Large-Scale Outbreak of Mycoplasma pneumoniae Infection, Marseille, France, 2023-2024.

We report a large-scale outbreak of Mycoplasma pneumoniae respiratory infections encompassing 218 cases (0.8% of 26,449 patients tested) during 2023-2024 in Marseille, France. The bacterium is currently circulating and primarily affects children <15 years of age. High prevalence of co-infections warrants the use of a syndromic diagnostic strategy.

Incidental diagnosis of mpox virus infection in patients undergoing sexually transmitted infection screening-findings from a study in France.

OBJECTIVES: This study aimed to investigate the prevalence of mpox virus (MPXV) infections in the general population consulting for routine sexually transmitted infections (STIs) in our Marseille public hospital. In fact, the recent worldwide MPXV outbreak mainly impacted men who have sex with men and the prevalence of MPXV infections in the general population remains poorly defined. METHODS: All samples addressed routinely to our microbiological laboratory for STIs between July 1 and October 15, 2022 were screened with MPXV-specific quantitative polymerase chain reaction. RESULTS: A total of 2688 samples from 1896 patients suspected of having STIs were tested and eight (0.4%) patients were incidentally diagnosed with MPXV infection, including six men and two women. MPXV was detected in rectal swabs (n = 2), urine (n = 2), vaginal swabs (n = 2), a urethral swab (n = 1), and a skin swab (n = 1). CONCLUSIONS: This study suggests that some MPXV infections are likely to be underdiagnosed because of their non-specific clinical presentation and/or insufficient clinical knowledge of the disease. Our data showed that systematic screening was particularly useful for detecting MPXV in patients without classic lesions or cases of asymptomatic carriage in patients reporting recent high-risk exposure and in patients presenting no obvious risk factor.

Coxiella burnetii Femoro-Popliteal Bypass Infection: A Case Report.

Cardiovascular infections are the most severe and potentially lethal among the persistent focalized Coxiella burnetii infections. While aortic infections on aneurysms or prostheses are well-known, with specific complications (risk of fatal rupture), new non-aortic vascular infections are increasingly being described thanks to the emerging use of 18-fluorodeoxyglucose positron emission tomography (18F-FDG PET-scan). Here, we describe an infection of a femoro-popliteal bypass that would not have been diagnosed without the use of PET-scan. It is well-known that vascular prosthetic material is a site favorable for bacterial persistence, but the description of unusual anatomical sites, outside the heart or aorta, should raise the clinicians' awareness and generalize the indications for PET-scan, with careful inclusion of the upper and lower limbs (not included in PET-scan for cancer), particularly in the presence of vascular prostheses. Future studies will be needed to precisely determine their optimal management.

Protection from successive Omicron variants with SARS-CoV-2 vaccine and monoclonal antibodies in kidney transplant recipients.

Introduction: Kidney transplant recipients (KTRs) are at high risk of severe COVID-19, even when they are fully vaccinated. Additional booster vaccinations or passive immunization with prophylactic monoclonal antibodies are recommended to increase their protection against severe COVID-19. Methods: Here, we describe the neutralization of SARS-CoV-2 Delta, Omicron BA.1, BA.2, BA.4, and BA.5 variants, firstly by 39 serum samples from vaccinated KTRs exhibiting anti-spike antibody concentrations ≥264 binding antibody units (BAU)/mL and, secondly, by tixagevimab/cilgavimab. Results: No neutralization was observed for 18% of the KTRs, while serum from only 46% of patients could neutralize the five variants. Cross-neutralization of the Delta and Omicron variants occurred for 65-87% of sera samples. The anti-spike antibody concentration correlated with neutralization activity for all the variants. The neutralization titers against the Delta variant were higher in vaccinated KTRs who had previously presented with COVID-19, compared to those KTRs who had only been vaccinated. Breakthrough infections occurred in 39% of the KTRs after the study. Tixagevimab/cilgavimab poorly neutralizes Omicron variants, particularly BA.5, and does not neutralize BQ.1, which is currently the most prevalent strain. Discussion: As a result, sera from seropositive vaccinated KTRs had poor neutralization of the successive Omicron variants. Several Omicron variants are able to escape tixagevimab/cilgavimab.

Observational Cohort Study of Evolving Epidemiologic, Clinical, and Virologic Features of Monkeypox in Southern France.

We enrolled 136 patients with laboratory-confirmed monkeypox during June 4-August 31, 2022, at the University Hospital Institute Méditerranée Infection in Marseille, France. The median patient age was 36 years (interquartile range 31-42 years). Of 136 patients, 125 (92%) were men who have sex with men, 15 (11%) reported previous smallpox vaccinations, and 21 (15.5%) were HIV-positive. The most frequent lesion locations were the genitals (68 patients, 53%), perianal region (65 patients, 49%), and oral/perioral area (22 patients, 17%). Lesion locations largely corresponded with the route of contamination. Most (68%) patients had isolated anal, genital, or oral lesions when they were first seen, including 56 (61%) who had >1 positive site without a visible lesion. Concurrent sexually transmitted infections were diagnosed in 19 (15%) patients, and 7 patients (5%) were asymptomatic. We recommend vaccination campaigns, intensified testing for sexually transmitted infections, and increased contact tracing to control the ongoing monkeypox outbreak.

Evidence of antibodies against SARS-CoV-2 in wild mustelids from Brittany (France).

In the French region of Brittany, mainly in the department of the Côtes d'Armor, during the first half of 2021, seropositivity for SARS-CoV-2 was detected in five wild mustelids out of 33 animals tested (15.6%). Anti-SARS-CoV-2 IgG was detected against at least four out of five recombinant viral proteins (S1 receptor binding domain, nucleocapsid, S1 subunit, S2 subunit and spike) in three pine martens (Martes martes) and in two badgers (Meles meles) using the automated western blot technique. An ELISA test also identified seropositive cases, although these did not align with western blot results. Although the 171 qPCRs carried out on samples from the 33 mustelids were all negative, these preliminary results from this observational study nevertheless bear witness to infections of unknown origin. The epidemiological surveillance of Covid-19 in wildlife must continue, in particular with effective serology tools.

High Individual Heterogeneity of Neutralizing Activities against the Original Strain and Nine Different Variants of SARS-CoV-2.

BACKGROUND: Since the beginning of the COVID-19 pandemic, several SARS-CoV-2 variants have sequentially emerged. In France, most cases were due to spike D641G-harbouring viruses that descended initially from the Wuhan strain, then by the variant of B.1.160 lineage we called Marseille-4 since the summer of 2020, which was followed by the Alpha and Beta variants in early 2021, then the Delta variant currently. METHODS: We determined the neutralising antibody (nAb) titres in sera from convalescent individuals previously infected by these four major local variants and from vaccine recipients to the original Wuhan strain and nine variants, including two recent circulating Delta isolates. RESULTS: The results show high inter-individual heterogeneity in nAbs, especially according to the variant tested. The major variations among nAbs are based on the genotype responsible for the infection. Patients previously infected with the beta and B.1.160 variants had the lowest nAb titres. We show that this heterogeneity is well explained by spike protein mutants modelling using in silico approaches. The highest titres were observed in individuals vaccinated with the Pfizer/BioNTech COVID-19 vaccine, even against the delta variant. CONCLUSIONS: Immunity acquired naturally after infection is highly dependent on the infecting variant, and, unexpectedly, mRNA-based vaccine efficacy was shown to be often better than natural immunity in eliciting neutralising antibodies.

Early combination therapy with hydroxychloroquine and azithromycin reduces mortality in 10,429 COVID-19 outpatients.

We evaluated the age-specific mortality of unselected adult outpatients infected with SARS-CoV-2 treated early in a dedicated COVID-19 day hospital and we assessed whether the use of hydroxychloroquine (HCQ) + azithromycin (AZ) was associated with improved survival in this cohort. A retrospective monocentric cohort study was conducted in the day hospital of our center from March to December 2020 in adults with PCR-proven infection who were treated as outpatients with a standardized protocol. The primary endpoint was 6-week mortality, and secondary endpoints were transfer to the intensive care unit and hospitalization rate. Among 10,429 patients (median age, 45 [IQR 32-57] years; 5597 [53.7%] women), 16 died (0.15%). The infection fatality rate was 0.06% among the 8315 patients treated with HCQ+AZ. No deaths occurred among the 8414 patients younger than 60 years. Older age and male sex were associated with a higher risk of death, ICU transfer, and hospitalization. Treatment with HCQ+AZ (0.17 [0.06-0.48]) was associated with a lower risk of death, independently of age, sex and epidemic period. Meta-analysis evidenced consistency with 4 previous outpatient studies (32,124 patients-Odds ratio 0.31 [0.20-0.47], I2 = 0%). Early ambulatory treatment of COVID-19 with HCQ+AZ as a standard of care is associated with very low mortality, and HCQ+AZ improve COVID-19 survival compared to other regimens.

Contagion Management at the Méditerranée Infection University Hospital Institute.

The Méditerranée Infection University Hospital Institute (IHU) is located in a recent building, which includes experts on a wide range of infectious disease. The IHU strategy is to develop innovative tools, including epidemiological monitoring, point-of-care laboratories, and the ability to mass screen the population. In this study, we review the strategy and guidelines proposed by the IHU and its application to the COVID-19 pandemic and summarise the various challenges it raises. Early diagnosis enables contagious patients to be isolated and treatment to be initiated at an early stage to reduce the microbial load and contagiousness. In the context of the COVID-19 pandemic, we had to deal with a shortage of personal protective equipment and reagents and a massive influx of patients. Between 27 January 2020 and 5 January 2021, 434,925 nasopharyngeal samples were tested for the presence of SARS-CoV-2. Of them, 12,055 patients with COVID-19 were followed up in our out-patient clinic, and 1888 patients were hospitalised in the Institute. By constantly adapting our strategy to the ongoing situation, the IHU has succeeded in expanding and upgrading its equipment and improving circuits and flows to better manage infected patients.

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

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.

Sunbathing, a possible risk factor of murine typhus infection in Greece.

BACKGROUND: There are few studies about the presence of murine typhus in Greece. Our objective was to conduct a large scale retrospective investigation to determine the clinical and epidemiological features of patients diagnosed with murine typhus in Greece. METHODOLOGY/PRINCIPAL FINDINGS: From 2012 to 2019 serum samples from hospitalized patients and outpatients throughout Greece suspected for murine typhus infection were tested by immunofluorescence assay for Rickettsia typhi. Immunofluorescence positive samples obtained since 2016 were also tested by qPCR targeting R. typhi. Clinical and epidemiological data were retrospectively collected for the patients with confirmed murine typhus. Overall, we tested 5,365 different patients and, in total, 174 patients from all geographic regions of Greece were diagnosed with murine typhus. The most frequently reported sign or symptom was fever (89%), followed by headache (84%) and rash (81%). The classical triad of fever, headache, and rash was present in 72% of patients during their illness. Severe infections with complications including acute renal failure or septic shock were not recorded. The majority of cases (81%) occurred during May-October and peaked in June and September. Most of patients (81%) infected in Athens, recalled that their only activity the last weeks before symptoms onset was swimming on the beach and 59% of them also reported an insect bite while sunbathing. CONCLUSIONS/SIGNIFICANCE: Our results may reflect the reemergence of murine typhus in Greece and we highlight the importance of awareness of this difficult-to-recognize undifferentiated febrile illness.

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

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 JessTM 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.

Sero-epidemiology investigation of Coxiella burnetii in domestic ruminants throughout most Greek regions.

Q fever is not considered as a public health problem in Greece where most regions are considered as Coxiella burnetii free possibly because of the low interest for this agent. Our objective was to conduct a large-scale study to investigate the sero-epidemiology of C. burnetii in domestic ruminants throughout the most of Greek regions. We tested serum samples obtained from goats, sheep and bovines from different regions of Greece. All sera were tested for C. burnetii IgG antibodies by a commercial ELISA according to the manufacturer's recommendations. We tested 1,173 goats and sheep obtained from 177 different herds and totally 194 (17%) animals from 78 (44%) herds were positive for C. burnetii. Positive animals were present in seven (88%) different regions and seropositivity varied widely among these regions. The highest percentage was observed in Peloponnese (44%), where all the tested herds presented animals with C. burnetii antibodies. Ιn all Aegean Islands except the island of Limnos we detected goats and sheep positive for C. burnetii with seroposivity varying between 2% in Kos to 37% in Rhodes. Finally, in 22 (85%) Greek prefectures we found C. burnetii IgG-positive animals whereas in 14 (54%) prefectures more than 50% of tested herds had seropositive animals. We also tested 28 cows from five different herds in Macedonia and Aegean Islands and six (21%) of them, obtained from two (40%) herds were positive. Considering the importance of C. burnetii for public health, our data reflect the lack of awareness by veterinarians, physicians and competent authorities as we provide evidence of C. burnetii seropositivity in productive animals throughout the most of Greek territories. Due to the increased risk of inhalation of the bacterium by people who entered the affected farms we raise the question of Q fever emergence in Greece.

Respiratory Syncytial Virus Infection: Its Propensity for Bacterial Coinfection and Related Mortality in Elderly Adults.

Respiratory syncytial virus (RSV) is an increasingly recognized cause of acute respiratory infection (ARI) in adults. We compared the crude in-hospital mortality of patients with RSV infection alone with that of patients with RSV-bacterial coinfection. Overall, 12 144 hospitalized patients with ARI were screened for RSV detection by polymerase chain reaction between February 2014 and April 2019. In total, 701 (5.8%) had a positive RSV result, including 85 (12.1%) with bacterial coinfection. RSV-bacterial coinfection was associated with an increase in crude in-hospital mortality in patients >65 years old (hazard ratio, 2.94; 95% CI, 1.30-6.60; P = .010). Optimized prevention and management strategies to reduce this burden are needed.

Evaluating ELISA, Immunofluorescence, and Lateral Flow Assay for SARS-CoV-2 Serologic Assays.

BACKGROUND: The SARS-CoV-2 outbreak has emerged at the end of 2019. Aside from the detection of viral genome with specific RT-PCR, there is a growing need for reliable determination of the serological status. We aimed at evaluating five SARS-CoV-2 serology assays. METHODS: An in-house immunofluorescence assay (IFA), two ELISA kits (EUROIMMUN® ELISA SARS-CoV-2 IgG and NovaLisa® SARS-CoV-2 IgG and IgM) and two lateral flow assays (T-Tek® SARS-CoV-2 IgG/IgM Antibody Test Kit and Sure Bio-tech® SARS-CoV-2 IgM/IgG Antibody Rapid Test) were compared on 40 serums from RT-PCR-confirmed SARS-CoV-2 infected patients and 10 SARS-CoV-2 RT-PCR negative subjects as controls. RESULTS: Control subjects tested negative for SARS-CoV-2 antibodies with all five systems. Estimated sensitivities varied from 35.5 to 71.0% for IgG detection and from 19.4 to 64.5% for IgM detection. For IgG, in-house IFA, EuroImmun, T-Tek and NovaLisa displayed 50-72.5% agreement with other systems except IFA vs EuroImmun and T-Tek vs NovaLisa. Intermethod agreement for IgM determination was between 30 and 72.5%. DISCUSSION: The overall intermethod agreement was moderate. This inconsistency could be explained by the diversity of assay methods, antigens used and immunoglobulin isotype tested. Estimated sensitivities were low, highlighting the limited value of antibody detection in CoVID-19. CONCLUSION: Comparison of five systems for SARS-CoV-2 IgG and IgM antibodies showed limited sensitivity and overall concordance. The place and indications of serological status assessment with currently available tools in the CoVID-19 pandemic need further evaluations.

Tularemia: A Case Series of Patients Diagnosed at the National Reference Center for Rickettsioses From 2008 to 2017.

BACKGROUND: We describe the epidemiological, clinical, and prognostic aspects of 177 tularemia cases diagnosed at the National Reference Center for rickettsioses, coxiellosis, and bartonelloses between 2008 and 2017. METHODS: All patients with a microbiological diagnosis of tularemia made in the laboratory were included. Clinical and epidemiological data were collected retrospectively from clinicians in charge of patients using a standardized questionnaire. Diagnostic methods used were indirect immunofluorescence serology, real-time polymerase chain reaction (PCR), and universal PCR targeting the 16S ribosomal ribonucleic acid gene. RESULTS: The series included 54 females and 123 males (sex ratio, 2.28; mean age, 47.38 years). Eighty-nine (50.2%) were confirmed as having tularemia on the basis of a positive Francisella tularensis PCR or seroconversion, and 88 (49.8%) were considered as probable due to a single positive serum. The regions of France that were most affected included Pays de la Loire (22% of cases), Nouvelle Aquitaine (18.6% of cases), and Grand Est (12.4% of cases). Patients became infected mainly through contact with rodents or game (38 cases, 21.4%), through tick-bites (23 cases, 12.9%), or during outdoor leisure activities (37 cases, 20.9%). Glandular and ulceroglandular forms were the most frequent (109 cases, 61.5%). Two aortitis, an infectious endocarditis, a myocarditis, an osteoarticular infection, and a splenic hematoma were also diagnosed. Tularemia was discovered incidentally in 54.8% of cases. Seventy-eight patients were hospitalized, and no deaths were reported. CONCLUSIONS: Our data suggest that in an endemic area and/or in certain epidemiological contexts, tularemia should be sought to allow an optimized antibiotic therapy and a faster recovery.

Capybara and Brush Cutter Involvement in Q Fever Outbreak in Remote Area of Amazon Rain Forest, French Guiana, 2014.

We investigated a Q fever outbreak that occurred in an isolated area of the Amazon Rain Forest in French Guiana in 2014. Capybara fecal samples were positive for Coxiella burnetii DNA. Being near brush cutters in use was associated with disease development. Capybaras are a putative reservoir for C. burnetii.

Metagenomic Analysis of Microdissected Valvular Tissue for Etiological Diagnosis of Blood Culture-Negative Endocarditis.

BACKGROUND: Etiological diagnosis is a key to therapeutic adaptation and improved prognosis, particularly for infections such as endocarditis. In blood culture-negative endocarditis (BCNE), 22% of cases remain undiagnosed despite an updated comprehensive syndromic approach. This prompted us to develop a new diagnostic approach. METHODS: Eleven valves from 10 BCNE patients were analyzed using a method that combines human RNA bait-depletion with phi29 DNA polymerase-based multiple displacement amplification and shotgun DNA sequencing. An additional case in which a microbe was serendipitously visualized by immunofluorescence was analyzed using the same method, but after laser capture microdissection. RESULTS: Background DNA prevented any diagnosis in cases analyzed without microdissection because the majority of sequences were contaminants. Moraxella sequences were dramatically enriched in the stained microdissected region of the additional case. A consensus genome sequence of 2.4 Mbp covering more than 94% of the Moraxella osloensis KSH reference genome was reconstructed with 234X average coverage. Several antibiotic-resistance genes were observed. Etiological diagnosis was confirmed using Western blot and specific polymerase chain reaction with sequencing on a different valve sample. CONCLUSIONS: Microdissection could be a key to the metagenomic diagnosis of infectious diseases when a microbe is visualized but remains unidentified despite an updated optimal approach. Moraxella osloensis should be tested in blood culture-negative endocarditis.

Western Immunoblotting for the Diagnosis of Enterococcus faecalis and Streptococcus gallolyticus Infective Endocarditis.

Blood culture-negative endocarditis (BCNE) remains a diagnostic challenge. In our center, despite a systematic and exhaustive microbiological diagnostics strategy, 22% of patients with BCNE remain without an identified etiology. In an effort to determine the relevance of using Western blot (WB) for the etiological diagnosis of BCNE in patients with early antibiotic use, we developed specific assays for the major infective endocarditis (IE) causative agents, namely, Staphylococcus aureus, Enterococcus faecalis, Streptococcus anginosus, and Streptococcus gallolyticus. Our technique was effective to identify the antigenic profiles of the four tested agents, but cross-reactions with S. aureus and S. anginosus antigens were frequent. A scoring method was developed for the diagnosis of E. faecalis and S. gallolyticus IE using the presence of reactivity to at least two antigenic bands for each bacterium and the positivity to at least one of the Ef300, Ef72, or Ef36 proteic bands for E. faecalis, and positivity for the two Sg75 and Sg97 proteic bands for S. gallolyticus. We tested these diagnostic criteria in a prospective cohort of 363 patients with suspected IE. Immunoblotting for the diagnosis of E. faecalis IE showed a sensitivity of 100% and a specificity of 99%. The positive and negative predictive values were 73 and 100%, respectively. Regarding S. gallolyticus infection, immunoblot had a sensitivity of 100% and a specificity of 95%. However, the positive predictive value was 22%, whereas the predictive negative value was 100%. Using WB, we identified a potential etiological agent in 4 of 14 BCNE cases with no identified pathogen. In conclusion, WB constitutes a promising and helpful method to diagnose E. faecalis or S. gallolyticus IE in patients with early antibiotic uptake and negative blood cultures.