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Høiby N. Louis Pasteur and the birth of microbiology in Denmark. APMIS 2022. Louis Pasteur's work initiated the birth of microbiology in Denmark. Carl Julius Salomonsen was the pioneer who inspired and taught Christian Gram, Thorvald Madsen and Bernhard Bang bacteriological techniques in his annual bacteriological course which he started in 1883 at the University of Copenhagen. These pioneers developed Danish human and veterinary microbiology and became world famous. Emil Chr. Hansen developed Danish technical/industrial microbiology in the Carlsberg Laboratory and purified yeast and designed equipment for the propagation of pure yeast which was used worldwide in beer brewing. He also became world famous. The fascinating birth and development of Danish microbiology is summarized in this article, which is dedicated to the 200th birthday of Louis Pasteur, December 27, and 100th birthday of the Danish Pasteur Society, October 25, 2022., (© 2022 Scandinavian Societies for Pathology, Medical Microbiology and Immunology.)

Background: Migrants account for 35% of HIV diagnoses in the European Union (ECDC/WHO 2014). Little is known about the impact of such a lifelong infection diagnosis on lives that are already disrupted by migration. In this paper, we assess the impact of HIV diagnosis on activity, union, well-being among African migrants living in France, the second group most affected by HIV after MSM. We compare it with the impact of the diagnosis of Hepatitis B, another lifelong infection affecting African migrants. Methods: We use the ANRS PARCOURS survey, a retrospective life-event survey led in 2012–2013 in 74 health structures in Paris greater area which collected 926 life histories of Sub-Saharan migrants living with HIV and 779 with Hepatitis B. We modelled the probability year by year since 18 years of age until data collection to lose one’s activity, to experience a conjugal break up and degradation of well-being and we estimated the impact of migration and of HIV and Hepatitis B diagnoses on these probabilities, after adjustment on other factors, thanks to discrete-time logistic regressions. Results: Migration entailed loss of activity and conjugal break up, though HIV diagnosis after migration did not statistically impact on these outcomes. Yet HIV diagnosis had a massive negative impact on well-being (aOR = 11.31 [4.64–27.56] for men and 5.75 [2.79–11.86] for women). This negative impact on well-being tended to diminish for persons diagnosed after 2004. The negative impact of HIV diagnosis on African migrants’ well-being seems to be attenuated in the last decade, which hints at a normalization of the subjective experience of HIV diagnosis. [ABSTRACT FROM AUTHOR]

Background: On admission to hospital, patients with community-acquired pneumonia (CAP), undergo extensive diagnostic testing. Two high-throughput laboratory-based PCR panels which return a result in 5.5 hours (h) have been developed to test for pathogens commonly associated with upper (Respiratory 1 Panel) and lower (Respiratory 3 Panel) respiratory tract infections (GeneFirst, Oxford). These could replace multiple diagnostic tests currently used. Methods: An online survey, completed by senior clinicians in the UK, France and Spain, was used to collect data on the diagnostic testing of immunocompetent and immunocompromised adults admitted to hospital with CAP, including the cost of diagnostics. Data were used to inform a cost-comparison model. For each country, the average cost of diagnostic testing per patient was calculated separately for immunocompetent and immunocompromised patients. The model compared three testing strategies with standard of care (SoC). In the Panel 1 strategy, the Respiratory 1 Panel was used for patients that would otherwise have tests which could be replaced by Respiratory 1 Panel, equivalent strategies for Respiratory 3 Panel and for both panels combined were assessed. Results: In total, 48 surveys were completed (UK = 17; France = 15; Spain = 16). Compared with SoC, the Panel 1 + 3 strategy was most favourable, resulting in cost savings for immunocompetent and immunocompromised patients respectively, of €22.09 (£18.50) and €26.12 (£21.88) in the UK, €99.60 and €108.77 in France and €27.07 and €51.87 in Spain. Conclusion: In all three countries, the use of these respiratory panels could reduce the average cost of diagnostics used for patients admitted to hospital with CAP. [ABSTRACT FROM AUTHOR]

Background: Rapid antiretroviral therapy (ART) initiation has been proven beneficial for patients and the community. We aimed to analyze recent changes in timing of ART initiation in France and consequences of early start. Methods: We selected from a prospective nationwide cohort, on 12/31/2017, patients with HIV-1 infection diagnosed between 01/01/2010 and 12/31/2015. We described time from (1) diagnosis to first specialized medical encounter, (2) from this encounter to ART initiation, (3) from diagnosis to first undetectable HIV viral load (VL). We analyzed the determinants of measured temporal trends. A multivariate logistic regression was performed to assess characteristics related with 1-year retention in care. Results: In the 7 245 included patients, median time (1) from HIV diagnosis to first medical encounter was 13 (IQR: 6–32) days, (2) to ART initiation was 27 (IQR: 9–91) days, decreasing from 42 (IQR: 13–272) days in 2010 to 18 (IQR: 7–42) in 2015 (p<0.0001), (3) to first undetectable VL was 257 (IQR: 151–496) days, decreasing from 378 (IQR: 201–810) days in 2010 to 169 (IQR: 97–281) in 2015. After one year, proportion of patients alive and still in care was significantly lower in those in the lower quartile of time from first encounter to ART (<9 days) than those in the higher quartile (>90 days), 79.9% and 85.2%, respectively (p<0.0001). Conclusions: In a country with unrestricted rapid access to ART, keeping recently diagnosed HIV infected patients in care remains challenging. Starting ART rapidly did not seem to be profitable for all and every patient. [ABSTRACT FROM AUTHOR]

Study objective: To investigate the performance of a rapid RT-PCR assay to detect influenza A/B at emergency department admission. Methods: This single-center prospective study recruited adult patients attending the emergency department for influenza-like illness. Triage nurses performed nasopharyngeal swab samples and ran rapid RT-PCR assays using a dedicated device (cobas Liat, Roche Diagnostics, Meylan, France) located at triage. The same swab sample was also analyzed in the department of virology using conventional RT-PCR techniques. Patients were included 24 hours-a-day, 7 days-a-week. The primary outcome was the diagnostic accuracy of the rapid RT-PCR assay performed at triage. Results: A total of 187 patients were included over 11 days in January 2018. Median age was 70 years (interquartile range 44 to 84) and 95 (51%) were male. Nine (5%) assays had to be repeated due to failure of the first assay. The sensitivity of the rapid RT-PCR assay performed at triage was 0.98 (95% confidence interval (CI): 0.91–1.00) and the specificity was 0.99 (95% CI: 0.94–1.00). A total of 92 (49%) assays were performed at night-time or during the weekend. The median time from patient entry to rapid RT-PCR assay results was 46 [interquartile range 36–55] minutes. Conclusion: Rapid RT-PCR assay performed by nurses at triage to detect influenza A/B is feasible and highly accurate. [ABSTRACT FROM AUTHOR]

Annual incidence rates of varicella infection in the general population in France have been rather stable since 1991 when clinical surveillance started. Rates however show a statistically significant increase over time in children aged 0–3 years, and a decline in older individuals. A significant increase in day-care enrolment and structures’ capacity in France was also observed in the last decade. In this work we investigate the potential interplay between an increase of contacts of young children possibly caused by earlier socialization in the community and varicella transmission dynamics. To this aim, we develop an age-structured mathematical model, informed with historical demographic data and contact matrix estimates in the country, accounting for longitudinal linear increase of early childhood contacts. While the reported overall varicella incidence is well reproduced independently of mixing variations, age-specific empirical trends are better captured by accounting for an increase in contacts among pre-school children in the last decades. We found that the varicella data are consistent with a 30% increase in the number of contacts at day-care facilities, which would imply a 50% growth in the contribution of 0-3y old children to overall yearly infections in 1991–2015. Our findings suggest that an earlier exposure to pathogens due to changes in day-care contact patterns, represents a plausible explanation for the epidemiological patterns observed in France. Obtained results suggest that considering temporal changes in social factors in addition to demographic ones is critical to correctly interpret varicella transmission dynamics. [ABSTRACT FROM AUTHOR]

Objective: HIV testing is an important tool in the management of the HIV epidemic among key populations. We aimed to explore the dynamic of first-time HIV testing in France for sub-Saharan migrants after their arrival. Methods: ANRS-Parcours is a retrospective life-event survey conducted from 2012 to 2013 in healthcare facilities in the Paris region, among 926 sub-Saharan HIV-infected migrants and 763 non-infected migrants. After describing the time to first HIV test in France and associated circumstances, we performed a discrete-time logistic regression to analyze the influence of socioeconomic position, contact with the healthcare system and sexual behaviors, on first-time HIV testing in France in migrants who arrived after 2000. Results: Median first-time HIV testing occurred during the second year spent in France for non-infected men and women in both groups, and during the first year for men of the HIV group. The probability of testing increased with hospitalization and pregnancy for women of both groups. For non-infected men unemployment and absence of a residence permit were associated with an increased probability of HIV testing [respectively, OR = 2.2 (1.2–4.1) and OR = 2.0 (1.1–3.5)]. Unemployment was also associated with an increased probability of first-time HIV-testing for women of the HIV group [OR: 1.7 (1.0–2.7)]. Occasional and multiple sexual relationships were associated with an increased probability of first-time testing only for HIV-infected women [OR: 2.2 (1.2–4.0) and OR = 2.4 (1.3–4.6)]. Conclusion: Access to first HIV testing in France is promoted by contact with the health care system and is facilitated for unemployed and undocumented migrants after arrival.However, testing should be offered more systematically and repeated in order to reduce time between HIV infection and diagnosis, especially for deprived people which are particularly vulnerable regarding HIV infection. [ABSTRACT FROM AUTHOR]

Objective: Side effects of antiretroviral therapy (ART) can have a negative impact on health-related quality of life threatening long-term retention in HIV care and adherence to ART. The aim of the French community-based survey EVE was to document personal experiences with side effects, the related physician-patient communication, and solutions found to deal with them. Design: Cross-sectional study of women between September 2013 to September 2014 Methods: An anonymous online questionnaire included the HIV Symptom Distress Module, which explores 20 symptoms. Results: In all, 301 women on ART participated in the study (median age: 49 years; median duration of ART: 14 years). They reported having experienced a median of 12 symptoms (Q1-Q3: 9–15) during the previous 12 months. Overall, 56% of them reported having found at least a partial solution to dealing with their symptoms. Women reporting financial difficulties were twice less likely to have found solutions to coping with their side effects (AOR: 0.5; 95% CI: 0.3–0.8). Feeling supported by the health-care provider (AOR: 2.1; 95% CI: 1.1–3.9) and being in contact with HIV/AIDS organisations (AOR: 1.9; 95% CI: 1.2–3.2) were positively associated with coping. Seventeen percent reported having modified their ART regimen to improve tolerance, with only 2 in 3 informing their physician afterwards. Reporting financial difficulties and living with more bothersome symptoms increased the risk of ART regimen modification without health-care provider consultation. Conclusion: The EVE study has called attention to the large number of side effects experienced by WLWHIV, only half of whom have found self-care strategies to manage their symptoms. Modification of ART regimen by the women themselves was not uncommon. [ABSTRACT FROM AUTHOR]

Human leptospirosis is a zoonotic and potentially fatal disease that has increasingly been reported in both developing and developed countries, including France. However, our understanding of the basic aspects of the epidemiology of this disease, including the source of Leptospira serogroup Australis infections in humans and domestic animals, remains incomplete. We investigated the genetic diversity of Leptospira in 28 species of wildlife other than rats using variable number tandem repeat (VNTR) and multispacer sequence typing (MST). The DNA of pathogenic Leptospira was detected in the kidney tissues of 201 individuals out of 3,738 tested individuals. A wide diversity, including 50 VNTR profiles and 8 MST profiles, was observed. Hedgehogs and mustelid species had the highest risk of being infected (logistic regression, OR = 66.8, CI95% = 30.9–144 and OR = 16.7, CI95% = 8.7–31.8, respectively). Almost all genetic profiles obtained from the hedgehogs were related to Leptospira interrogans Australis, suggesting the latter as a host-adapted bacterium, whereas mustelid species were infected by various genotypes, suggesting their interaction with Leptospira was different. By providing an inventory of the circulating strains of Leptospira and by pointing to hedgehogs as a potential reservoir of L. interrogans Australis, our study advances current knowledge on Leptospira animal carriers, and this information could serve to enhance epidemiological investigations in the future. [ABSTRACT FROM AUTHOR]

Species cooccurrence patterns give significant insights into the processes shaping communities. While biotic interactions have been widely studied using cooccurrence analyses in animals and larger plants, studies about cooccurrences among micro-organisms are still relatively rare. We examined stream diatom cooccurrences in France through a national database of samples. In order to test the relative influence of environmental, biotic and spatial constraints on species’ incidence distribution, cooccurrence and nestedness patterns of real communities were compared with the patterns generated from a set of standard and environmentally constrained null models. Real communities showed a higher level of segregation than the most conservative standard null models, but a general aggregation of cooccurrences when compared to environmentally constrained null models. We did not find any evidence of limiting similarity between cooccurring species. Aggregations of species cooccurrences were associated with the high levels of nestedness. Altogether, these results suggested that biotic interactions were not structuring cooccurrences of diatom species at our study scale. Instead, the patterns were more likely to be related with colonization patterns, mass effect, and local temporal dynamics of diatom biofilms. We further highlight that the association of standard and environmentally constrained null models may give realistic insight into the cooccurrence patterns of microbial communities. [ABSTRACT FROM AUTHOR]

Context: HIV self-tests are currently being introduced in France with the aim of promoting screening both for the general population and for high-risk populations. Objective: The current study aimed to identify and compare the information and support needs of the different target population groups. Methods: The Delphi process was used to synthesize expert opinions for each population group. Experts were chosen for their experience and expertise in the area of HIV and HIV screening for each population. Each group developed recommendations for a specific population: six high HIV prevalence populations (men who have sex with men; transgender people; substance users; migrants from sub-Saharan Africa; French West Indies; French Guiana) and two low prevalence populations (the general population; people under 25). Each group included expertise from four areas: research, screening and care, policy-making, and community groups. Results: A final total of 263 recommendations were grouped into eight main themes: Communicating at both national and community levels about self-test arrival (24% of all recommendations); Providing information adapted to the different community groups’ needs (23%); Providing counselling on self-test use and access to care (15%); Making self-tests available to all in terms of accessibility and cost (13%); Preparing community healthcare and screening systems for the arrival of the self-test (11%); Approving only high quality self-tests (6%); Defending self-test users’ legal rights (5%); Evaluating self-test use (3%). Although a large number of recommendations were common to several groups of experts, the study highlighted a certain number of recommendations specific to each different population group, particularly with regard to information content and access both to information and to the self-tests themselves. Conclusion: Results from the current study should make a significant contribution to policy decisions concerning catering for the specific access, information and support needs of different potential HIV self-test user groups in France. [ABSTRACT FROM AUTHOR]