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Article ; Online: Nouvelles AMM : ripretinib dans le traitement des GIST avancées à partir de la quatrième ligne.

Lemaître, Joséphine / Watson, Sarah

2022 Volume 109, Issue 3, Page(s) 250–252

Title translation	New drug approvals: Ripretinib for advanced gastrointestinal stromal tumors (GIST) in fourth or later-line therapy.
MeSH term(s)	Antineoplastic Agents/pharmacology ; Antineoplastic Agents/therapeutic use ; Drug Approval ; Drug Resistance, Neoplasm ; Gastrointestinal Neoplasms/drug therapy ; Gastrointestinal Neoplasms/pathology ; Gastrointestinal Stromal Tumors/drug therapy ; Gastrointestinal Stromal Tumors/pathology ; Humans ; Mutation ; Naphthyridines/therapeutic use ; Protein Kinase Inhibitors/pharmacology ; Protein Kinase Inhibitors/therapeutic use ; Proto-Oncogene Proteins c-kit/genetics ; Proto-Oncogene Proteins c-kit/therapeutic use ; Urea/analogs & derivatives ; Urea/therapeutic use
Chemical Substances	Antineoplastic Agents ; Naphthyridines ; Protein Kinase Inhibitors ; Urea (8W8T17847W) ; ripretinib (9XW757O13D) ; Proto-Oncogene Proteins c-kit (EC 2.7.10.1)
Language	French
Publishing date	2022-01-31
Publishing country	France
Document type	Letter
ZDB-ID	213270-9
ISSN	1769-6917 ; 0007-4551
ISSN (online)	1769-6917
ISSN	0007-4551
DOI	10.1016/j.bulcan.2022.01.002
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Article ; Online: flepiMoP: The evolution of a flexible infectious disease modeling pipeline during the COVID-19 pandemic.

Lemaitre, Joseph C / Loo, Sara L / Kaminsky, Joshua / Lee, Elizabeth C / McKee, Clifton / Smith, Claire / Jung, Sung-Mok / Sato, Koji / Carcelen, Erica / Hill, Alison / Lessler, Justin / Truelove, Shaun

Epidemics

2024 Volume 47, Page(s) 100753

Abstract: The COVID-19 pandemic led to an unprecedented demand for projections of disease burden and healthcare utilization under scenarios ranging from unmitigated spread to strict social distancing policies. In response, members of the Johns Hopkins Infectious ... ...

Abstract	The COVID-19 pandemic led to an unprecedented demand for projections of disease burden and healthcare utilization under scenarios ranging from unmitigated spread to strict social distancing policies. In response, members of the Johns Hopkins Infectious Disease Dynamics Group developed flepiMoP (formerly called the COVID Scenario Modeling Pipeline), a comprehensive open-source software pipeline designed for creating and simulating compartmental models of infectious disease transmission and inferring parameters through these models. The framework has been used extensively to produce short-term forecasts and longer-term scenario projections of COVID-19 at the state and county level in the US, for COVID-19 in other countries at various geographic scales, and more recently for seasonal influenza. In this paper, we highlight how the flepiMoP has evolved throughout the COVID-19 pandemic to address changing epidemiological dynamics, new interventions, and shifts in policy-relevant model outputs. As the framework has reached a mature state, we provide a detailed overview of flepiMoP's key features and remaining limitations, thereby distributing flepiMoP and its documentation as a flexible and powerful tool for researchers and public health professionals to rapidly build and deploy large-scale complex infectious disease models for any pathogen and demographic setup.
Language	English
Publishing date	2024-03-02
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2467993-8
ISSN	1878-0067 ; 1755-4365
ISSN (online)	1878-0067
ISSN	1755-4365
DOI	10.1016/j.epidem.2024.100753
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Article ; Online: Epidemicity of cholera spread and the fate of infection control measures.

Trevisin, Cristiano / Lemaitre, Joseph C / Mari, Lorenzo / Pasetto, Damiano / Gatto, Marino / Rinaldo, Andrea

Journal of the Royal Society, Interface

2022 Volume 19, Issue 188, Page(s) 20210844

Abstract: The fate of ongoing infectious disease outbreaks is predicted through reproduction numbers, defining the long-term establishment of the infection, and epidemicity indices, tackling the reactivity of the infectious pool to new contagions. Prognostic ... ...

Abstract	The fate of ongoing infectious disease outbreaks is predicted through reproduction numbers, defining the long-term establishment of the infection, and epidemicity indices, tackling the reactivity of the infectious pool to new contagions. Prognostic metrics of unfolding outbreaks are of particular importance when designing adaptive emergency interventions facing real-time assimilation of epidemiological evidence. Our aim here is twofold. First, we propose a novel form of the epidemicity index for the characterization of cholera epidemics in spatial models of disease spread. Second, we examine in hindsight the survey of infections, treatments and containment measures carried out for the now extinct 2010-2019 Haiti cholera outbreak, to suggest that magnitude and timing of non-pharmaceutical and vaccination interventions imply epidemiological responses recapped by the evolution of epidemicity indices. Achieving negative epidemicity greatly accelerates fading of infections and thus proves a worthwhile target of containment measures. We also show that, in our model, effective reproduction numbers and epidemicity indices are explicitly related. Therefore, providing an upper bound to the effective reproduction number (significantly lower than the unit threshold) warrants negative epidemicity and, in turn, a rapidly fading outbreak preventing coalescence of sparse local sub-threshold flare-ups.
MeSH term(s)	Basic Reproduction Number ; Cholera/epidemiology ; Cholera/prevention & control ; Disease Outbreaks/prevention & control ; Epidemics ; Haiti/epidemiology ; Humans ; Infection Control
Language	English
Publishing date	2022-03-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2156283-0
ISSN	1742-5662 ; 1742-5689
ISSN (online)	1742-5662
ISSN	1742-5689
DOI	10.1098/rsif.2021.0844
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Article ; Online: Nocardia neocaledoniensis as Rare Cause of Spondylodiscitis.

Choquet, Emeline / Rodriguez-Nava, Veronica / Peltier, François / Wankap-Mogo, Rodrigue / Bergeron, Emmanuelle / Joseph, Cédric / Lemaitre, Nadine

Emerging infectious diseases

2023 Volume 29, Issue 2, Page(s) 444–446

Abstract: Nocardia neocaledoniensis is a rare species of Nocardia bacteria, identified in 2004 in hypermagnesian ultramafic soil of New Caledonia. Culture of this opportunistic pathogen from spinal biopsy samples confirmed N. neocaledoniensis spondylodiscitis in ... ...

Abstract	Nocardia neocaledoniensis is a rare species of Nocardia bacteria, identified in 2004 in hypermagnesian ultramafic soil of New Caledonia. Culture of this opportunistic pathogen from spinal biopsy samples confirmed N. neocaledoniensis spondylodiscitis in an immunocompromised man. Isolation of this unusual species from spinal biopsy samples illustrates its underappreciated ability to cause invasive infection.
MeSH term(s)	Humans ; Male ; Discitis/diagnosis ; Nocardia/genetics ; Nocardia Infections/diagnosis ; Nocardia Infections/drug therapy ; Bacteria ; RNA, Ribosomal, 16S
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2023-01-24
Publishing country	United States
Document type	Letter
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid2902.221389
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Article ; Online: Range of reproduction number estimates for COVID-19 spread.

Pasetto, Damiano / Lemaitre, Joseph C / Bertuzzo, Enrico / Gatto, Marino / Rinaldo, Andrea

Biochemical and biophysical research communications

2020 Volume 538, Page(s) 253–258

Abstract: To monitor local and global COVID-19 outbreaks, and to plan containment measures, accessible and comprehensible decision-making tools need to be based on the growth rates of new confirmed infections, hospitalization or case fatality rates. Growth rates ... ...

Abstract	To monitor local and global COVID-19 outbreaks, and to plan containment measures, accessible and comprehensible decision-making tools need to be based on the growth rates of new confirmed infections, hospitalization or case fatality rates. Growth rates of new cases form the empirical basis for estimates of a variety of reproduction numbers, dimensionless numbers whose value, when larger than unity, describes surging infections and generally worsening epidemiological conditions. Typically, these determinations rely on noisy or incomplete data gained over limited periods of time, and on many parameters to estimate. This paper examines how estimates from data and models of time-evolving reproduction numbers of national COVID-19 infection spread change by using different techniques and assumptions. Given the importance acquired by reproduction numbers as diagnostic tools, assessing their range of possible variations obtainable from the same epidemiological data is relevant. We compute control reproduction numbers from Swiss and Italian COVID-19 time series adopting both data convolution (renewal equation) and a SEIR-type model. Within these two paradigms we run a comparative analysis of the possible inferences obtained through approximations of the distributions typically used to describe serial intervals, generation, latency and incubation times, and the delays between onset of symptoms and notification. Our results suggest that estimates of reproduction numbers under these different assumptions may show significant temporal differences, while the actual variability range of computed values is rather small.
MeSH term(s)	Basic Reproduction Number ; COVID-19/epidemiology ; COVID-19/transmission ; Humans ; Models, Statistical ; Stochastic Processes
Language	English
Publishing date	2020-12-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	205723-2
ISSN	1090-2104 ; 0006-291X ; 0006-291X
ISSN (online)	1090-2104 ; 0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2020.12.003
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Article ; Online: Assessing the impact of non-pharmaceutical interventions on SARS-CoV-2 transmission in Switzerland.

Lemaitre, Joseph C / Perez-Saez, Javier / Azman, Andrew S / Rinaldo, Andrea / Fellay, Jacques

Swiss medical weekly

2020 Volume 150, Page(s) w20295

Abstract: Following the rapid dissemination of COVID-19 cases in Switzerland, large-scale non-pharmaceutical interventions (NPIs) were implemented by the cantons and the federal government between 28 February and 20 March 2020. Estimates of the impact of these ... ...

Abstract	Following the rapid dissemination of COVID-19 cases in Switzerland, large-scale non-pharmaceutical interventions (NPIs) were implemented by the cantons and the federal government between 28 February and 20 March 2020. Estimates of the impact of these interventions on SARS-CoV-2 transmission are critical for decision making in this and future outbreaks. We here aim to assess the impact of these NPIs on disease transmission by estimating changes in the basic reproduction number (R0) at national and cantonal levels in relation to the timing of these NPIs. We estimated the time-varying R0 nationally and in eleven cantons by fitting a stochastic transmission model explicitly simulating within-hospital dynamics. We used individual-level data from more than 1000 hospitalised patients in Switzerland and public daily reports of hospitalisations and deaths. We estimated the national R0 to be 2.8 (95% confidence interval 2.1–3.8) at the beginning of the epidemic. Starting from around 7 March, we found a strong reduction in time-varying R0 with a 86% median decrease (95% quantile range [QR] 79–90%) to a value of 0.40 (95% QR 0.3–0.58) in the period of 29 March to 5 April. At the cantonal level, R0 decreased over the course of the epidemic between 53% and 92%. Reductions in time-varying R0 were synchronous with changes in mobility patterns as estimated through smartphone activity, which started before the official implementation of NPIs. We inferred that most of the reduction of transmission is attributable to behavioural changes as opposed to natural immunity, the latter accounting for only about 4% of the total reduction in effective transmission. As Switzerland considers relaxing some of the restrictions of social mixing, current estimates of time-varying R0 well below one are promising. However, as of 24 April 2020, at least 96% (95% QR 95.7–96.4%) of the Swiss population remains susceptible to SARS-CoV-2. These results warrant a cautious relaxation of social distance practices and close monitoring of changes in both the basic and effective reproduction numbers.
MeSH term(s)	Betacoronavirus/isolation & purification ; COVID-19 ; Communicable Disease Control/methods ; Communicable Disease Control/organization & administration ; Communicable Disease Control/statistics & numerical data ; Communicable Diseases, Emerging/prevention & control ; Coronavirus Infections/epidemiology ; Coronavirus Infections/prevention & control ; Coronavirus Infections/transmission ; Disease Transmission, Infectious/prevention & control ; Disease Transmission, Infectious/statistics & numerical data ; Hospitalization/statistics & numerical data ; Humans ; Models, Statistical ; Mortality ; Pandemics/prevention & control ; Pandemics/statistics & numerical data ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/prevention & control ; Pneumonia, Viral/transmission ; SARS-CoV-2 ; Space-Time Clustering ; Stochastic Processes
Keywords	covid19
Language	English
Publishing date	2020-05-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2036179-8
ISSN	1424-3997 ; 1424-7860
ISSN (online)	1424-3997
ISSN	1424-7860
DOI	10.4414/smw.2020.20295
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Article ; Online: The Gut Microbial Metabolite Trimethylamine N-oxide, Incident CKD, and Kidney Function Decline.

Journal of the American Society of Nephrology : JASN

2024

Abstract: ... Cystatin C were measured up to 4 times during follow-up and used to compute eGFR. Incident CKD was defined ...

Abstract	Background: Trimethylamine N-oxide (TMAO) is a gut microbiota-derived metabolite of dietary phosphatidylcholine and carnitine. Experimentally, TMAO causes kidney injury and tubulointerstitial fibrosis. Little is known about prospective associations between TMAO and kidney outcomes, especially incident CKD. We hypothesized that higher plasma TMAO levels would be associated with higher risk of incident CKD and greater rate of kidney function decline. Methods: We included 10,564 participants from two community-based, prospective cohorts with estimated glomerular filtration rate (eGFR) ≥ 60 mL/min/1.73m2 to assess incident CKD. TMAO was measured using targeted mass spectrometry at baseline and one follow-up visit. Creatinine and Cystatin C were measured up to 4 times during follow-up and used to compute eGFR. Incident CKD was defined as an eGFR decline ≥ 30% from baseline and a resulting eGFR<60 ml/min/1.73 m2. Time-varying Cox models assessed the association of serial TMAO measures with incident CKD, adjusting for sociodemographic, lifestyle, diet, and cardiovascular disease risk factors. Linear mixed models assessed the association with annualized eGFR change in 10,009 participants with at least one follow-up eGFR measure without exclusions for baseline eGFR levels. Results: During a median follow-up of 9.4 years (interquartile range: 9.1-11.6 years), 979 incident CKD events occurred. Higher TMAO levels associated with higher risk of incident CKD (2nd to 5th vs. 1st quintile HR[95%CI]= 1.65 [1.22-2.23], 1.68 [1.26-2.25], 2.28 [1.72-3.02], and 2.24[1.68-2.98], respectively) and greater annualized eGFR decline ( 2nd to 5th vs. 1st quintile annualized eGFR change= -0.21 [-0.32, -0.09], -0.17 [-0.29, -0.05], -0.35 [-0.47, -0.22], and -0.43[-0.56, -0.30], respectively) with monotonic dose-response relationships. These associations were consistent across different racial/ethnic groups examined. The association with eGFR decline was similar to or larger than that seen for established CKD risk factors including diabetes, per 10 mmHg of higher systolic blood pressure, per 10 years of older age, and Black race. Conclusions: In community-based US adults, higher serial measures of plasma TMAO were associated with higher risk of incident CKD and greater annualized kidney function decline.
Language	English
Publishing date	2024-04-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	1085942-1
ISSN	1533-3450 ; 1046-6673
ISSN (online)	1533-3450
ISSN	1046-6673
DOI	10.1681/ASN.0000000000000344
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Article ; Online: Lactic acidosis after allogeneic haematopoietic stem cell transplantation potentially related to letermovir.

Manczak, Bérénice / Verdier, Marie-Clémence / Dewulf, Joseph P / Lemaitre, Florian / Haufroid, Vincent / Hantson, Philippe

British journal of clinical pharmacology

2023 Volume 89, Issue 5, Page(s) 1686–1689

Abstract: ... SLCO1B1*5/*15 (c.521T>C homozygous carrier and c.388A>G heterozygous carrier) with a predicted ...

Abstract	A 53-year-old woman with a history of acute myeloid leukaemia received a second allogeneic haematopoietic stem cell transplant and was prescribed, among other medications, acyclovir and letermovir (480-mg daily oral dose) for prophylaxis of, respectively, herpes simplex and cytomegalovirus infection. The patient was admitted in the intensive care unit for dyspnoea and oliguria. Laboratory investigations revealed acute kidney injury but also a severe and progressive lactic acidosis. Liver function tests were within normal range. The combination of lactic acidosis, hypoglycaemia and acylcarnitine profile in plasma raised the suspicion of mitochondrial toxicity. Letermovir therapy was interrupted, and determination of plasma letermovir pharmacokinetics revealed a prolonged terminal half-life (38.7 h) that was not significantly influenced by continuous venovenous haemofiltration. Exploration for genetic polymorphisms revealed that the patient was SLCO1B15/15 (c.521T>C homozygous carrier and c.388A>G heterozygous carrier) with a predicted nonfunctional organic anion transporting polypeptide 1B1 protein. The relationship between letermovir accumulation and development of lactic acidosis requires further observations.
MeSH term(s)	Female ; Humans ; Middle Aged ; Acidosis, Lactic/therapy ; Acidosis, Lactic/drug therapy ; Antiviral Agents/therapeutic use ; Cytomegalovirus Infections/drug therapy ; Acetates/pharmacokinetics ; Hematopoietic Stem Cell Transplantation/adverse effects ; Liver-Specific Organic Anion Transporter 1
Chemical Substances	letermovir (1H09Y5WO1F) ; Antiviral Agents ; Acetates ; SLCO1B1 protein, human ; Liver-Specific Organic Anion Transporter 1
Language	English
Publishing date	2023-02-19
Publishing country	England
Document type	Case Reports
ZDB-ID	188974-6
ISSN	1365-2125 ; 0306-5251 ; 0264-3774
ISSN (online)	1365-2125
ISSN	0306-5251 ; 0264-3774
DOI	10.1111/bcp.15686
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Article ; Online: Trimethylamine N-oxide is associated with long-term mortality risk: the multi-ethnic study of atherosclerosis.

Wang, Meng / Li, Xinmin S / Wang, Zeneng / de Oliveira Otto, Marcia C / Lemaitre, Rozenn N / Fretts, Amanda / Sotoodehnia, Nona / Budoff, Matthew / Nemet, Ina / DiDonato, Joseph A / Tang, Wai Hong Wilson / Psaty, Bruce M / Siscovick, David S / Hazen, Stanley L / Mozaffarian, Dariush

European heart journal

2023 Volume 44, Issue 18, Page(s) 1608–1618

Abstract: Aims: Little is known about associations of trimethylamine N-oxide (TMAO), a novel gut microbiota-generated metabolite of dietary phosphatidylcholine and carnitine, and its changes over time with all-cause and cause-specific mortality in the general ... ...

Abstract	Aims: Little is known about associations of trimethylamine N-oxide (TMAO), a novel gut microbiota-generated metabolite of dietary phosphatidylcholine and carnitine, and its changes over time with all-cause and cause-specific mortality in the general population or in different race/ethnicity groups. The study aimed to investigate associations of serially measured plasma TMAO levels and changes in TMAO over time with all-cause and cause-specific mortality in a multi-ethnic community-based cohort. Methods and results: The study included 6,785 adults from the Multi-Ethnic Study of Atherosclerosis. TMAO was measured at baseline and year 5 using mass spectrometry. Primary outcomes were adjudicated all-cause mortality and cardiovascular disease (CVD) mortality. Secondary outcomes were deaths due to kidney failure, cancer, or dementia obtained from death certificates. Cox proportional hazards models with time-varying TMAO and covariates assessed the associations with adjustment for sociodemographics, lifestyles, diet, metabolic factors, and comorbidities. During a median follow-up of 16.9 years, 1704 participants died and 411 from CVD. Higher TMAO levels associated with higher risk of all-cause mortality [hazard ratio (HR): 1.12, 95% confidence interval (CI): 1.08-1.17], CVD mortality (HR: 1.09, 95% CI: 1.00-1.09), and death due to kidney failure (HR: 1.44, 95% CI: 1.25-1.66) per inter-quintile range, but not deaths due to cancer or dementia. Annualized changes in TMAO levels associated with higher risk of all-cause mortality (HR: 1.10, 95% CI: 1.05-1.14) and death due to kidney failure (HR: 1.54, 95% CI: 1.26-1.89) but not other deaths. Conclusion: Plasma TMAO levels were positively associated with mortality, especially deaths due to cardiovascular and renal disease, in a multi-ethnic US cohort.
MeSH term(s)	Adult ; Humans ; Risk Factors ; Biomarkers ; Methylamines/metabolism ; Cardiovascular Diseases ; Renal Insufficiency/etiology ; Atherosclerosis/complications ; Neoplasms/complications ; Dementia
Chemical Substances	trimethyloxamine (FLD0K1SJ1A) ; Biomarkers ; Methylamines
Language	English
Publishing date	2023-03-08
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	603098-1
ISSN	1522-9645 ; 0195-668X
ISSN (online)	1522-9645
ISSN	0195-668X
DOI	10.1093/eurheartj/ehad089
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Article ; Online: Assessing the impact of non-pharmaceutical interventions on SARS-CoV-2 transmission in Switzerland

Lemaitre, Joseph C / Perez-Saez, Javier / Azman, Andrew S / Rinaldo, Andrea / Fellay, Jacques

Swiss Medical Weekly ; ISSN 1424-3997

2020

Keywords	General Medicine ; covid19
Language	English
Publisher	EMH Swiss Medical Publishers, Ltd.
Publishing country	ch
Document type	Article ; Online
DOI	10.4414/smw.2020.20295
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