Genetic diversity of Leptospira strains circulating in humans and dogs in France in 2019-2021

Leptospirosis is a bacterial zoonotic disease. Humans and dogs are susceptible hosts, with similar clinical manifestations ranging from a febrile phase to multiple organ dysfunction. The incidence of leptospirosis in mainland France is relatively high, at about 1 case per 100,000 inhabitants, but our knowledge of the strains circulating in humans and dogs remains limited. We studied the polymorphism of the lfb1 gene sequences in an exhaustive database, to facilitate the identification of Leptospira strains. We identified 46 species-groups (SG) encompassing the eight pathogenic species of Leptospira. We sequenced the lfb1 gene amplification products from 170 biological samples collected from 2019 to 2021: 110 from humans and 60 from dogs. Epidemiological data, including vaccination status in dogs, were also collected. Three Leptospira species displaying considerable diversity were identified: L. interrogans, with eight lfb1 species-groups (including five new lfb1 species-groups) in humans and dogs; L. kirschneri, with two lfb1 species-groups in humans and dogs; and L. borgpetersenii, with one lfb1 species-group in humans only. The lfb1 species-group L. interrogans SG1, corresponding to serovar Icterohaemorrhagiae or Copenhageni, was frequently retrieved from both humans and dogs (n=67/110; 60.9% and n=59/60; 98.3% respectively). A high proportion of the affected dogs developed the disease despite vaccination (n=30/60; 50%). Genotyping with the polymorphic lfb1 gene is both robust and simple. This approach provided the first global picture of the Leptospira strains responsible for acute infections in mainland France, based on biological samples but without the need for culture. Identification of the Leptospira strains circulating and their changes over time will facilitate more precise epidemiological monitoring of susceptible and reservoir species. It should also facilitate the monitoring of environmental contamination, making it possible to implement preventive measures and to reduce the burden of this disease.

Genetic Diversity and Population Structure of Mycobacterium bovis at the Human-Animal-Ecosystem Interface in France: “A One Health Approach”

Mycobacterium bovis infects cattle and wildlife, and also causes a small proportion of tuberculosis cases in humans. In most European countries, M. bovis infections in cattle have been drastically reduced, but not eradicated. Here, to determine the M. bovis circulation within and between the human, cattle, and wildlife compartments, we characterized by spoligotyping and mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing the genetic diversity of M. bovis isolates collected from humans, cattle, and wildlife in France from 2000 to 2010. We also assessed their genetic structure within and among the different host groups, and across time and space. The M. bovis genetic structure and its spatiotemporal variations showed different dynamics in the human and animal compartments. Most genotypes detected in human isolates were absent in cattle and wildlife isolates, possibly because in patients, M. bovis infection was contracted abroad or was the reactivation of an old lesion. Therefore, they did not match the genetic pool present in France during the study period. However, some human-cattle exchanges occurred because some genotypes were common to both compartments. This study provides new elements for understanding M. bovis epidemiology in France, and calls for increased efforts to control this pathogen worldwide.

Epidemiology of infection by pulmonary non-tuberculous mycobacteria in French Guiana 2008–2018

Introduction

Unlike diseases caused by Mycobacterium tuberculosis, M. leprae and M. ulcerans, the epidemiology of pulmonary non-tuberculous mycobacteria (PNTM) has not received due attention in French Guiana. The main objective of the current study was to define the incidence of these PNTM infections: NTM pulmonary diseases (NTM-PD) and casual PNTM isolation (responsible of latent infection or simple colonization). The secondary objectives were to determine species diversity and geographic distribution of these atypical mycobacteria.

Methods

A retrospective observational study (2008–2018) of French Guiana patients with at least one PNTM positive respiratory sample in culture was conducted. Patients were then classified into two groups: casual PNTM isolation or pulmonary disease (NTM-PD), according to clinical, radiological and microbiological criteria defined by the American Thoracic Society / Infectious Disease Society of America (ATS / IDSA) in 2007.

Results

178 patients were included, out of which 147 had casual PNTM isolation and 31 had NTM-PD. Estimated annual incidence rate of respiratory isolates was 6.17 / 100,000 inhabitants per year while that of NTM-PD was 1.07 / 100,000 inhabitants per year. Among the 178 patients, M. avium complex (MAC) was the most frequently isolated pathogen (38%), followed by M. fortuitum then M. abscessus (19% and 6% of cases respectively), the latter two mycobacteria being mainly found in the coastal center region. Concerning NTM-PD, two species were mainly involved: MAC (81%) and M. abscessus (16%).

Discussion/Conclusion

This is the first study on the epidemiology of PNTM infections in French Guiana. PNTM’s incidence looks similar to other contries and metropolitan France and NTM-PD is mostly due to MAC and M.abscessus. Although French Guiana is the French territory with the highest tuberculosis incidence, NTM should not be overlooked.

Analyzing and Modeling the Spread of SARS-CoV-2 Omicron Lineages BA.1 and BA.2, France, September 2021-February 2022

We analyzed 324,734 SARS-CoV-2 variant screening tests from France enriched with 16,973 whole-genome sequences sampled during September 1, 2021–February 28, 2022. Results showed the estimated growth advantage of the Omicron variant over the Delta variant to be 105% (95% CI 96%–114%) and that of the BA.2 lineage over the BA.1 lineage to be 49% (95% CI 44%–52%). Quantitative PCR cycle threshold values were consistent with an increased ability of Omicron to generate breakthrough infections. Epidemiologic modeling shows that, in spite of its decreased virulence, the Omicron variant can generate important critical COVID-19 activity in hospitals in France. The magnitude of the BA.2 wave in hospitals depends on the level of relaxing of control measures but remains lower than that of BA.1 in median scenarios.

Association between the COVID-19 pandemic and pertussis derived from multiple nationwide data sources, France, 2013 to 2020

BackgroundInterventions to mitigate the COVID-19 pandemic may impact other respiratory diseases.AimsWe aimed to study the course of pertussis in France over an 8-year period including the beginning of the COVID-19 pandemic and its association with COVID-19 mitigation strategies, using multiple nationwide data sources and regression models.MethodsWe analysed the number of French pertussis cases between 2013 and 2020, using PCR test results from nationwide outpatient laboratories (Source 1) and a network of the paediatric wards from 41 hospitals (Source 2). We also used reports of a national primary care paediatric network (Source 3). We conducted a quasi-experimental interrupted time series analysis, relying on negative binomial regression models. The models accounted for seasonality, long-term cycles and secular trend, and included a binary variable for the first national lockdown (start 16 March 2020).ResultsWe identified 19,039 pertussis cases from these data sources. Pertussis cases decreased significantly following the implementation of mitigation measures, with adjusted incidence rate ratios of 0.10 (95% CI: 0.04-0.26) and 0.22 (95% CI: 0.07-0.66) for Source 1 and Source 2, respectively. The association was confirmed in Source 3 with a median of, respectively, one (IQR: 0-2) and 0 cases (IQR: 0-0) per month before and after lockdown (p = 0.0048).ConclusionsThe strong reduction in outpatient and hospitalised pertussis cases suggests an impact of COVID-19 mitigation measures on pertussis epidemiology. Pertussis vaccination recommendations should be followed carefully, and disease monitoring should be continued to detect any resurgence after relaxation of mitigation measures.

Effect of change in vaccine schedule on pertussis epidemiology in France: a modelling and serological study

BACKGROUND

In April-May, 2013, France modified its pertussis vaccination schedule, which uses the acellular pertussis vaccine, from three primary doses at 2, 3, and 4 months of age and a first booster at 16-18 months of age (former schedule) to two primary doses at 2 and 4 months of age and a first booster at 11 months of age (new schedule). We aimed to assess the subsequent effect of the vaccine schedule change on pertussis epidemiology in France.

METHODS

In this modelling study, using data collected between Jan 1, 2012, and Dec 31, 2019, from French national surveillance sources, we analysed the PCR test results of nasopharyngeal swabs collected from symptomatic outpatients aged 2-20 years with suspected pertussis. We developed a negative binomial regression model for the number of confirmed pertussis cases by year and age to assess the relative risks of pertussis depending on vaccine schedule. The linear predictor included the year, the age group, the population size, and a proxy of waning immunity. We tested different models in which waning immunity could vary with vaccine schedule and type of primary vaccine. The models were fitted to the 2012-18 data via Bayesian Markov chain Monte Carlo sampling, and the 2019 data were left out for external model validation. We also compared the anti-pertussis toxin (PT) antibody concentrations in leftover sera from children not tested for pertussis or recent respiratory tract infection aged 2-5 years born before and after the vaccine schedule change.

FINDINGS

We collected data on 7493 confirmed cases of pertussis. The model that best fitted the 2012-18 epidemiological data supported a faster waning of immunity following vaccination with the new vaccine schedule. 3 years after vaccination, the risk of developing pertussis was 1·7 (95% CI 1·4-2·0) times higher for children vaccinated according to the new schedule than those vaccinated according to the former schedule. The model correctly predicted the age distribution of cases in 2019. Geometric mean concentrations (GMC) of anti-PT IgG were 50% lower in children aged 2 years vaccinated with the new schedule (GMC=5·85 IU/mL [95% CI 4·08-8·39]) than in children of the same age vaccinated with the former schedule (GMC=11·62 IU/mL [95% CI 9·05-14·92]; p=0·0016), and 43% lower in children aged 3 years vaccinated with the new schedule (GMC=3·88 IU/mL [95% CI 2·82-5·34]) than those with the former schedule (GMC=6·80 IU/mL [95% CI 4·77-9·70]; p=0·026).

INTERPRETATION

A shorter-lived protection induced by the new vaccine schedule recommended in France since 2013 is associated with an increase of pertussis cases in children aged 2-5 years. If similar findings are observed in other countries and clinical trials, these findings should be considered in future pertussis vaccination policies.

FUNDING

INCEPTION, Labex-IBEID, Institut Pasteur, and Santé Publique France.

SARS-CoV-2 variants of concern are associated with lower RT-PCR amplification cycles between January and March 2021 in France

SARS-CoV-2 variants raise concern regarding the mortality caused by COVID-19 epidemics. We analyse 88,375 cycle amplification (Ct) values from variant-specific RT-PCR tests performed between January 26 and March 13, 2021. We estimate that on March 12, nearly 85% of the infections were caused by the Alpha variant and that its transmission advantage over wild type strains was between 38 and 44%. We also find that tests positive for Alpha and Beta/Gamma variants exhibit significantly lower cycle threshold (Ct) values.

Rapid spread of the SARS-CoV-2 Delta variant in some French regions, June 2021

We analysed 9,030 variant-specific RT-PCR tests performed on SARS-CoV-2-positive samples collected in France between 31 May and 21 June 2021. This analysis revealed rapid growth of the Delta variant in three of the 13 metropolitan French regions and estimated a +79% (95% confidence interval: 52-110%) transmission advantage compared with the Alpha variant. The next weeks will prove decisive and the magnitude of the estimated transmission advantages of the Delta variant could represent a major challenge for public health authorities.

The SARS-CoV-2 B.1.351 lineage (VOC β) is outgrowing the B.1.1.7 lineage (VOC α) in some French regions in April 2021

To assess SARS-CoV-2 variants spread, we analysed 36,590 variant-specific reverse-transcription-PCR tests performed on samples from 12 April-7 May 2021 in France. In this period, contrarily to January-March 2021, variants of concern (VOC) β (B.1.351 lineage) and/or γ (P.1 lineage) had a significant transmission advantage over VOC α (B.1.1.7 lineage) in Île-de-France (15.8%; 95% confidence interval (CI): 15.5-16.2) and Hauts-de-France (17.3%; 95% CI: 15.9-18.7) regions. This is consistent with VOC β's immune evasion abilities and high proportions of prior-SARS-CoV-2-infected persons in these regions.

Detecting Rapid Spread of SARS-CoV-2 Variants, France, January 26-February 16, 2021

Variants of severe acute respiratory syndrome coronavirus 2 raise concerns regarding the control of coronavirus disease epidemics. We analyzed 40,000 specific reverse transcription PCR tests performed on positive samples during January 26–February 16, 2021, in France. We found high transmission advantage of variants and more advanced spread than anticipated.

Epidemiology of Human Leptospirosis in French Guiana (2007-2014): A Retrospective Study

Leptospirosis is a worldwide zoonotic bacterial infection with a rising incidence. French Guiana is mostly covered by Amazonian rain forest. Despite a potentially favorable environment, leptospirosis has been barely studied in French Guiana. The objective of this study was to describe the current trends of leptospirosis epidemiology in French Guiana. A cross-sectional study was performed in the two main hospitals of French Guiana. Cases of leptospirosis from 2007 to 2014 were retrospectively identified with a systematic screening of serological and polymerase chain reaction results to classify them as confirmed, probable, or excluded cases. Medical files were reviewed to collect epidemiological data. Among the 72 included patients, 55 (76.4%) cases were confirmed and 17 (23.6%) were probable. The median age was 39 years (range: 16-82 years) and the M/F sex ratio 6.2. Sixty-two (86.1%) patients required hospitalization, including 12 (16.7%) in the intensive care unit. Three (4.2%) patients died. The monthly distribution of cases was correlated with rainfall (P = 0.004) and moisture (P = 0.038). Professional exposure was frequently identified (especially gold mining and construction). Among 16 different serogroups identified by microagglutination test, Icterohaemorrhagiae was the most frequent (38.0%). This study revealed an epidemiology close to that observed in Brazilian regions, and professional and climatic risk factors. The high diversity of serogroups may reveal a complex environmental reservoir requiring further investigations. Only 20% of leptospirosis patients were suspected as such on hospital admission, thus emphasizing the need to inform local physicians.

[Evaluation of a in house serology reagent for the diagnosis of cat-scratch disease defined by PCR]

AIM OF THE STUDY

evaluate the sensitivity and the specificity of the cat scratch disease serology by indirect immunofluorescence assay, realized from an in-house antigenic suspension, with PCR defined cases. Describe the epidemiological characteristics of the cases.

METHODS

the antigenic suspension is realized by culture of a Houston 1 ATCC 49882 B. henselae reference strain on horse blood agar suspended in egg formoled PBS. Real time PCR from clinical samples is performed by amplification of a 998-bp 16S rDNA sequence with Bart and r-BH primers.

RESULTS

In 57 out of 92 (62%) positive patients in PCR, the serology is positive in IgG at low or significative level or positive in IgG with presence of IgM or shows a seroconversion. The specificity in serum samples from 40 control patients is 100%. The average age of the 165 positive patients in PCR is 27.6 years old (3-80). The localization of the lymph nodes is more often axillary (47%) than inguinal (32%) or cervical (16%).

CONCLUSION

Our in-house indirect immunofluorescence assay for the cat scratch disease serology shows a sensitivity equivalent to other technics described in the literature, with an excellent specificity.

[Contribution of PCR for detection of Mycobacterium tuberculosis complex in respiratory and nonrespiratory specimens]

AIM OF THE STUDY

To evaluate the sensitivity of PCR versus culture of complex tuberculosis mycobacteria and to determine the delay between PCR results and identification of mycobacteria in culture.

MATERIALS AND METHODS

Ninety-nine pulmonary and 66 extrapulmonary specimens were analyzed. Samples were inoculated on liquid (MGIT, Bactec) and solid media (Coletsos) and respectively incubated 6 and 12 weeks. Identification was performed by reverse hybridization of PCR products to their complementary probes immobilized on membrane strips (Genotype MTBC, HAIN). Specimens DNA detection was realized by PCR (Cobas Amplicor Mycobacterium tuberculosis test, Roche).

RESULTS

Sensitivity of PCR for acid fast bacilli smear positive pulmonary (50/50) and extrapulmonary (7/7) specimens was 100%. Delay between PCR result and identification was 11 days for pulmonary specimens and 8 days for extrapulmonary specimens. Sensitivity of PCR for smear negative samples was, respectively, of 78.7% (37/47) and 51.8% (29/56) for pulmonary and extrapulmonary specimens. In case of PCR positive result of a smear negative sample, a gap of respectively 13 and 12 days was obtained for pulmonary and extrapulmonary specimens compared to identification.

CONCLUSION

Positive PCR result for respiratory specimens allows a gap of 11 to 13 days in diagnosis in comparison with identification of mycobacteria in culture.

[Retrospective study of Lyme borreliosis positive serologies in 2003]

PURPOSES OF THE STUDY

To estimate the percentage of positive sera for Lyme borreliosis antibodies, to precise the characteristics of clinical cases diagnosed from serological data and to determine their geographical distribution in France.

MATERIALS AND METHODS

Studied sera were those received by the Pasteur-Cerba laboratory in 2003. IgG and IgM isotypes were detected using the Dade Behring kits. Antibody specificity was analysed with the Meridian's western blot.

RESULTS

1504/16 176 (9%) sera were positive for IgG isotype, and 978/3298 (29%) for IgM. The specificity was confirmed by western blot in 49% cases for IgG and in 54% for IgM. The highest positive serology rates were found in eastern and centre regions and in Aquitaine. Forty-two cases have been investigated leading to the identification of 16 borreliosis cases, each suffering of an erythema migrans. Five of them had neurological signs. Patient mean age was 40 years. 87% of patients had risk factors and 69% reported previous tick bites, mainly on lower limbs.

CONCLUSION

A low rate of positive borreliosis sera was found, suggesting that serology prescription should be limited to patients suffering of compatible clinical signs, as recommended by the EUCALB. Erythema migrans was the most frequent clinical manifestation and neurological signs were present in 30% of cases. Finally, the geographical case distribution was similar to that provided by the study of the Sentinelle network in 1999-2000.

Comparaison de deux techniques d’hybridation moléculaire dans l’identification de mycobactéries en pratique courante

AIM OF THE STUDY

To evaluate the performance of two commercial methods for identification of Mycobacterium species: InnoLiPA Mycobacteria first version (Innogenetics) versus Genotype MTBC and Genotype Mycobacterium (HAIN) on, respectively, 2123 and 2164 distinct isolates.

MATERIALS AND METHODS

Both techniques are based on the reverse hybridization of PCR products to their complementary probes immobilized on membrane strips. The InnoLiPA assay targets the 16S-23S rRNA spacer region. The HAIN test is composed of two kits: Genotype MTBC, for identification of tuberculosis complex mycobacteria, is based on gyrB DNA sequence polymorphism. Genotype Mycobacterium kit targets the 23S rDNA for identification of mycobacteria other than tuberculosis (MOTT) and tuberculosis complex mycobacteria. Both assays identify complex tuberculosis mycobacteria and respectively, eight and 12 species of MOTT. Moreover, the Genotype MTBC allows species differentiation within the M. tuberculosis complex.

RESULTS

Eighty-eight percent and 95% of mycobacteria were identified by InnoLiPA and HAIN, respectively. Hybridization remained negative for 11% of isolates with InnoLiPA and 4% with HAIN. An identification of MOTT was obtained by conventional identification in all cases after the use of InnoLiPA. MOTT and one M. tuberculosis was obtained after HAIN procedure. Unidentified species were complementary to a specific probe in 5% of the cases with InnoLiPA and 17% with HAIN.

CONCLUSION

HAIN identifies more mycobacteria species than does InnoLiPA and allows identification in the M. tuberculosis complex. However, failure in identification occurs only with MOTT with InnoLiPA when one M. tuberculosis was found among mycobacteria non identified with HAIN.