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The nature and dynamics of mutations associated with the emergence, spread, and vanishing of SARS‐CoV‐2 variants causing successive waves are complex. We determined the kinetics of the most common French variant ("Marseille‐4") for 10 months since its onset in July 2020. Here, we analyzed and classified into subvariants and lineages 7453 genomes obtained by next‐generation sequencing. We identified two subvariants, Marseille‐4A, which contains 22 different lineages of at least 50 genomes, and Marseille‐4B. Their average lifetime was 4.1 ± 1.4 months, during which 4.1 ± 2.6 mutations accumulated. Growth rate was 0.079 ± 0.045, varying from 0.010 to 0.173. Most of the lineages exhibited a bell‐shaped distribution. Several beneficial mutations at unpredicted sites initiated a new outbreak, while the accumulation of other mutations resulted in more viral heterogenicity, increased diversity and vanishing of the lineages. Marseille‐4B emerged when the other Marseille‐4 lineages vanished. Its ORF8 gene was knocked out by a stop codon, as reported in SARS‐CoV‐2 of mink and in the Alpha variant. This subvariant was associated with increased hospitalization and death rates, suggesting that ORF8 is a nonvirulence gene. We speculate that the observed heterogenicity of a lineage may predict the end of the outbreak. [ABSTRACT FROM AUTHOR]

Objectives: We evaluated the 6-week mortality of SARS-CoV-2 hospitalized patients treated using a standardized protocol in 2020 in Marseille, France.Methods: A retrospective monocentric cohort study was conducted in the standard hospital wards at the Institut Hospitalo-Universitaire Méditerranée Infection, between March and December 2020 in adults with SARS-CoV-2 PCR-proven infection.Results: Of the 2111 hospitalized patients (median age, 67 [IQR 55-79] years; 1154 [54.7%] men), 271 were transferred to the intensive care unit (12.8%) and 239 died (11.3%; the mean age of patients who died was 81.2 (±9.9)). Treatment with hydroxychloroquine plus azithromycin (HCQ-AZ), used in 1270 patients, was an independent protective factor against death (0.68 [0.52 - 0.88]). This effect was consistent for all subgroups of age, comorbidities, severity of the disease and comedications with zinc or corticosteroids. Zinc was independently protective against death (0.39 [0.23 - 0.67]), in a subgroup analysis of patients treated with HCQ-AZ without dexamethasone. The use of high-flow oxygen therapy in elderly patients who were not eligible for intensive care unit transfer saved 19 patients (33.9%).Conclusions: In our 2020 cohort, treating COVID-19 with HCQ-AZ was associated with lower mortality. These results need to be analyzed in the context of academic discussions about observational studies versus randomized clinical trials. More data will deserve to be analyzed in the SARS-Cov 2 variants, vaccination and post-vaccination era. [ABSTRACT FROM AUTHOR]

One thousand one hundred and nineteen cases of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) Omicron variant cases have been diagnosed at the Institut Hospitalo‐Universitaire Méditerranée Infection, Marseille, France, between November 28, 2021, and December 31, 2021. Among the 825 patients with known vaccination status, 383 (46.4%) were vaccinated, of whom 91.9% had received at least two doses of the vaccine. Interestingly, 26.3% of cases developed SARS‐CoV‐2 infection within 21 days following the last dose of vaccine suggesting possible early production of anti‐SARS‐CoV‐2 facilitating antibodies. Twenty‐one patients have been hospitalized, one patient required intensive care, and another patient who received a vaccine booster dose died. Highlights: Significantly low rates of hospitalization, transfer to Intensive Care Unit and death were observed in patients infected with Omicron as compared to those infected with Delta variant of severe acute respiratory syndrome coronavirus 2 during the same period,26.3% of patients infected with Omicron get infected during the 3 weeks following COVID‐19 vaccination raising the question of facilitating antibodies. [ABSTRACT FROM AUTHOR]

We detected SARS-CoV-2 of PANGO lineage R.1 with the spike substitution E484K in three patients. Eleven other sequences in France and 8,831 worldwide were available from GISAID, 92% originating from Japan. The three genome sequences from our institute were phylogenetically closest to another from Guinea-Conakry, where one of the patients had travelled. These viruses did not exhibit any unusual features in cell culture. Spike structural predictions indicated a 1.3-time higher transmissibility index than for the globally spread B.1.1.7 variant but also an affinity loss for gangliosides that might have slowed dissemination. The spread of new SARS-CoV-2 mutants/variants is still not well understood and therefore difficult to predict, and this hinders implementation of effective preventive measures, including adapted vaccines. [ABSTRACT FROM AUTHOR]

From January 18th to August 13th, 2021, 13,804 unvaccinated and 1,156 patients who had received at least one COVID-19 vaccine dose were tested qPCR-positive for SARS-CoV-2 in our center. Among vaccinated patients, 949, 205 and 2 had received a single, two or three vaccine doses, respectively. Most patients (80.3%) had received the Pfizer-BioNTech vaccine. The SARS-CoV-2 variants infecting vaccinated patients varied over time, reflecting those circulating in the Marseille area, with a predominance of the Marseille-4/20A.EU2 variant from weeks 3 to 6, of the Alpha/20I variant from weeks 7 to 25, and of the Delta/21A variant from week 26. SARS-CoV-2 infection was significantly more likely to occur in the first 13 days post-vaccine injection in those who received a single dose (48.9%) than two doses (27.4%, p < 10–3). Among 161 patients considered as fully vaccinated, i.e., > 14 days after the completion of the vaccinal scheme (one dose for Johnson and Johnson and two doses for Pfizer/BioNTech, Moderna and Sputnik vaccines), 10 (6.2%) required hospitalization and four (2.5%) died. Risks of complications increased with age in a nonlinear pattern, with a first breakpoint at 54, 33, and 53 years for death, transfer to ICU, and hospitalization, respectively. Among patients infected by the Delta/21A or Alpha/20I variants, partial or complete vaccination exhibited a protective effect with a risk divided by 3.1 for mortality in patients ≥ 55 years, by 2.8 for ICU transfer in patients ≥ 34 years, and by 1.8 for hospitalization in patients ≥ 54 years. Compared to partial vaccination, complete vaccination provided an even stronger protective effect, confirming effectiveness to prevent severe forms of COVID-19. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 bla CTX-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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Previous reports have suggested that children are less affected than adults by SARS-CoV-2. We analyzed SARS-CoV-2 diagnoses between February 27, 2020, and March 14, 2020, and mortality among positive patients in Marseille university hospitals. Of 4050 tested individuals, 228 were positive. Deaths occurred in 2/99 documented cases (both > 85 year-old). Children were majorly asymptomatic. Incidence increased by 7.4-fold between 1–5 and 45–65 years then decreased. It was significantly lower among 0–1 year- (0%) and 1–5 (1.1%) and 5–10 (3.6%)-year-old children than among subjects > 18 years (6.5%). Viral loads did not differ between children and adults. Children may not contribute significantly to virus circulation. [ABSTRACT FROM AUTHOR]

Homeless people are often exposed to unhygienic environments as well as to animals carrying arthropods which both transmit zoonotic infections and human louse-borne pathogens. We attempted to determine the prevalence of antibodies against several vector-borne and zoonotic pathogens among homeless adults living in Marseille. During the 2005–2015 period, we collected sera samples from 821 homeless adults living in shelters. Antibodies against Bartonella quintana, Bartonella henselae, Borrelia recurrentis, Coxiella burnetii, Francisella tularensis (with a cut-off of 1:100), Rickettsia akari, Rickettsia conorii, Rickettsia felis, Rickettsia prowazekii, and Rickettsia typhi (with a cut-off of 1:64) were searched by microimmunofluorescence (MIF). MIF-positive serum samples were confirmed by cross-adsorption to characterise cross-reacting antigens and immunoblotting. Positive sera by Western blot were further tested using qPCR. We evidenced a prevalence of 4.9% seroreactivity to at least one pathogen including phase II C. burnetii (2.1%), B. quintana (1.7%), R. conorii (0.4%), R. prowazekii (0.4%), R. typhi (0.1%), B. recurrentis (0.1%), and F. tularensis (0.1%). No DNA from any pathogens was detected. A comparison with studies conducted prior to the 2000–2003 period showed a decrease in the overall seroprevalence of several vector-borne and zoonotic infections. [ABSTRACT FROM AUTHOR]

The presence of Acinetobacter baumannii was demonstrated in body lice, however, little is known about the mechanism of natural lice infection. In 2013 and 2014, cross-sectional one-day studies were therefore performed within two Marseille homeless shelters to assess the presence of A. baumannii DNA on human skin, blood and in body lice collected from the same homeless individuals. All 332 participants completed questionnaires, were examined for dermatologic signs, and provided four skin samples (hair, neck, armpits, and pelvic belt), blood samples and body lice (if any). We developed a new real-time PCR tool targeting the ompA/motB gene for the detection of A. baumannii for all collected samples. Blood culture was also performed. Body lice were found in 24/325 (7.4%) of subjects. We showed a prevalence of A. baumannii DNA skin-carriage in 33/305 (10.8%) of subjects. No difference was found in A. baumannii DNA prevalence according to body sites. A strong association between body lice infestation (OR = 3.07, p = 0.029) and A. baumannii DNA skin-carriage was noted. In lice, A. baumannii DNA was detected in 59/219 arthropods (26.9%). All blood cultures and real-time PCR on blood samples were negative for A. baumannii. Lice probably get infected with A. baumannii while biting through the colonized skin and likely transmit the bacteria in their feces. We found no evidence that lice facilitate the invasion of A. baumannii into the blood stream. Further investigations are needed to compare phenotypic and genotypic features of A. baumannii isolates from human skin and lice from the same individuals. [ABSTRACT FROM AUTHOR]

The prevalence of body lice among 2,288 sheltered homeless persons in the city of Marseille during 2000-2017 was 12.2% and significantly decreased over time. We report a positive association between body lice infestations and older age, duration of stays in France for migrants, frequent consumption of alcohol, and tobacco smoking. [ABSTRACT FROM AUTHOR]

Enterococci are gram-positive cocci responsible for various infections worldwide, and their prevalence of antibiotic resistance greatly varies worldwide. This study investigates the prevalence of resistance to antibiotics in enterococci from patients admitted in the four university hospitals of Marseille between January 2013 and September 2014. Two thousand nine hundred seventy-six patients-bacteria couples were identified (2,507 Enterococcus faecalis and 469 Enterococcus faecium) in the four university hospitals of Marseille. 1.3%, 8.9%, 1.4%, and 0% of E. faecalis strains were resistant to amoxicillin, gentamicin, teicoplanin, and vancomycin, respectively, and 83.9%, 49.2%, 1.3%, and 0.2% of E. faecium strains were resistant to amoxicillin, gentamicin, teicoplanin, and vancomycin, respectively. Resistance to aminoglycosides and vancomycin in strains isolated from blood cultures was significantly lower than that of most European countries included in the 2012 European Antimicrobial Resistance Surveillance Network report. Our low percentage of antibiotic resistance in enterococci is likely due to a low level of E. faecium infections, underlining the need to implement surveillance systems, especially to monitor the E. faecalis/ E. faecium ratio evolution in blood cultures and others. [ABSTRACT FROM AUTHOR]

Background: In France, there was a reluctance to accept vaccination against the A/H1N1 pandemic influenza virus despite government recommendation and investment in the vaccine programme. Methods and Findings: We examined the willingness of different populations to accept A/H1N1vaccination (i) in a French hospital among 3315 employees immunized either by in-house medical personnel or mobile teams of MDs and (ii) in a shelter housing 250 homeless persons. Google was used to assess the volume of enquiries concerning incidence of influenza. We analyzed the information on vaccination provided by Google, the website of the major French newspapers, and PubMed. Two trust Surveys were used to assess public opinion on the trustworthiness of people in different professions. Paramedics were significantly more reluctant to accept immunisation than qualified medical staff. Acceptance was significantly increased when recommended directly by MDs. Anecdotal cases of directly observed severe infections were followed by enhanced acceptance of paramedical staff. Scientific literature was significantly more in favour of vaccination than Google and French newspaper websites. In the case of the newspaper websites, information correlated with their recognised political reputations, although they would presumably claim independence from political bias. The Trust Surveys showed that politicians were highly distrusted in contrast with doctors and pharmacists who were considered much more trustworthy. Conclusions: The low uptake of the vaccine could reflect failure to convey high quality medical information and advice relating to the benefits of being vaccinated. We believe that the media and internet contributed to this problem by raising concerns within the general population and that failure to involve GPs in the control programme may have been a mistake. GPs are highly regarded by the public and can provide face-to-face professional advice and information. The top-down strategy of vaccine programme management and information delivered by the Ministry of Health could have aggravated the problem, because the general population does not always trust politicians. [ABSTRACT FROM AUTHOR]

The article presents a study which examines the effect of standardized diagnostic and therapeutic protocol on the mortality of infective endocarditis (IE) patients in the Cardiology Department of La Timone Hospital in Marseille, France. Subjects of the study were divided to before and after groups of the therapeutic protocol of the researchers. Results show that mortality rates in both approaches provided positive results. It notes that the researchers' approach has a substantial impact on IE.

The article focuses on the detection of Amoeba-resistant bacteria (ARB) in human and environmental samples wherein their habitat is regarded as a reservoir of human pathogens. It states that co-culture with amoeba is an efficient tool, yet, only water samples from cooling towers and hospital water supply has been studied as possible ARB reservoirs. It presents the study on ARB population of diverse soil and sand sources in proximity to human environments in the city of Marseilles, France. It also provides information on the result of the study in which the ability to grow within lyse amoebae was demonstrated, and 20 of the isolates including Streptococcus pneumoniae were described as human pathogens.

The objective of this paper is to describe the surveillance system MIDaS and to show how this system has been used for evaluating the consequences of the French COVID-19 lockdown on the bacterial mix of AP-HM and the antibiotic resistance. MIDas is a kind of surveillance activity hub, allowing the automatic construction of surveillance control boards. We investigated the diversity and resistance of bacterial agents from respiratory, blood, and urine samples during the lockdown period (from week 12 to 35 of 2020), using the same period of years from 2017 to 2019 as control. Taking into account the drop in patient recruitment, several species have exhibited significant changes in their relative abundance (either increasing or decreasing) with changes up to 9%. The changes were more important for respiratory and urine samples than for blood samples. The relative abundance in respiratory samples for the whole studied period was higher during the lockdown. A significant increase in the percentage of wild phenotypes during the lockdown was observed for several species. The use of the MIDaS syndromic collection and surveillance system made it possible to efficiently detect, analyze, and follow changes of the microbiological population as during the lockdown period. [ABSTRACT FROM AUTHOR]

(1) Background: We collected COVID-19 mortality data and the age distribution of the deceased in France and other European countries, as well as specifically in the cities of Paris and Marseille, and compared them. (2) Methods: Data on mortality related to COVID-19 and the associated age distribution were collected from government institutions in various European countries. In France, data were obtained from INSEE and Santé Publique France. All-cause mortality was also examined in order to study potential excess mortality using EuroMOMO. The Marseille data came from the epidemiological surveillance system. (3) Results: France is one of the European countries most impacted by COVID-19. Its proportion of deaths in people under 60 years of age is higher (6.5%) than that of Italy (4.6%) or Spain (4.7%). Excess mortality (5% more deaths) was also observed. Ile-de-France and the Grand-Est are the two French regions with the highest mortality. The proportion of deaths in the under-60 age group was considerable in Ile-de-France (9.9% vs. 4.5% in the Southern region). There are significantly higher numbers of patients hospitalized, in intensive care and deceased in Paris than in Marseille. (4) Conclusions: No patient management, i.e., from screening to diagnosis, including biological assessment and clinical examination, likely explains the high mortality associated with COVID-19. [ABSTRACT FROM AUTHOR]

Background: The Hospital-University Institute (IHU) Méditerranée Infection features a 27,000 square meter building hosting 700 employees and 75 hospitalized patients in the center of Marseille, France. Method: Previous preparedness in contagious disease management allowed the IHU to manage the COVID-19 outbreak by continuing adaptation for optimal diagnosis, care and outcome. We report here the output of this management. Results: From 5 March 2020, and 26 April 2021, 608,313 PCR tests were provided for 424,919 patients and 44,089 returned positive. A total of 23,390 patients with COVID-19 were followed at IHU with an overall case fatality ratio of 1.7%. Of them 20,270 were followed as outpatients with an overall CFR of 0.17%. We performed 24,807 EKG, 5759 low dose CT Scanner, and 18,344 serology. Of the 7643 nasopharyngeal samples inoculated in cell cultures 3317 (43.3%) yielded SARS-Cov-2 isolates. Finally, 7370 SARS-Cov-2 genomes were analyzed, allowing description of the first genetic variants and their implication in the epidemiologic curves. Continuous clinical care quality evaluation provided the opportunity for 155 publications allowing a better understanding of the disease and improvement of care and 132 videos posted on the IHU Facebook network, totaling 60 million views and 390,000 followers, and dealing with COVID-19, outbreaks, epistemology, and ethics in medicine. Conclusions: During this epidemic, IHU Méditerranée Infection played the role for which it has been created; useful clinical research to guarantee a high-quality diagnostic and care for patient and a recognized expertise. [ABSTRACT FROM AUTHOR]

SARS-CoV-2 nasopharyngeal shedding contributes to the spread of the COVID-19 epidemic. Among 3271 COVID-19 patients treated at the Hospital University Institute Méditerranée Infection, Marseille, France from 3 March to 27 April 2020, tested at least twice by qRT-PCR, the median SARS-CoV-2 nasopharyngeal shedding duration was 6 days (range 2–54 days). Compared with short shedders (qRT-PCR positivity < 10 days), 34 (1.04%) persistent shedders (qRT-PCR positivity ≥ 17 days; mean ± SD: 23.3 ± 3.8 days) were significantly older, with associated comorbidities, exhibiting lymphopenia, eosinopenia, increased D-dimer and increased troponin (p < 0.05), and were hospitalized in intensive care unit in 17.7% vs. 1.1% of cases (p < 0.0001). Viral culture was positive in six persistent shedders after day 10, including in one patient after day 17, and no viral co-pathogen was detected in 33 tested patients. Persistent shedders received azithromycin plus hydroxychloroquine ≥ 3 days in 26/34 (76.5%) patients, a figure significantly lower than in short shedders (86.6%) (p = 0.042). Accordingly, mortality was 14.7% vs. 0.5% (p < 0.0001). Persistent shedding was significantly associated with persistent dyspnea and anosmia/ageusia (p < 0.05). In the context of COVID-19 treatment, including treatment with azithromycin plus hydroxychloroquine, the persistence of SARS-CoV-2 nasopharyngeal shedding was a rare event, most frequently encountered in elderly patients with comorbidities and lacking azithromycin plus hydroxychloroquine treatment. [ABSTRACT FROM AUTHOR]

We report a case of infectious endocarditis attributable to Legionella longbeachae. L. longbeachae is usually associated with lung infections. It is commonly found in composted waste wood products. L. longbeachae should be regarded as an agent of infectious endocarditis, notably in the context of gardening involving handling of potting soils. [ABSTRACT FROM AUTHOR]

Urban outbreaks of Q fever have occurred after exposure to slaughterhouses or parturient cats, We detected an outbreak of Q fever in a homeless shelter in Marseilles. Investigations showed that the main factors exposing persons to Coxiella bumetii were an abandoned slaughterhouse, used for an annual Muslim sheep feast, and wind. [ABSTRACT FROM AUTHOR]

• The severe acute respiratory syndrome (SARS-CoV-2) Marseille-4 variant caused an epidemic that started in August and is still ongoing. • This variant harbours 13 hallmark mutations, including one in the spike receptor binding domain. • The variant predominated in Marseille from September 2020 and caused a re-infection in 11 patients. • Hypoxemia was more frequent than with clade 20A strains that circulated before May 2020. • The sudden appearance of Marseille-4 points towards an animal reservoir, possibly mink. In Marseille, France, following a first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak in March–May 2020, a second epidemic phase occurred from June, involving 10 new variants. The Marseille-4 variant caused an epidemic that started in August and is still ongoing. The 1038 SARS-CoV-2 whole genome sequences obtained in our laboratory by next-generation sequencing with Illumina technology were analysed using Nextclade and nextstrain/ncov pipelines and IQ-TREE. A Marseille-4-specific qPCR assay was implemented. Demographic and clinical features were compared between patients with the Marseille-4 variant and those with earlier strains. Marseille-4 harbours 13 hallmark mutations. One leads to an S477N substitution in the receptor binding domain of the spike protein targeted by current vaccines. Using a specific qPCR, it was observed that Marseille-4 caused 12–100% of SARS-CoV-2 infections in Marseille from September 2020, being involved in 2106 diagnoses. This variant was more frequently associated with hypoxemia than were clade 20A strains before May 2020. It caused a re-infection in 11 patients diagnosed with different SARS-CoV-2 strains before June 2020, suggesting either short-term protective immunity or a lack of cross-immunity. Marseille-4 should be considered as a major SARS-CoV-2 variant. Its sudden appearance points towards an animal reservoir, possibly mink. The protective role of past exposure and current vaccines against this variant should be evaluated. [ABSTRACT FROM AUTHOR]

• The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positivity rate was 9.0% among homeless people. • SARS-CoV-2 positivity correlated with symptoms. • Positivity among homeless people increased with younger age and one shelter. 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. 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. 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). Symptom screening alone is insufficient to prevent SARS-CoV-2 transmission in vulnerable sheltered people. Systematic testing should be promoted. [ABSTRACT FROM AUTHOR]

• Two third of COVID-19 patients do not complaint of a shortness of breath. • The LDCT scan showed signs compatible with pneumonia in two third of them. • Asymptomatic hypoxemia was present in one third of them at admission. • Patient with asymptomatic hypoxemia have a very poor outcome. • Lack of shortness of breath is not a sign of wellbeing in patient with COVID-19. Describe and evaluate the outcome of a coronavirus disease-2019 (COVID-19) patient without shortness of breath. 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. 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). 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. [ABSTRACT FROM AUTHOR]

• Comparable bell-shaped distributions for SARS-CoV-2 and endemic coronaviruses. • Different age distributions for SARS-CoV-2 and other respiratory viruses. • Fewer children among all SARS-CoV-2-positive than all endemic coronavirus-positive. • SARS-CoV-2 was the only respiratory virus to spare children. The SARS-CoV-2 epidemic presents a poorly understood epidemiological cycle. We aimed to compare the age and weekly distributions of the five human coronaviruses, including SARS-CoV-2, that circulated in southeastern France. We analyzed all available diagnoses of respiratory viruses, including SARS-CoV-2, performed between 09/2013 and 05/2020 at the University Hospital Institute Méditerranée Infection in Marseille, southeastern France. For SARS-CoV-2, positive children <15 years of age represented 3.4% (228/6,735) of all positive cases, which is significantly less than for endemic coronaviruses (46.1%; 533/1,156; p < 0.001). Among 10,026 patients tested for SARS-CoV-2 and endemic coronaviruses in 2020, children <15 years represented a significantly lower proportion of all positive cases for SARS-CoV-2 than for endemic coronaviruses [2.2% (24/1,067) vs. 33.5% (149/445), respectively; p < 0.001]. Epidemic curves for endemic coronaviruses and SARS-CoV-2 in 91,722 patients showed comparable bell-shaped distributions with a slight time lag. In contrast, the age distribution of endemic coronaviruses and 14 other respiratory viruses differed significantly compared to that of SARS-CoV-2, which was the only virus to relatively spare children. We observed for SARS-CoV-2 a temporal distribution resembling that of endemic coronaviruses but an age distribution that relatively spares the youngest subjects, who are those the most exposed to endemic coronaviruses. [ABSTRACT FROM AUTHOR]

• Risk factors for acquisition of pathogens among medical students have not been clearly identified. • The relationship between symptoms and the carriage of pathogens also remain poorly understood. • This study showed that 35.8%, 63.5% and 3.6% students reported at least one respiratory, gastro-intestinal and vaginal symptom during travel. • Acquisition of pathogens was high, including viruses and bacteria. • Risk factors for these infectious in medical students were identified. To investigate symptoms of infections and their risk factors among French medical students undertaking an internship abroad. Clinical follow up, and qPCR-based respiratory, gastrointestinal, and vaginal pathogen carriages were prospectively assessed pre-travel and post-travel, in a cohort of medical students departing from Marseille, France. 293 students were included. 63.5%, 35.8%, and 3.6% of students reported gastrointestinal, respiratory, and vaginal symptoms, respectively. The acquisition rate of Enteroaggregative Escherichia coli and Enteropathogenic E. coli was 40.9% and 18.6%, respectively. A significant increase was observed for rhinovirus and Streptococcus pneumoniae by comparing the prevalence of pathogens in pre-travel and post-travel samples. Gardnerella vaginalis and Atopobium vaginae acquisition rates were 12.9% and 13.9%, respectively. Being female, primarily traveling to Vietnam, and living in basic accommodation conditions were independent risk factors for reporting respiratory symptoms. Students reporting respiratory symptoms were three times more likely to acquire S. pneumoniae. Traveling primarily to north India and Senegal were independent risk factors for diarrhea. This study makes it possible to identify the leading infectious diseases linked to travel in a group of French medical students undertaking an internship abroad and the risk factors on which to base targeting students for reinforced pre-travel advice. [ABSTRACT FROM AUTHOR]

• The COVID19 pandemics affected suddenly the Jewish community of Marseille, France. The investigations of COVID-19 epidemic clusters showed that many small gathering for Purim Jewish celebration, in March 2020 accelerated the virus spreading in community settings. • A total of 6 clusters were linked to religious and social activities: a ski trip, organized meals for the Purim Jewish celebration in community and family settings on March 10, a religious service and a charity gala. • A considerable proportion (40%) of the patients were infected by index patients during the presymptomatic period. • Clinical and PCR attack rates were 3.3 and 2.7 fold lower in children than in adults, especially when children were in close contacts with the infected adults; and thus suggesting a lower susceptibility of children for the COVID19. We investigated possible COVID-19 epidemic clusters and their common sources of exposure that led to a sudden increase in the incidence of COVID-19 in the Jewish community of Marseille between March 15 and March 20, 2020. All data were generated as part of routine work at Marseille university hospitals. Biological diagnoses were made by RT-PCR testing. A telephone survey of families in which a laboratory confirmed case was diagnosed was conducted to determine possible exposure events. As of March 30, 2020, 63 patients were linked to 6 epidemic clusters. The 6 clusters were linked to religious and social activities: a ski trip, organized meals for the Purim Jewish celebration in community and family settings on March 10, a religious service and a charity gala. Notably, 40% of the patients were infected by index patients during the presymptomatic period, which was 2.5 days before symptom onset. When considering household members, all 12 patients who tested negative and who did not develop any relevant clinical symptoms compatible with COVID-19 were 1–16 years of age. The clinical attack rate (symptoms compatible with COVID-19, and biologically confirmed by PCR) in adults was 85% compared to 26% in children. Family and community gatherings for the Purim Jewish celebration probably accelerated the spread of COVID-19 in the Marseille Jewish community, leading to multiple epidemic clusters. This investigation of family clusters suggested that all close contacts of patients with confirmed COVID-19 who were not infected were children. [ABSTRACT FROM AUTHOR]

Many studies have evaluated the use of hydroxychloroquine in COVID-19. Most retrospective observational studies demonstrate a benefit of using HCQ on mortality, but not most randomized clinical trials. We analyzed raw data collected from a cohort of 30,423 patients with COVID-19 cared for at IHU Méditerranée Infection in Marseille France and extracted from the DRYAD open data platform. We performed univariate and multivariable logistic regressions with all-cause mortality within six weeks. Multivariable logistic regressions were adjusted for sex, age group (<50, 50–69, 70–89 and ​> ​89 years), periods (or variants), and type of patient management. Among 30,202 patients for whom information on treatment was available, 191/23,172 (0.82%) patients treated with HCQ-AZ died, compared to 344/7030 (4.89%) who did not receive treatment with HCQ-AZ. HCQ-AZ therapy was associated with a lower mortality than treatment without HCQ-AZ (odds ratio (OR) 0.16; 95% confidence interval (CI), 0.14–0.19). After adjustment for sex, age, period, and patient management, HCQ-AZ was associated with a significantly lower mortality rate (adjusted OR (aOR) 0.55, 95% CI 0.45–0.68). On a subsample of 21,664 patients with available variant information, results remained robust after adjustment on sex, age, patient management and variant (aOR 0.55; 95% CI 0.44–0.69). On a subsample of 16,063 patients, HCQ-AZ was still associated with a significantly lower mortality rate (aOR 0.47, 95%CI 0.29–0.75) after adjustment for sex, age, period, patient management, vaccination status and comorbidities. Analysis of this large online database showed that HCQ-AZ was consistently associated with the lowest mortality. [ABSTRACT FROM AUTHOR]

• The number of COVID-19 cases in Marseille, France, peaked in March-April. • Resurgence was observed in June-August. • Patients in the two periods did not present marked age and sex differences. • Markers of severity were less prevalent in the summer period. • A 10 times decrease in the lethality rate was observed in June-August. To describe the characteristics of COVID-19 patients seen in March-April and June-August 2020 in Marseille, France with the aim to investigate possible changes in the disease between these two time periods. Demographics, hospitalization rate, transfer to intensive care unit (ICU), lethality, clinical and biological parameters were investigated. Compared to those seen in March-April, COVID-19 patients seen in June-August were significantly younger (39.2 vs. 45.3 years), more likely to be male (52.9% vs. 45.6%), and less likely to be hospitalized (10.7 vs. 18.0%), to be transferred to ICU (0.9% vs. 1.8%) and to die (0.1% vs. 1.1%). Their mean fibrinogen and D-dimer blood levels were lower (1.0 vs. 1.5 g/L and 0.6 vs. 1.1 μg/mL, respectively). By contrast, their viral load was higher (cycle threshold ≤16 = 5.1% vs. 3.7%). Patients in the two periods did not present marked age and sex differences, but markers of severity were undoubtedly less prevalent in the summer period, associating with a 10 times decrease in the lethality rate. [ABSTRACT FROM AUTHOR]

• There were fewer common respiratory virus-associated deaths in Southeastern France hospitals during 2019–2020 vs 2018–2019. • The majority were due to decreases in influenza A virus and respiratory syncytial virus (RSV)-associated deaths. • 55 deaths were associated with a SARS-CoV-2 diagnosis. • There was similar respiratory virus-associated mortality among hospitalized patients. • SARS-CoV-2 infections had a limited impact on the number of deaths of any cause among hospitalized people. Respiratory viruses are a major cause of mortality worldwide and in France, where they cause several thousands of deaths every year. University Hospital Institute-Méditerranée Infection performs real-time surveillance of all diagnoses of infections and associated deaths in public hospitals in Marseille, Southeastern France. This study compared mortality associated with diagnoses of respiratory viruses during the colder months of 2018–2019 and 2019–2020 (week 47–week 14). In 2018–2019, 73 patients (0.17% of 42,851 hospitalized patients) died after being diagnosed with a respiratory virus; 40 and 13 deaths occurred in patients diagnosed with influenza A virus and respiratory syncytial virus (RSV), respectively. In 2019–2020, 50 patients (0.10% of 49,043 patients hospitalized) died after being diagnosed with a common respiratory virus; seven and seven deaths occurred in patients diagnosed with influenza A virus and RSV, respectively. Additionally, 55 patients died after being diagnosed with SARS-CoV-2. The proportion of respiratory virus-associated deaths among hospitalized patients was thus significantly lower for common respiratory viruses in 2019–2020 than in 2018–2019 (102 versus 170 per 100,000 hospitalized patients; p = 0.003), primarily as a consequence of a decrease in influenza A virus (–83%) and RSV (–46%)-associated deaths. Overall, the proportion of respiratory virus-associated deaths among hospitalized patients was higher, but not significantly, in 2019–2020 than in 2018–2019 (214 versus 170 per 100,000 hospitalized patients; p = 0.08, Yates-corrected Chi-square test). These findings put into perspective the death burden of SARS-CoV-2 infections in this geographical area. [ABSTRACT FROM AUTHOR]

Among the multiple SARS-CoV-2 variants identified since summer 2020, several have co-circulated, creating opportunities for coinfections and potentially genetic recombinations that are common in coronaviruses. Viral recombinants are indeed beginning to be reported more frequently. Here, we describe a new SARS-CoV-2 recombinant genome that is mostly that of a Omicron 21L/BA.2 variant but with a 3′ tip originating from a Omicron 21K/BA.1 variant. Two such genomes were obtained in our institute from adults sampled in February 2022 in university hospitals of Marseille, southern France, by next-generation sequencing carried out with the Illumina or Nanopore technologies. The recombination site was located between nucleotides 26,858-27,382. In the two genomic assemblies, mean sequencing depth at mutation-harboring positions was 271 and 1362 reads and mean prevalence of the majoritary nucleotide was 99.3 ± 2.2% and 98.8 ± 1.6%, respectively. Phylogeny generated trees with slightly different topologies according to whether genomes analyzed were depleted or not of the 3′ tip. This 3′ terminal end brought in the Omicron 21L/BA.2 genome a short transposable element of 41 nucleotides named S2m that is present in most SARS-CoV-2 except a few variants among which the Omicron 21L/BA.2 variant and may be involved in virulence. Importantly, this recombinant is not detected by currently used qPCR that screen for variants in routine diagnosis. The present observation emphasizes the need to survey closely the genetic pathways of SARS-CoV-2 variability by whole genome sequencing, and it could contribute to gain a better understanding of factors that lead to observed differences between epidemic potentials of the different variants. • We described a new recombinant consiting in a Omicron 21L/BA.2 variant with the 3′ tip of a Omicron 21K/BA.1 variant. • This recombinant is not detected by routine variants screening qPCR. • It recovered from a 21K/BA.1 genome a short transposable element named S2m that lacks in 21L/BA.2 genomes. • S2m might increase viral virulence. [ABSTRACT FROM AUTHOR]

• Since 2003, we have systematically investigated respiratory and gastrointestinal infections of viral origin in patients who are admitted to our hospital (IHU Marseille, France) with lung or intestinal symptoms with an epidemiological syndromic surveillance MIDaS. • The measures taken to control COVID-19 were effective against lower respiratory tract infections viruses and gastroenteritis agents • But these measures were no efficacy on the agents of the common winter cold (rhinovirus, parainfluenza 3 virus, NL63 coronavirus and SARS-CoV-2). • More specific measures for preventing COVID-19 and upper respiratory tract infections need to be discovered to limit the spread of this epidemic. We systematically survey respiratory and gastrointestinal infections of viral origin in samples sent to our university hospital institute in Marseille, southern France. Here, we evaluated whether the measures implemented to fight COVID-19 had an effect on the dynamics of viral respiratory or gastrointestinal infections. We analysed PCR performed and positive for the diagnoses of viral respiratory and gastrointestinal infections over five years (January 2017-February 2021). Data were collected from our epidemiological surveillance system (MIDaS). Dates and contents of French measures against SARS-CoV-2 were collected from: https://www.gouvernement.fr/info-coronavirus/les-actions-du-gouvernement. Over the 2017-2021 period, 990,364 analyses were carried out for respiratory infections not including SARS-CoV-2, 510,671 for SARS-CoV-2 and 27,719 for gastrointestinal infections. During winter 2020–2021, when the most restrictive lockdown measures were in place in France, a marked decrease of infections with influenza viruses (one case versus 1,839-1,850 cases during 2017-2020 cold seasons) and with the RSV (56 cases versus 988-1,196 cases during 2017-2020 cold seasons) was observed, demonstrating the relative effectiveness of these measures on their occurrence. SARS-CoV-2 incidence seemed far less affected. Rhinoviruses, parainfluenza 3 virus, and the coronavirus NL63 remained at comparable levels. Also, the norovirus winter season positivity rates decreased continuously and significantly over time from 9.3% in 2017–2018 to 2.0% in 2020–2021. The measures taken to control COVID-19 were effective against lower respiratory tract infections viruses and gastroenteritis agents, but not on the agents of the common winter cold and SARS-CoV-2. This suggests that more specific measures to prevent COVID-19 and upper respiratory tract infections need to be discovered to limit the spread of this epidemic. [ABSTRACT FROM AUTHOR]

To compare the demographics, clinical characteristics and severity of patients infected with nine different SARS-CoV-2 variants, during three phases of the COVID-19 epidemic in Marseille. A single centre retrospective cohort study was conducted in 1760 patients infected with SARS-CoV-2 of Nextstrain clades 20A, 20B, and 20C (first phase, February–May 2020), Pangolin lineages B.1.177 (we named Marseille-2) and B.1.160 (Marseille-4) variants (second phase, June–December 2020), and B.1.1.7 (alpha), B.1.351 (beta), P.1 (gamma) and A.27 (Marseille-501) variants (third phase, January 2021-today). Outcomes were the occurrence of clinical failures, including hospitalisation, transfer to the intensive-care unit, and death. During each phase, no major differences were observed with regards to age and gender distribution, the prevalence of chronic diseases, and clinical symptoms between variants circulating in a given phase. The B.1.177 and B.1.160 variants were associated with more severe outcomes. Infections occurring during the second phase were associated with a higher rate of death as compared to infections during the first and third phases. Patients in the second phase were more likely to be hospitalised than those in the third phase. Patients infected during the third phase were more frequently obese than others. A large cohort study is recommended to evaluate the transmissibility and to better characterise the clinical severity of emerging variants. • Monitoring the epidemiology of SARS-CoV-2 variants is very important for epidemic control • No major differences were observed between COVID-19 patients infected with variants circulating in each phase of epidemic. • Infections occurring in the second phase were associated with a higher mortality compared with the first and third episodes • More research on clinical severity of COVID-19 in patients infected with variants harbouring the N501Y mutations is needed. [ABSTRACT FROM AUTHOR]

Abstract: Homeless populations are particularly exposed to many vector-borne diseases because of their poor living conditions. We tested sera from 299 homeless people recruited in 2010 and 2011 in Marseilles, France for antibodies to Rickettsia typhi by microimmunofluorescence using a titer of 1:25 as a cut-off titer, and we confirmed the results by Western blot and cross-adsorption studies. Sixty-three persons (22%) had antibodies against R. typhi. The murine typhus seroprevalence rates have significantly increased in homeless populations between the 2000–2003 and 2010–2011 periods. These findings indicate that the homeless are increasingly exposed to flea-borne murine typhus in Marseilles. One might suggest that multiple strikes of sanitation workers resulting in the increase of waste and construction sites combined with the poor living conditions of the homeless expose this population to rodents and their fleas. Further annual studies are necessary to follow rodent-associated diseases among homeless people in Marseille. [Copyright &y& Elsevier]

To compare the clinical and epidemiological aspects associated with different predominant lineages circulating in Marseille from March 2020 to January 2021. In this single-centre retrospective cohort study, characteristics of patients infected with four different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants were documented from medical files. The outcome was the occurrence of clinical failure, defined as hospitalization (for outpatients), transfer to the intensive care unit (inpatients) and death (all). A total of 254 patients were infected with clade 20A (20AS), 85 with Marseille-1 (M1V), 190 with Marseille-4 (M4V) and 211 with N501Y (N501YV) variants. 20AS presented a bell-shaped epidemiological curve and nearly disappeared around May 2020. M1V reached a very weak peak, then disappeared after six weeks. M4V appeared in July presented an atypical wave form for 7 months. N501YV has only recently appeared. Compared with 20AS, patients infected with M1V were less likely to report dyspnoea (adjusted odds ratio (OR) 0.50, p 0.04), rhinitis (aOR 0.57, p 0.04) and to be hospitalized (aOR 0.22, p 0.002). Patients infected with M4V were more likely to report fever than those with 20AS and M1V (aOR 2.49, p < 0.0001 and aOR 2.30, p 0.007, respectively) and to be hospitalized than those with M1V (aOR 4.81, p 0.003). Patients infected with N501YV reported lower rate of rhinitis (aOR 0.50, p 0.001) and anosmia (aOR 0.57, p 0.02), compared with those infected with 20AS. A lower rate of hospitalization was associated with N501YV infection compared with 20AS and M4V (aOR 0.33, p < 0.0001 and aOR 0.27, p < 0.0001, respectively). The four lineages have presentations that differ from one another, epidemiologically and clinically. This supports SARS-CoV-2 genomic surveillance through next-generation sequencing. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Abstract: The European hedgehog (Erinaceus europaeus) is a synanthropic nocturnal insectivore commonly found in the countryside and in the parks and gardens. Because hedgehogs are already involved in the transmission of a number of zoonoses, including salmonellosis and ringworm, we decided to study their possible role in the epidemiology of the spotted fever group of Rickettsia. We collected ticks and fleas from a hedgehog that was captured in the city of Marseilles in France. Using a genus-specific quantitative PCR (qPCR) analysis followed by a species-specific qPCR analysis for positive samples, we observed that 91.7% (11/12) of the Rhipicephalus sanguineus ticks were positive for Rickettsia massiliae and 99.2% (128/129) of the Archaeopsylla erinacei fleas were positive for Rickettsia felis. Hedgehogs carry infected ectoparasites and then likely ensure the dissemination of spotted fever group Rickettsiae, and their epidemiological role requires further investigation. [Copyright &y& Elsevier]

Bartonella rattimassiliensis is a facultative intracellular bacterium isolated from the blood of Rattus norvegkus in Marseille. The present study reports the draft genome of B. rattimassiliensis strain 15908 (CIP 107705T). [ABSTRACT FROM AUTHOR]

Summary: Objectives: The aim of this study was to examine the mechanisms by which weather conditions, the incidence of Leptospira in reservoir populations, and various socio-ecological factors are driving the emergence of leptospirosis in Marseille, France. Methods: Over the last 30 years our laboratory has surveyed all human cases of leptospirosis in Marseille using clinical, epidemiological, serological, and molecular tools. Data for the weather conditions in Marseille were collected from the official meteorological station, and garbage management strikes were monitored through the local press. Rats were trapped in alleys near to where the patients may have acquired leptospirosis. Results: Three new cases of autochthonous leptospirosis are reported. The global tendency for rainfall showed a slight increase over the period under analysis. The index case of leptospirosis occurred after a heavy rainfall with flooding. Over the last 10 years Marseille has undergone 82 days of garbage management strikes. Leptospira DNA was detected in two of 11 rats. Conclusions: The emergence of leptospirosis has become a public health problem in Marseille, and is associated with a combination of heavy rainfall and garbage collection strikes in which garbage is left on the street and thereby contributes to the expansion of the rat population on the surface. [ABSTRACT FROM AUTHOR]

Background: Infection with Bartonella quintana can cause trench fever, endocarditis, bacillary angiomatosis, and peliosis. An outbreak of bacteremia due to B. quintana has been reported among homeless people in Seattle, and the seroprevalence is high among homeless people in both the United States and Europe. Body lice are known to be the vectors of B. quintana. Methods: We studied all the homeless people who presented in 1997 to the emergency departments of the University Hospital, Marseilles, France. Blood was collected for microimmunofluorescence testing for antibodies against B. quintana and for culture of the bacterium. Body lice were collected and analyzed by the polymerase chain reaction and sequencing of a portion of the citrate synthase gene of B. quintana. Results: In 10 of 71 homeless patients (14 percent), blood cultures were positive for B. quintana, and 21 of the patients (30 percent) had high titers of antibody against the organism. A total of 17 patients (24 percent) had evidence of recent infection (bacteremia or seroconversion). Tests of lice from 3 of the 15 patients from whom they were collected were positive for B. quintana. The homeless people with B. quintana bacteremia were more likely to have been exposed to lice (P=0.002), were more likely to have headaches (P=0.03) and severe leg pain (P<0.001), and had lower platelet counts (P=0.006) than the homeless people who were seronegative for B. quintana and did not have bacteremia; 8 of the 10 patients with bacteremia were afebrile. Five patients had chronic bacteremia, as indicated by positive blood cultures over a period of several weeks. Conclusions: In an outbreak of urban trench fever among homeless people in Marseilles, B. quintana infections were associated with body lice in patients with nonspecific symptoms or no symptoms. (N Engl J Med 1999;340:184-9.) [ABSTRACT FROM AUTHOR]

Reports cases of Brill-Zinsser disease in Marseilles, France. Human beings regarded as the principal reservoir of rickettsia prowazekii; Increased prevalence of body-louse infestation among poor and homeless; Immediate intervention to combat the louse epidemic to eradicate the disease; Consequences of Brill-Zinsser disease occurring among the poor and homeless.