Respiratory pathogens among ill pilgrims and the potential benefit of using point-of-care rapid molecular diagnostic tools during the Hajj.

We investigated respiratory pathogens among ill Hajj pilgrims from Marseille. We also discuss the potential role of point-of-care (POC) rapid molecular diagnostic tools for this purpose. Clinical data were collected using a standardised questionnaire. Influenza A and B viruses, human rhinovirus and human coronaviruses, Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae and Klebsiella pneumoniae were investigated using real-time PCR in respiratory samples obtained during travel, at the onset of symptoms. 207 participants were included. A cough, expectoration, rhinitis and a sore throat were the most frequent respiratory symptoms, followed by loss of voice and dyspnoea. 38.7% and 25.1% of pilgrims reported a fever and influenza-like symptoms, respectively. 59.4% pilgrims received antibiotics. Rhinovirus (40.6%) was the most frequent pathogen, followed by S. aureus (35.8%) and H. influenzae (30.4%). Virus and bacteria co-infections were identified in 28.5% of participants. 25.1% pilgrims who were positive for respiratory bacteria did not receive antibiotic treatment. In the context of the Hajj pilgrimage, it is important to detect infections that can be easily managed with appropriate treatment, and those that can affect prognosis, requiring hospitalisation. POC rapid molecular diagnostic tools could be used for patient management at small Hajj medical missions and to rationalise antibiotic consumption among Hajj pilgrims.

MALDI-TOF mass spectrometry identification of mosquitoes collected in Vietnam.

BACKGROUND: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a tool that has revolutionised clinical microbiology and has recently been described as an innovative and effective approach to arthropod identification. METHODS: In this study, mosquitoes were captured in Vietnam using four different methods (human landing catch, CDC light traps, BG-Sentinel traps, animal-baited net traps). A total of 4215 mosquitoes were captured and morphologically identified as belonging to three genera: Aedes, Anopheles and Culex. We randomly selected 1253 mosquitoes, including 662 specimens of 14 Anopheles species, 200 specimens of two Aedes species and 391 morphologically unidentified Culex specimens, for molecular and MALDI-TOF MS analysis. The DNA from 98 mosquitoes (69 Anopheles specimens, 23 Culex specimens and six Aedes sp. specimens) was subjected to molecular analysis, either to confirm our morphological identification or the MALDI-TOF MS results, as well as to identify the Culex species that were morphologically identified at the genus level and to resolve the discrepancies between the morphological identification and the MALDI-TOF MS identification. RESULTS: High-quality MS spectra were obtained for 1058 of the 1253 specimens (84%), including 192/200 for Aedes, 589/662 for Anopheles and 277/391 for Culex. The blind test showed that 986/997 (99%) of the specimens were correctly identified by MALDI-TOF MS, with log score values ranging from 1.708 to 2.843. Eleven specimens of Culex could not be identified based on morphological features, MALDI-TOF MS or molecular analysis. CONCLUSIONS: This study enabled us to identify several species of mosquitoes from Vietnam using MALDI-TOF MS, and to enrich our database of MALDI-TOF MS reference spectra.

Epidemiology and genomic characterisation of travel-associated and locally-acquired influenza, Marseille, France.

BACKGROUND: The purpose of the study was to challenge the hypothesis of an introduction of influenza viruses by international travellers and subsequent local circulation in Marseille, France. METHODS: We analysed the epidemiological data of PCR-confirmed cases over an eight-year period and compared the genomic data of local and imported influenza viruses during a six-month period. RESULTS: Between June 2013 and December 2020, 12,434 patients in the Assistance Publique-Hospitaux de Marseille were diagnosed with an influenza virus infection at the laboratory of the Institut Hospitalo-Universitaire Méditerranéee Infection of Marseille. Half of the patients were below the age of 20. Most of the imported cases were diagnosed outside of epidemic periods. Fourteen genomes of the influenza A virus, including six in international travellers returning from Europe or from the Arabian Peninsula and eight from patients who had not travelled were analysed. Sequences of influenza A/H1N1 virus genomes detected in subjects who had travelled to Saudi Arabia were in the same clade and differed from sequences detected later in a traveller returning from Italy, and in non-travellers who were infected in Marseille. This suggests that influenza viruses imported from Saudi Arabia did not subsequently circulate in Marseille. CONCLUSION: Future studies with higher numbers of genomes are needed to confirm this result.

Epidemiological Investigations of Infectious Diseases among Mobile Populations at the University Hospital Institute Mediterranean Infection in Marseille, France.

We review the most recent work conducted by our group on the circulation of infectious agents in mobile populations, including pilgrims participating in the Hajj (Mecca, Saudi Arabia) and the Grand Magal of Touba (Senegal) pilgrimages, homeless people, and medical students participating in an elective abroad. Using a similar epidemiological study design with standardized questionnaires and molecular assays allows comparison of different populations of travelers. The main infectious pathogens and antibiotic resistance genes linked to travel were identified in certain specific populations of travelers, as well as in a group of homeless migrant people in Marseille. The role of several risk factors has also been demonstrated, allowing identifying individuals at increased risk of disease or pathogen carriage on which to base targeted preventive measures. Such results, together with those obtained through international surveillance networks allow better description of the epidemiology of travel-associated infectious diseases.

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.

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.

Screening Strategy of Active Pulmonary Tuberculosis in Sheltered Homeless People in Marseille, 2019.

We aimed to assess the reliability of a screening questionnaire for Active Pulmonary Tuberculosis (APTB) in a population of sheltered homeless persons (HP). Participants from two homeless shelters completed a questionnaire specially designed to identify patients at high-risk of APTB (available at www.tb-screen.ch), underwent a Chest X-ray (CXR), and provided sputum samples. Computed Tomography (CT) scanning was subsequently performed on those which had images consistent with APTB. Microscopical examination, real-time polymerase chain reaction (qPCR) and culture testing were applied for Mycobacterium tuberculosis complex detection. Additionally, we retrospectively selected 16 HP hospitalised in our hospital between 2017 and 2019 with biologically confirmed tuberculosis and typical CXR images, and retrospectively documented a screening questionnaire by reviewing their medical files. Overall, the population (n = 383 HP) was predominantly migrants (87%). Forty-seven individuals (11.7%) had positive screening questionnaire scores and four (2.4%) displayed abnormal CXR features consistent with APTB. Three of them three underwent CT scanning that ruled out APTB and one was lost to follow-up. None tested positive through microbiological investigation. Fifteen (of 16, 93.8%) hospitalised patients with biologically confirmed APTB had a positive screening questionnaire score. The sensitivity and specificity of questionnaire for confirmed APTB were 93.8% and 87.7%, respectively. Screening questionnaires can be used as a first assessment tool in people arriving at homeless shelters and to refer those screening positive for a CXR.

Screening of SARS-CoV-2 among homeless people, asylum-seekers and other people living in precarious conditions in Marseille, France, March-April 2020.

BACKGROUND: Surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among sheltered homeless and other vulnerable people might provide the information needed to prevent its spread within accommodation centres. METHODS: Data were obtained from 698 participants in different accommodation centres (411 homeless individuals, 77 asylum-seekers, 58 other people living in precarious conditions and 152 employees working in these accommodation centres) who completed questionnaires and had nasal samples collected between 26 March and 17 April 2020. SARS-CoV-2 carriage was assessed by quantitative PCR. RESULTS: We found a high acceptance rate (78.9%) for testing. Overall, 49 people (7.0%) were positive for SARS-CoV-2, including 37 homeless individuals (of 411, 9.0%) and 12 employees (of 152, 7.9%). SARS-CoV-2 positivity correlated with symptoms, although 51% of patients who tested positive did not report respiratory symptoms or fever. Among homeless people, being young (18-34 years) (odds ratio 3.83, 95% confidence interval 1.47-10.0, p = 0.006) and being housed in one specific shelter (odds ratio 9.13, 95% confidence interval 4.09-20.37, p < 0.001) were independent factors associated with SARS-CoV-2 positivity (rates of 11.4% and 20.6%, respectively). DISCUSSION: Symptom screening alone is insufficient to prevent SARS-CoV-2 transmission in vulnerable sheltered people. Systematic testing should be promoted.

Variations in respiratory pathogen carriage among a homeless population in a shelter for men in Marseille, France, March-July 2020: cross-sectional 1-day surveys.

We aimed to compare respiratory pathogen carriage by PCR during three different time periods in 2020 in sheltered homeless people in Marseille, France. The overall prevalence of respiratory pathogen carriage in late March-early April (69.9%) was significantly higher than in late April (42.3%) and mid-July (45.1%). Bacterial carriage significantly decreased between late March-early April and late April. SARS-CoV-2 was detected only in late March-early April samples (20.6%). Measures aiming at mitigating SARS-CoV-2 transmission were effective and also impacted bacterial carriage. Seasonal variations of bacterial carriage between winter and summer in this population were not marked.

Enteric pathogenic bacteria and resistance gene carriage in the homeless population in Marseille, France.

We aimed to assess the prevalence of pathogenic bacteria and resistance genes in rectal samples collected among homeless persons in Marseille, France. In February 2014 we enrolled 114 sheltered homeless adults who completed questionnaires and had rectal samples collected. Eight types of enteric bacteria and 15 antibiotic resistance genes (ARGs) were sought by real-time polymerase chain reaction (qPCR) performed directly on rectal samples. ARG-positive samples were further tested by conventional PCR and sequencing. We evidenced a 17.5% prevalence of gastrointestinal symptoms, a 9.6% prevalence of enteric pathogenic bacteria carriage, including Escherichia coli pathotypes (8.7%) and Tropheryma whipplei (0.9%). Only 2 persons carried blaCTX-M-15 resistance genes (1.8%), while other genes, including carbapenemase-encoding genes and colistin-resistance genes, (mcr-1 to mcr-6, mcr-8) were not detected. Our results suggest that sheltered homeless persons in Marseille do not have a high risk of harbouring gastrointestinal antibiotic resistant bacteria.

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

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.

Vaccine-preventable diseases other than tuberculosis, and homelessness: A scoping review of the published literature, 1980 to 2020.

BACKGROUND: Homelessness may result in the breakdown of regular health services, including routine vaccination programmes. A scoping review was conducted to describe vaccine-preventable diseases (VPD) other than tuberculosis in people experiencing homelessness (PEH). METHODS: We followed the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR). We searched peer-reviewed literature published in English, French, Spanish or Portuguese reporting the outbreak of VPD or VPD prevalence in both infant and adult homeless populations published between 1980 and 2020, using PubMed/Medline, SciELO, Google Scholar, and Web of Science databases. Relevant information from the studies was charted in Microsoft Excel and results were summarised using a descriptive analytical method. RESULTS: Eighty-one articles were included. A high prevalence of past hepatitis B virus (HBV) and hepatitis A virus (HAV) infections were observed through serosurveys, mostly in high income countries or high-middle income countries (USA, Canada, France, Iran or Brazil). Ten outbreaks of HAV infection were also reported, with lethality rates ranging from 0 to 4.8%. The studies identified numerous risk factors positively associated with HBV infection, including older age, homosexual or bisexual practice, injected drug use (IDU), and, with HAV infection including IDU, having sexual partner(s) with a history of unspecified hepatitis, insertive anal penetration, or originating from a country with a high prevalence of anti-HAV antibody. Eleven outbreaks of pneumococcal infection affecting PEH were reported in Canada and USA, with lethality rates from 0 to 15.6%. Six diphtheria outbreaks were reported. Vaccination status was rarely documented in these studies. CONCLUSIONS: The literature suggests that homeless populations generally experience a high VPD burden suggesting the need for a national vaccination programme and planning for delivering vaccines in this population.

Pneumococcal infections and homelessness.

Objective: To assess the prevalence of pneumococcal nasopharyngeal carriage, the role of potential risk factors, and the pneumococcal vaccination coverage among sheltered homeless people in Marseille, France. Methods: During the winters 2015-2018, we enrolled 571 sheltered homeless males and 54 non-homeless controls. Streptococcus pneumoniae was directly searched from nasal/pharyngeal samples using real-time polymerase chain reaction. Results: The homeless people were mostly migrants from African countries, with a mean age of 43 years. Pneumococcal vaccination coverage was low (3.1%). The overall pneumococcal carriage rate was 13.0% and was significantly higher in homeless people (15.3% in 2018) than in controls (3.7%), with p = 0.033. Among homeless people, being aged ≥ 65 years (1.97, 95% CI; 1.01-3.87), living in a specific shelter (OR = 1.80, 95% CI: 1.06-3.05), and having respiratory signs and symptoms at the time of enrolment (OR = 2.55, 95% CI: 1.54-4.21) were independently associated with pneumococcal carriage. Conclusion: Pneumococcal nasopharyngeal carriage, which is a precursor for pneumococcal disease in at-risk individuals, is frequent among French homeless people. Studies conducted in other countries have also reported outbreaks of pneumococcal infections in homeless people. Pneumococcal vaccination should be systematically considered for sheltered homeless people in France, as is being done in Canada since 2008.

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

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.

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

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 blaCTX-M-A (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.