 patients, 76 from patients diagnosed with seasonal HCoVs and 303 from coronavirus-negative control sera. We also compared this assay with the EUROIMMUN® SARS-CoV-2 IgG ELISA kit. Among 223 sera obtained from RT-PCR-confirmed COVID-19 patients, 180/223 (81%) exhibited reactivity against the nucleocapsid and 70/223 (31%) against the spike protein. Nucleocapsid reactivity was further detected in 9/76 (14%) samples collected from patients diagnosed with seasonal HCoVs and in 15/303 (5%) coronavirus-negative control samples. In the subset of sera collected more than 2 weeks after the onset of symptoms, the sensitivity was 94% and the specificity 93%, the latter value probably reflecting cross-reactivity of SARS-CoV-2 with other coronaviruses. The automated Western immunoblotting presented a substantial agreement (90%) with the compared ELISA (Cohen's Kappa=0.64). Automated Western immunoblotting may be used as a second line test to monitor exposure of people to HCoVs including SARS-CoV-2.
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http://dx.doi.org/10.1007/s10096-021-04203-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7928199PMC
March 2021

The Grand Magal of Touba was spared by the COVID-19 pandemic.

Int J Infect Dis 2021 Apr 9;105:470-471. Epub 2021 Jan 9.

IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.

In the context of the coronavirus disease-2019 (COVID-19) pandemic, all mass gathering (MG) events have been cancelled. The Grand Magal took place on October 6, 2020, in Touba, Senegal, which was the only MG event organized in 2020. This Muslim pilgrimage gathers about four million Muslim Mourides from Senegal and beyond. No significant increase in COVID-19 cases was therefore observed at the national level in the weeks following the Grand Magal. This successful strategy is an invitation to better promote community commitments by public authorities in their various strategies.
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http://dx.doi.org/10.1016/j.ijid.2021.01.006DOI Listing
April 2021

Acquisition of multidrug-resistant bacteria and encoding genes among French pilgrims during the 2017 and 2018 Hajj.

Eur J Clin Microbiol Infect Dis 2021 Jan 7. Epub 2021 Jan 7.

IRD, AP-HM, SSA, VITROME, Aix Marseille University, Marseille, France.

The objective of this study is to determine the acquisition of multidrug-resistant (MDR) bacteria and antibiotic resistance-encoding genes by French Hajj pilgrims and associated risk factors. Pilgrims traveling during the 2017 and 2018 Hajj were recruited. All pilgrims underwent two successive systematic nasopharyngeal and rectal swabs, pre- and post-Hajj. Specific culture media were used to screen for MDR bacteria, including methicillin-resistant Staphylococcus aureus (MRSA), carbapenem-resistant bacteria, and extended spectrum beta-lactamase producing Enterobacteriaceae (ESBL-E). qPCR was used to identify antibiotic resistance-encoding genes from cultured isolates. Direct screening of genes encoding for colistin resistance (mcr-1, 2, 3, 4, 5, and 8) from nasopharyngeal and rectal swabs was performed using qPCR, and positive qPCR results were simultaneously tested by sequencing. There were 268 pilgrims included. The percentage of pilgrims acquiring MDR bacteria during the Hajj was 19.4%. A total of 81 strains were isolated (1 carbapenem-resistant Acinetobacter baumannii, 12 MRSA, and 68 ESBL-E). ESBL-E strains were found in rectal samples of 6.0% pilgrims pre-Hajj and of 16.4% pilgrims post-Hajj. Only 0.4% pilgrims were positive for CARB post-Hajj and 1.9% carried nasal MRSA pre- and post-Hajj. In addition, 23 (8.6%) post-Hajj rectal swabs were positive for mcr genes (19 mcr-1 gene and 4 mcr-4 gene). No significant association was found between co-factors and acquisition of MDR bacteria or mcr genes. MDR bacteria and genes are acquired by pilgrims during the Hajj mass gathering. Rationalization of antibiotic consumption and implementation of measures to prevent transmission of bacteria among pilgrims during the event are of paramount importance.
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http://dx.doi.org/10.1007/s10096-020-04122-0DOI Listing
January 2021

Clinical Features and Mortality Associated with Severe Malaria in Adults in Southern Mauritania.

Trop Med Infect Dis 2020 Dec 22;6(1). Epub 2020 Dec 22.

Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, 13005 Marseille, France.

Severe malaria in adults is not well-studied in Sahelian Africa. Clinical features and mortality associated with severe malaria in adult patients hospitalized in Kiffa, southern Mauritania, were analysed. Patients over 15 years old admitted for severe malaria between August 2016 and December 2019 were included in the present retrospective study. The World Health Organization (WHO) criteria were used to define severe malaria. The presenting clinical characteristics and outcome were compared. Of 4266 patients hospitalized during the study period, 573 (13.4%) had a positive rapid diagnostic test for malaria, and 99 (17.3%; mean age, 37.5 years; range 15-79 years; sex-ratio M/F, 2.1) satisfied the criteria for severe malaria. On admission, the following signs and symptoms were observed in more than one-fourth of the patients: fever (98%), impairment of consciousness (81.8%), multiple convulsions (70.7%), cardiovascular collapse (61.6%), respiratory distress (43.4%), severe anaemia ≤ 80 g/L (36.4%), haemoglobinuria (27.3%), and renal failure (25.3%). Patients were treated with parenteral quinine or artemether. Fourteen (14.1%) patients died. Multiple convulsions, respiratory distress, severe anaemia, haemoglobinuria.
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http://dx.doi.org/10.3390/tropicalmed6010001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7838900PMC
December 2020

Natural history of COVID-19 and therapeutic options.

Expert Rev Clin Immunol 2020 12 24;16(12):1159-1184. Epub 2020 Dec 24.

Institut Hospitalo-Universitaire Méditerranée Infection , Marseille, France.

: COVID-19 presents benign forms in young patients who frequently present with anosmia. Infants are rarely infected, while severe forms occur in patients over 65 years of age with comorbidities, including hypertension and diabetes. Lymphopenia, eosinopenia, thrombopenia, increased lactate dehydrogenase, troponin, C-reactive protein, D-dimers and low zinc levels are associated with severity.: The authors review the literature and provide an overview of the current state of knowledge regarding the natural history of and therapeutic options for COVID-19. : Diagnosis should rely on PCR and not on clinical presumption. Because of discrepancies between clinical symptoms, oxygen saturation or radiological signs on CT scans, pulse oximetry, and radiological investigation should be systematic. The disease evolves in successive phases: an acute virological phase, and, in some patients, a cytokine storm phase; an uncontrolled coagulopathy; and an acute respiratory distress syndrome. Therapeutic options include antivirals, oxygen therapy, immunomodulators, anticoagulants and prolonged mechanical treatment. Early diagnosis, care, and implementation of an antiviral treatment; the use of immunomodulators at a later stage; and the quality of intensive care are critical regarding mortality rates. The higher mortality observed in Western countries remains unexplained. Pulmonary fibrosis may occur in some patients. Its future is unpredictable.
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http://dx.doi.org/10.1080/1744666X.2021.1847640DOI Listing
December 2020

Identification of Lice Stored in Alcohol Using MALDI-TOF MS.

J Med Entomol 2021 May;58(3):1126-1133

Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille, France.

Lice pose major public and veterinary health problems with economic consequences. Their identification is essential and requires the development of an innovative strategy. MALDI-TOF MS has recently been proposed as a quick, inexpensive, and accurate tool for the identification of arthropods. Alcohol is one of the most frequently used storage methods and makes it possible to store samples for long periods at room temperature. Several recent studies have reported that alcohol alters protein profiles resulting from MS analysis. After preliminary studies on frozen lice, the purpose of this research was to evaluate the influence of alcohol preservation on the accuracy of lice identification by MALDI-TOF MS. To this end, lice stored in alcohol for variable periods were submitted for MS analysis and sample preparation protocols were optimized. The reproducibility and specificity of the MS spectra obtained on both these arthropod families allowed us to implement the reference MS spectra database (DB) with protein profiles of seven lice species stored in alcohol. Blind tests revealed a correct identification of 93.9% of Pediculus humanus corporis (Linnaeus, 1758) and 98.4% of the other lice species collected in the field. This study demonstrated that MALDI-TOF MS could be successfully used for the identification of lice stored in alcohol for different lengths of time.
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http://dx.doi.org/10.1093/jme/tjaa266DOI Listing
May 2021

Acquisition of multidrug-resistant bacteria and colistin resistance genes in French medical students on internships abroad.

Travel Med Infect Dis 2021 Jan-Feb;39:101940. Epub 2020 Nov 26.

Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France. Electronic address:

Background: Acquisition of multidrug resistant bacteria (MDR) and colistin resistance genes by international travellers has been demonstrated. Studies conducted in medical students during internships abroad are scant.

Methods: Nasopharyngeal, rectal, and vaginal swabs samples were collected from 382 French medical students before and after travel to investigate the acquisition of MDR bacteria. The bacterial diversity in the samples was assessed by culture on selective media. We also genetically characterised the isolates of MDR bacteria including Extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E), methicillin-resistant Staphylococcus aureus (MRSA), and Carbapenemase-producing Enterobacteriacae (CPE) using the real-time polymerase chain reaction method. The samples were collected from 293 students and were investigated for mcr colistin-resistance genes using RT-PCR directly on the samples, followed by conventional PCR and sequencing.

Results: A proportion of 29.3% (112/382) of the participants had acquired ESBL-E and 2.6% (10/382) had acquired CPE. The most common species and ESBL-E encoding gene were Escherichia coli (125/127 isolates, 98.4%) and bla (121/127, 95.3%), respectively. A proportion of 6.8% (20/293) of the participants had acquired mcr-1 genes, followed by mcr-3 (1/293, 0.3%) and mcr-8 (1/293, 0.3%). We found that taking part in humanitarian missions to orphanages (aRR = 2.01, p < 0.0001), being in contact with children during travel (aRR = 1.78, p = 0.006), the primary destination of travel being Vietnam (aRR = 2.15, p < 0.0001) and north India (aRR = 2.41, p = 0.001), using antibiotics during travel (aRR = 1.77, p = 0.01), and studying in 2018 (aRR = 1.55, p = 0.03) were associated with the acquisition of ESBL-E. When the primary destination of travel was Vietnam (aRR = 2.74, p < 0.0001) and the year of study was 2018 (aRR = 1.93, p < 0.002), this was associated with acquisition of colistin resistance genes.

Conclusion: Medical students are at a potential risk of acquiring ESBL-E, CPE and colistin resistance genes. A number of risk factors have been identified, which may be used to develop targeted preventive measures.
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http://dx.doi.org/10.1016/j.tmaid.2020.101940DOI Listing
November 2020

Prevalence and risk factors for lung involvement on low-dose chest CT (LDCT) in a paucisymptomatic population of 247 patients affected by COVID-19.

Insights Imaging 2020 Nov 17;11(1):117. Epub 2020 Nov 17.

Radiology Department, La Timone Hospital, Assistance Publique Des Hôpitaux de Marseille, 264 Rue Saint Pierre, 13005, Marseille 05, France.

Background: Low-dose chest CT (LDCT) showed high sensitivity and ability to quantify lung involvement of COVID-19 pneumopathy. The aim of this study was to describe the prevalence and risk factors for lung involvement in 247 patients with a visual score and assess the prevalence of incidental findings.

Methods: For 12 days in March 2020, 250 patients with RT-PCR positive tests and who underwent LDCT were prospectively included. Clinical and imaging findings were recorded. The extent of lung involvement was quantified using a score ranging from 0 to 40. A logistic regression model was used to explore factors associated with a score ≥ 10.

Results: A total of 247 patients were analyzed; 138 (54%) showed lung involvement. The mean score was 4.5 ± 6.5, and the mean score for patients with lung involvement was 8.1 ± 6.8 [1-31]. The mean age was 43 ± 15 years, with 121 males (48%) and 17 asymptomatic patients (7%). Multivariate analysis showed that age > 54 years (odds ratio 4.4[2.0-9.6] p < 0.001) and diabetes (4.7[1.0-22.1] p = 0.049) were risk factors for a score ≥ 10. Multivariate analysis including symptoms showed that only age > 54 years (4.1[1.7-10.0] p = 0.002) was a risk factor for a score ≥ 10. Rhinitis (0.3[0.1-0.7] p = 0.005) and anosmia (0.3[0.1-0.9] p = 0.043) were protective against lung involvement. Incidental imaging findings were found in 19% of patients, with a need for follow-up in 0.6%.

Conclusion: The prevalence of lung involvement was 54% in a predominantly paucisymptomatic population. Age ≥ 55 years and diabetes were risk factors for significant parenchymal lung involvement. Rhinitis and anosmia were protective against LDCT abnormalities.
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http://dx.doi.org/10.1186/s13244-020-00939-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7670109PMC
November 2020

Pattern of SARS-CoV-2 infection among dependant elderly residents living in long-term care facilities in Marseille, France, March-June 2020.

Int J Antimicrob Agents 2020 Dec 13;56(6):106219. Epub 2020 Nov 13.

Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France. Electronic address:

Objectives: This study aimed to report the results of SARS-CoV-2 PCR-based screening campaigns conducted on dependent elderly residents (compared with staff members) in long-term care facilities (LTCFs) in Marseille, France, and the follow-up of positive cases.

Methods: Data from 1691 elderly residents and 1000 members of staff were retrospectively collected through interviewing the medical teams in 24 LTCFs and using the hospitals' electronic health recording systems.

Results: Elderly residents were predominantly female (64.8%) with a mean age of 83.0 years. SARS-CoV-2 detection among residents (226, 13.4%) was significantly higher than among staff members (87, 8.7%) (P < 0.001). Of the 226 infected residents, 37 (16.4%) were detected on a case-by-case basis due to their COVID-19 symptoms and 189 (83.6%) were detected through mass screening. Most (77.0%) had possible COVID-19 symptoms, including respiratory symptoms and signs (44.5%) and fever (46.5%); 23.0% were asymptomatic. A total of 116 (51.4%) patients received a course of oral hydroxychloroquine and azithromycin (HCQ-AZM) for ≥ 3 days; 47 (20.8%) died. Through multivariate analysis, the death rate was positively associated with being male (30.7% vs. 14.0%, OR = 3.95, P = 0.002), aged > 85 years (26.1% vs. 15.6%, OR = 2.43, P = 0.041) and receiving oxygen therapy (39.0% vs. 12.9%, OR = 5.16, P < 0.001) and negatively associated with being diagnosed through mass screening (16.9% vs. 40.5%, OR = 0.20, P= 0.001) and receiving HCQ-AZM treatment ≥ 3 days (15.5% vs. 26.4%, OR = 0.37, P = 0.02).

Conclusion: The high proportion of asymptomatic COVID-19 patients and independent factors for mortality suggest that early diagnosis and treatment of COVID-19 patients in LTCFs may be effective in saving lives.
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http://dx.doi.org/10.1016/j.ijantimicag.2020.106219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7661959PMC
December 2020

Molecular detection of microorganisms in lice collected from farm animals in Northeastern Algeria.

Comp Immunol Microbiol Infect Dis 2021 02 23;74:101569. Epub 2020 Oct 23.

Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France. Electronic address:

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http://dx.doi.org/10.1016/j.cimid.2020.101569DOI Listing
February 2021

Molecular Detection of Microorganisms Associated with Small Mammals and Their Ectoparasites in Mali.

Am J Trop Med Hyg 2020 12 29;103(6):2542-2551. Epub 2020 Oct 29.

IHU-Méditerranée Infection, Marseille, France.

Small mammals are the natural reservoirs for many zoonotic pathogens. Using molecular tools, we assessed the prevalence of bacteria and protozoans in small mammals and their ectoparasites in Faladjè, Bougouni, and Bamoko, Mali. A total of 130 small mammals belonging to 10 different species were captured, of which 74 (56.9%) were infested by ectoparasites, including , , , sensu lato, and spp. nymphs. DNA of was found in 14/75 (18.7%), 6/48 (12.5%), and 3/7 (42.8%) small mammals from Faladjè, Bougouni, and Bamako, respectively. In Faladjè, DNA was detected in 31/68 (45.6%) of and 14/22 (63.6%) of . In Bougouni, it was found in 2/26 (7.7%) of and 10/42 (23.8%) of . The sequences of obtained from small mammals were close to those of , , and uncultured spp. In Faladjè, DNA was detected in 64.4% (29/45) of spp. ticks, 4.5% (2/44) of , 12.5% (1/8) of , and 1.5% (1/68) of . We found DNA of in from Faladjè and DNA of and in from Bougouni. The results of our study show that several small mammal species harbor and may serve as potential reservoirs of spp., likely to play a major role in the maintenance, circulation, and potential transmission of bacteria in Mali. The pathogenicity of these bacteria for humans or animals remains to be demonstrated.
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http://dx.doi.org/10.4269/ajtmh.19-0727DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7695096PMC
December 2020

Low-dose chest CT for diagnosing and assessing the extent of lung involvement of SARS-CoV-2 pneumonia using a semi quantitative score.

PLoS One 2020 3;15(11):e0241407. Epub 2020 Nov 3.

Department of Radiology, La Timone Hospital, Assistance Publique des Hôpitaux de Marseille, Marseille, France.

Objectives: The purpose is to assess the ability of low-dose CT (LDCT) to determine lung involvement in SARS-CoV-2 pneumonia and to describe a COVID19-LDCT severity score.

Materials And Methods: Patients with SARS-CoV-2 infection confirmed by RT-PCR were retrospectively analysed. Clinical data, the National Early Warning Score (NEWS) and imaging features were recorded. Lung features included ground-glass opacities (GGO), areas of consolidation and crazy paving patterns. The COVID19-LDCT score was calculated by summing the score of each segment from 0 (no involvement) to 10 (severe impairment). Univariate analysis was performed to explore predictive factor of high COVID19-LDCT score. The nonparametric Mann-Whitney test was used to compare groups and a Spearman correlation used with p<0.05 for significance.

Results: Eighty patients with positive RT-PCR were analysed. The mean age was 55 years ± 16, with 42 males (53%). The most frequent symptoms were fever (60/80, 75%) and cough (59/80, 74%), the mean NEWS was 1.7±2.3. All LDCT could be analysed and 23/80 (28%) were normal. The major imaging finding was GGOs in 56 cases (67%). The COVID19-LDCT score (mean value = 19±29) was correlated with NEWS (r = 0.48, p<0.0001). No symptoms were risk factor to have pulmonary involvement. Univariate analysis shown that dyspnea, high respiratory rate, hypertension and diabetes are associated to a COVID19-LDCT score superior to 50.

Conclusions: COVID19-LDCT score did correlate with NEWS. It was significantly different in the clinical low-risk and high-risk groups. Further work is needed to validate the COVID19-LDCT score against patient prognosis.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0241407PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7608883PMC
November 2020

Asymptomatic hypoxia in COVID-19 is associated with poor outcome.

Int J Infect Dis 2021 Jan 31;102:233-238. Epub 2020 Oct 31.

Aix Marseille Université, IRD, MEPHI, Marseille, France; IHU-Mediterranée Infection, Marseille, France.

Objectives: Describe and evaluate the outcome of a coronavirus disease-2019 (COVID-19) patient without shortness of breath.

Design And Methods: We retrospectively collected data from COVID-19 patients diagnosed and cared for in Marseille, France. We selected data from patients who at admission, had a low dose CT scanner, dyspnea status, and oxygen saturation available. Blood gas was analyzed in a sample subset of patients.

Results: Among 1712 patients with COVID-19, we report that 1107 (64.7%) do not complain of shortness of breath at admission. The low-dose computed tomography (LDCT) scan showed signs compatible with pneumonia in 757/1,107 (68.4%) of patients without dyspnea. In a subset of patients who had underwent at least one blood gas analysis (n = 161) and presented without dyspnea at admission, 28.1% (27/96) presented with a hypoxemia/hypocapnia syndrome. Asymptomatic hypoxia was associated with a very poor outcome (33.3% were transferred to the ICU and 25.9% died).

Conclusion: The absence of shortness of breath in an old patient with comorbidity merit medical attention and should not be considered as a good sign of well-being. The poor prognosis of asymptomatic hypoxia, highlight the severity of this mild clinical presentation. In these patients, pulse oximetry is an important mean to predict the outcome along with news score and LDCT scanner.
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http://dx.doi.org/10.1016/j.ijid.2020.10.067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7604151PMC
January 2021

The Impact of Renewing Long-Lasting Insecticide-Treated Nets in the Event of Malaria Resurgence: Lessons from 10 Years of Net Use in Dielmo, Senegal.

Am J Trop Med Hyg 2021 01;104(1):255-262

1VITROME, UMR 257 IRD, Campus UCAD-IRD, Dakar, Senegal.

The occurrence of malaria resurgences could threaten progress toward elimination of the disease. This study investigated the impact of repeated renewal of long-lasting insecticide-treated net (LLIN) universal coverage on malaria resurgence over a period of 10 years of net implementation in Dielmo (Senegal). A longitudinal study was carried out in Dielmo between August 2007 and July 2018. In July 2008, LLINs were offered to all villagers through universal campaign distribution which was renewed in July 2011, August 2014, and May 2016. Malaria cases were treated with artemisinin-based combination therapy. Two resurgences of malaria occurred during the 10 years in which LLINs have been in use. Since the third renewal of the nets, malaria decreased significantly compared with the first year the nets were implemented (adjusted incidence rate ratio) (95% CI) = 0.35 (0.15-0.85), during the ninth year after net implementation). During the tenth year of net implementation, no cases of malaria were observed among the study population. The use of nets increased significantly after the third time the nets were renewed when compared with the year after the first and the second times the nets were renewed ( < 0.001). The third renewal of nets, which took place after 2 years instead of 3 years together with a higher use of LLINs especially among the young, probably prevented the occurrence of a third malaria upsurge in this village.
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http://dx.doi.org/10.4269/ajtmh.20-0127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7790102PMC
January 2021

Bed bug bites.

Dermatol Ther 2020 11 7;33(6):e14341. Epub 2020 Oct 7.

IHU-Méditerranée Infection, Marseille, France.

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http://dx.doi.org/10.1111/dth.14341DOI Listing
November 2020

Establishing Medical Coverage and Epidemiological Surveillance during the Grand Magal of Touba in Senegal: A Public Health Need.

J Epidemiol Glob Health 2020 12 26;10(4):247-249. Epub 2020 Jun 26.

Aix Marseille University, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France.

The Grand Magal is a religious pilgrimage that takes place in Senegal. An estimated 4-5 million individuals yearly gather in the holy city of Touba. Pilgrims comes from the whole Senegal and surrounding countries and from countries outside of Africa where Mouride Senegalese emigrated. It is the largest Mass Gathering (MG) event of the Mouride community and the largest Muslim religious MG in West Africa. The context of the Grand Magal MG is unique given its location in a tropical developing country and its international component which may favour the globalization of local endemic diseases and warrants investment in modern methods for public health surveillance and planning of the event.
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http://dx.doi.org/10.2991/jegh.k.200620.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7758853PMC
December 2020

Dynamics and genetic diversity of Haemophilus influenzae carriage among French pilgrims during the 2018 Hajj: A prospective cohort survey.

Travel Med Infect Dis 2020 Nov - Dec;38:101883. Epub 2020 Sep 18.

Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France. Electronic address:

Background: To investigate the genetic diversity of Haemophilus influenzae positive samples among French pilgrims attending the 2018 Hajj pilgrimage.

Method: After screening by qPCR, multilocus sequence typing was performed for all H. influenzae-positive samples. The following housekeeping genes were amplified and assigned: adk, atpG, frdB, fucK, mdh, pgi and recA.

Results: 121 pilgrims were included. H. influenzae was positive in 35.5% pre-Hajj samples, 12.4% at day five post-arrival, 15.7% at day 12 post-arrival, and 43.0% post-Hajj. Of the 129 positive swabs for H. influenzae, only one sample at D12 was negative for all seven genes amplified by standard PCR. The adk, atpG, frdB, mdh, pgi, recA and fucK genes were positive in 123, 107, 122, 70, 127, 118 and 69 samples, respectively. One sequence of atpG and two of recA genes were not possible to assign. None of the sequences of fucK gene was successfully obtained. Consequently, a complete sequence type characterisation was not possible. Of the 128 obtained strains, 111 had distinct patterns of alleles.

Conclusion: H. influenzae genotypes acquired were completely different from those present at pre-Hajj. We observed a great biodiversity and a lack of clonality of H. influenzae among French pilgrims during the 2018 Hajj. Further studies aiming at studying the genome of Hajj-acquired H. influenzae isolates are needed to define the clinical burden of H. influenzae infection during Hajj and to evaluate the potential interest of vaccination in Hajj pilgrims.
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http://dx.doi.org/10.1016/j.tmaid.2020.101883DOI Listing
September 2020

MALDI-TOF MS identification of Cimex lectularius and Cimex hemipterus bedbugs.

Infect Genet Evol 2020 11 11;85:104536. Epub 2020 Sep 11.

Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France. Electronic address:

Bedbugs (Cimex lectularius and C. hemipterus) have reemerged as a major public health problem around the world. Their bites cause various skin lesions as well as discomfort and anxiety. Their role as potential vectors of various infectious agents is discussed. Accordingly, all suspected cases of bedbug infestations need to be documented thoroughly, with an unequivocal identification of the arthropods involved, if any are present. Although morphological identification is easily and quickly performed by entomologists or professionals, it can be challenging otherwise. Also, distinguishing Cimex lectularius and C. hemipterus requires entomological expertise. MALDI-TOF mass spectrometry has been recently presented as an additional tool for arthropod identification. In this study, we assess the use of MALDI-TOF MS for the identification of laboratory and wild strains of C. lectularius and C. hemipterus. Several body parts of laboratory reared C. lectularius specimens were used to develop a MALDI-TOF MS protocol for bedbug identification, which was later validated using five other laboratory and wild populations of C. hemipterus and C. lectularius. A total of 167C. lectularius and C. hemipterus bedbug specimens (98 laboratory specimens and 69 wild specimens) were submitted to MALDI-TOF MS analysis. 143/167 (85.63%) provided high quality MS spectra. The in-lab database was then upgraded with a total of 20 reference spectra from all bedbug populations and the rest of the MS spectra (123 bedbugs) were blind tested. All specimens were properly identified to the species level using MALDI-TOF MS and 86,25% (69/80) were aptly identified according to their origin with LSVs ranging from 1.867 to 2.861. MALDI-TOF MS appears as a reliable additional tool for the identification of these two anthropophilic species.
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http://dx.doi.org/10.1016/j.meegid.2020.104536DOI Listing
November 2020

Gastrointestinal symptoms and the acquisition of enteric pathogens in Hajj pilgrims: a 3-year prospective cohort study.

Eur J Clin Microbiol Infect Dis 2021 Feb 11;40(2):315-323. Epub 2020 Sep 11.

Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France.

The acquisition of enteric pathogens and risk factors for Hajj-associated diarrhea in Hajj pilgrims is poorly documented. Pilgrims from Marseille participating in the Hajj in 2016-2018 underwent successive systematic rectal swabbing before and after their travel. Carriage of the main enteric pathogens was assessed by real-time PCR. Baseline demographics, adherence to individual preventive measures, gastrointestinal symptoms, and treatments were recorded. A total of 376 pilgrims were included. The median age was 62.0 years. During the Hajj, 18.6% presented at least one gastrointestinal symptom, 13.8% had diarrhea, and 36.4% had acquired at least one enteric pathogen. Enteropathogenic Escherichia coli (EPEC) and Enteroaggregative E. coli (EAEC) were the pathogens most frequently acquired by pilgrims (17.6% and 14.4%, respectively). Being female was associated with increased frequency of gastrointestinal symptoms during the pilgrimage (aOR = 2.38, p = 0.004). Enterohemorrhagic Escherichia coli (EHEC) acquisition was associated with a four-fold higher risk of reporting at least one gastrointestinal symptom and diarrhea (aOR = 3.68 and p = 0.01 and aOR = 3.96 and p = 0.01, respectively). Pilgrims who suffered from diarrhea were more likely to wash their hands more often (aOR = 2.07, p = 0.03) and to be either overweight (aOR = 2.71, p = 0.03) or obese (aOR = 2.51, p = 0.05). Enteric bacteria such as E. coli that are frequently associated with traveler's diarrhea due to the consumption of contaminated food and drink were frequently found in pilgrims. Respecting strict measures regarding food and water quality during the Hajj and adherence to preventive measures such as good personal hygiene and environmental management will help reduce the burden of gastrointestinal infections at the event.
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http://dx.doi.org/10.1007/s10096-020-04018-zDOI Listing
February 2021

Olfactory and gustative disorders for the diagnosis of COVID-19.

Travel Med Infect Dis 2020 Sep - Oct;37:101875. Epub 2020 Sep 6.

IHU-Méditerranée Infection, Marseille, France; Aix Marseille Uni., IRD, AP-HM, SSA, VITROME, Marseille, France. Electronic address:

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http://dx.doi.org/10.1016/j.tmaid.2020.101875DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7474847PMC
October 2020