Influence of conflicts of interest on public positions in the COVID-19 era, the case of Gilead Sciences

Funding and gifts from the pharmaceutical industry have an influence on the decisions made by physicians and medical experts. In the context of the coronavirus disease 2019 epidemic, several treatments are available to treat patients infected with the virus. Some are protected by patents, such as remdesivir, others0020stare not, such as hydroxychloroquine. We wanted to observe the possible correlation between the fact, for an academic doctor in infectious diseases, of having benefited from funding by Gilead Sciences, producer of remdesivir, and the public positions taken by this doctor towards hydroxychloroquine. Our results show a correlation (Spearman test, p = 0.017) between the amount received from the Gilead Sciences company and public opposition to the use of hydroxychloroquine in France. This should open up the debate on the role of the interest links of doctors with pharmaceutical companies in the medical and scientific public debate.

Clinical efficacy of chloroquine derivatives in COVID-19 infection: comparative meta-analysis between the big data and the real world

In the context of the current coronavirus disease 2019 (COVID-19) pandemic, we conducted a meta-analysis on the effects of chloroquine derivatives in patients, based on unpublished and published reports available publicly on the internet as of 27 May 2020. The keywords 'hydroxychloroquine', 'chloroquine', 'coronavirus', 'COVID-19' and 'SARS-Cov-2' were used in the PubMed, Google Scholar and Google search engines without any restrictions as to date or language. Twenty studies were identified involving 105 040 patients (19 270 treated patients) from nine countries (Brazil, China, France, Iran, Saudi Arabia, South Korea, Spain and the USA). Big data observational studies were associated with conflict of interest, lack of treatment dosage and duration, and absence of favourable outcome. Clinical studies were associated with favourable outcomes and details on therapy. Among clinical studies, three of four randomized controlled trials reported a significant favourable effect. Among clinical studies, a significant favourable summary effect was observed for duration of cough (OR 0.19, p 0.00003), duration of fever (OR 0.11, p 0.039), clinical cure (OR 0.21, p 0.0495), death (OR 0.32, p 4.1 × 10-6) and viral shedding (OR 0.43, p 0.031). A trend for a favourable effect was noted for the outcome 'death and/or intensive care unit transfer' (OR 0.29, p 0.069) with a point estimate remarkably similar to that observed for death (∼0.3). In conclusion, a meta-analysis of publicly available clinical reports demonstrates that chloroquine derivatives are effective to improve clinical and virological outcomes, but, more importantly, they reduce mortality by a factor of 3 in patients with COVID-19. Big data are lacking basic treatment definitions and are linked to conflict of interest. The retraction of the only big data study associated with a significantly deleterious effect the day after (June 5, 2020) the acceptance of the present work (June 4, 2020) confirms the relevance of this work.

Early treatment of COVID-19 patients with hydroxychloroquine and azithromycin: A retrospective analysis of 1061 cases in Marseille, France

BACKGROUND

In France, the combination hydroxychloroquine (HCQ) and azithromycin (AZ) is used in the treatment of COVID-19.

METHODS

We retrospectively report on 1061 SARS-CoV-2 positive tested patients treated for at least three days with the following regimen: HCQ (200 mg three times daily for ten days) + AZ (500 mg on day 1 followed by 250 mg daily for the next four days). Outcomes were death, clinical worsening (transfer to ICU, and >10 day hospitalization) and viral shedding persistence (>10 days).

RESULTS

A total of 1061 patients were included in this analysis (46.4% male, mean age 43.6 years - range 14-95 years). Good clinical outcome and virological cure were obtained in 973 patients within 10 days (91.7%). Prolonged viral carriage was observed in 47 patients (4.4%) and was associated to a higher viral load at diagnosis (p < .001) but viral culture was negative at day 10. All but one, were PCR-cleared at day 15. A poor clinical outcome (PClinO) was observed for 46 patients (4.3%) and 8 died (0.75%) (74-95 years old). All deaths resulted from respiratory failure and not from cardiac toxicity. Five patients are still hospitalized (98.7% of patients cured so far). PClinO was associated with older age (OR 1.11), severity of illness at admission (OR 10.05) and low HCQ serum concentration. PClinO was independently associated with the use of selective beta-blocking agents and angiotensin II receptor blockers (p < .05). A total of 2.3% of patients reported mild adverse events (gastrointestinal or skin symptoms, headache, insomnia and transient blurred vision).

CONCLUSION

Administration of the HCQ+AZ combination before COVID-19 complications occur is safe and associated with a very low fatality rate in patients.

SARS-CoV-2: fear versus data

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Comparison of incidence and mortality rates of four common coronaviruses circulating in France with those of SARS-CoV-2 in OECD countries.

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As of 2 March 2020, 90 307 patients had tested positive for SARS-CoV-2 worldwide, with 3086 deaths (mortality rate 3.4%).

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As of 2 March 2020, among OECD countries, 7476 patients had tested positive for SARS-CoV-2, with 96 deaths (mortality rate 1.3%)

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As of 2 March 2020, in France, 191 people had tested positive for SARS-CoV-2, with three deaths (mortality rate 1.6%).

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In OECD countries. the mortality rate for SARS-CoV-2 (1.3%) is not significantly different from that for common coronaviruses identified in public hospitals of Marseille, France (0.8%; P=0.11).

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The problem of SARS-CoV-2 is probably overestimated, as 2.6 million people die of respiratory infections each year compared with less than 4000 deaths for SARS-CoV-2 at the time of writing.

SARS-CoV-2, the novel coronavirus from China, is spreading around the world, causing a huge reaction despite its current low incidence outside China and the Far East. Four common coronaviruses are in current circulation and cause millions of cases worldwide. This article compares the incidence and mortality rates of these four common coronaviruses with those of SARS-CoV-2 in Organisation for Economic Co-operation and Development countries. It is concluded that the problem of SARS-CoV-2 is probably being overestimated, as 2.6 million people die of respiratory infections each year compared with less than 4000 deaths for SARS-CoV-2 at the time of writing.

Lactimicrobium massiliense gen. nov., sp. nov.; Anaerolactibacter massiliensis gen. nov., sp. nov.; Galactobacillus timonensis gen. nov., sp. nov. and Acidipropionibacterium timonense sp. nov. isolated from breast milk from healthy breastfeeding African women

Four strains isolated by microbial culturomics from breast milk of healthy mothers from Mali were not identified and characterized by taxono-genomics. This led us to propose the new genera and species Lactimicrobium massiliense, Anaerolactibacter massiliensis and Galactobacillus timonensis containing type strain Marseille-P4301^T (CSUR P4301^T), Marseille-P4302^T (CSUR P4302^T) and Marseille-P4641^T (CSUR P4641^T), respectively. The strain Marseille-P4482 represents a novel species, Acidipropionibacterium timonense, in a previously known genus with type strain being Marseille-P4482^T (CSUR P4482^T).

Development of the recombinase-based in vivo expression technology in Streptococcus thermophilus and validation using the lactose operon promoter

AIMS

To construct and validate the recombinase-based in vivo expression technology (R-IVET) tool in Streptococcus thermophilus (ST).

METHODS AND RESULTS

The R-IVET system we constructed in the LMD-9 strain includes the plasmid pULNcreB allowing transcriptional fusion with the gene of the site-specific recombinase Cre and the chromosomal cassette containing a spectinomycin resistance gene flanked by two loxP sites. When tested in M17 medium, promoters of the genes encoding the protease PrtS, the heat-shock protein Hsp16 and of the lactose operon triggered deletion of the cassette, indicating promoter activity in these conditions. The lactose operon promoter was also found to be activated during the transit in the murine gastrointestinal tract.

CONCLUSIONS

The R-IVET system developed in ST is relatively stable, functional, very sensitive and can be used to assay activity of promoters, which are specifically active in in vivo conditions.

SIGNIFICANCE AND IMPACT OF THE STUDY

This first adaptation of R-IVET to ST provides a highly valuable tool allowing an exploration of the physiological state of ST in the GIT of mammals, fermentation processes or dairy products.

Expression of Helicobacter pylori urease subunit B gene in Lactococcus lactis MG1363 and its use as a vaccine delivery system against H. pylori infection in mice

The use of Lactococcus lactis as an antigen delivery vehicle for mucosal immunisation has been proposed. To determine whether L. lactis could effectively deliver Helicobacter pylori antigens to the immune system, a recombinant L. lactis expressing H. pylori urease subunit B (UreB) was constructed. Constitutive expression of UreB by a pTREX1 vector resulted in the intracellular accumulation of UreB to approximately 6.25% of soluble cellular protein. Five different oral regimens were used to vaccinate C57BL/6 mice and the immune response measured. One regimen, which consisted of four weekly doses of 10(10) bacteria, followed after an interval of approximately 4 weeks by three successive daily doses, was able to elicit a systemic antibody response to UreB in the mice, although subsequently, a similar regimen produced a significant antibody response in only one out of six mice. The other three regimes, in which mice were vaccinated with two or three sets of three consecutive daily doses of recombinant bacteria over 30 days, failed to elicit significant anti-UreB serum antibody responses. In three regimens, the immunised mice were then challenged by H. pylori strain SS1 and no protective effect was observed. These findings suggest that any adjuvant effects of L. lactis are unlikely to be sufficient to produce an effective immune response and to protect against H. pylori challenge, when used to deliver a weak immunogen, such as UreB.

Characterization of a novel integrative element, ICESt1, in the lactic acid bacterium Streptococcus thermophilus

The 35.5-kb ICESt1 element of Streptococcus thermophilus CNRZ368 is bordered by a 27-bp repeat and integrated into the 3' end of a gene encoding a putative fructose-1,6-biphosphate aldolase. This element encodes site-specific integrase and excisionase enzymes related to those of conjugative transposons Tn5276 and Tn5252. The integrase was found to be involved in a site-specific excision of a circular form. ICESt1 also encodes putative conjugative transfer proteins related to those of the conjugative transposon Tn916. Therefore, ICESt1 could be or could be derived from an integrative conjugative element.

Characterization of a mosaic ISS1 element and evidence for the recent horizontal transfer of two different types of ISS1 between Streptococcus thermophilus and Lactococcus lactis

A 12-kb region of the Streptococcus thermophilus CNRZ368 chromosome was found to contain two copies of IS981 (one complete and one truncated) and three copies of ISS1 (two complete, ISS1SA and ISS1SC, and one truncated, delta ISS1SB). Comparison of the nucleotide sequences of these ISS1 elements with those of previously identified iso-ISS1 elements from Lactococcus lactis and the Enterococcus genus indicated that the ISS1 group is divided into three distinct subgroups which we have named alpha, beta and gamma. Nucleotide sequences of elements belonging to the same subgroup share more than 97% identity whereas sequences of elements from different groups share only 75-85% identity. Sequence analysis of ISS1SA and delta ISS1SB showed that they are members of the alpha group. We found that ISS1SC from S. themophilus CNRZ368, an ISS1 from L. lactis IL964 and IS946 from L. lactis TEK1 resulted from recombinations between alpha and beta elements. In addition, ISS1W from L. lactis Wg2 resulted from a recombination event between a gamma element and an ISS1 belonging to an unidentified subgroup. ISS1 sequences belonging to the alpha and beta subgroups were found in both S. thermophilus and L. lactis and gamma sequences were found in both the Enterococcus genus and L. lactis. The quasi-identity of some ISS1 elements in S. thermophilus and L. lactis and the distribution of alpha and beta elements suggest that horizontal transfer of ISS1 elements recently took place from L. lactis to S. thermophilus, two lactic acid bacteria used in the manufacture of cheeses. Since the presence of IS981 in S. thermophilus CNRZ368 also probably resulted from a horizontal transfer from L. lactis [Guédon et al. (1995) Mol. Microbiol. 16, 69-78], the 12-kb region bearing IS981 and ISS1 elements could be due to the integration of a lactococcal DNA fragment into the chromosome.

Characterization and distribution of two insertion sequences, IS1191 and iso-IS981, in Streptococcus thermophilus: does intergeneric transfer of insertion sequences occur in lactic acid bacteria co-cultures?

A chromosomal repeated sequence from Streptococcus thermophilus was identified as a new insertion sequence (IS), IS1191. This is the first IS element characterized in this species. This 1313 bp element has 28 bp imperfect terminal inverted repeats and is flanked by short direct repeats of 8 bp. The single large open reading frame of IS1191 encodes a 391-amino-acid protein which displays homologies with transposases encodes by IS1201 from Lactobacillus helveticus (44.5% amino-acid sequence identity) and by the other ISs of the IS256 family. One of the copies of IS1191 is inserted into a truncated iso-IS981 element. The nucleotide sequences of two truncated iso-IS981s from S. thermophilus and the sequence of IS981 element from Lactococcus lactis share more than 99% identity. The distribution of these insertion sequences in L. lactis and S. thermophilus strains suggests that intergeneric transfers occur during cocultures used in the manufacture of cheese.

Physical and genetic map of Streptococcus thermophilus A054

The three restriction endonucleases SfiI, BssHII, and SmaI were found to generate fragments with suitable size distributions for mapping the genome of Streptococcus thermophilus A054. A total of 5, 8, and 24 fragments were produced with SfiI, BssHII, and SmaI, respectively. An average genome size of 1,824 kb was determined by summing the total fragment sizes obtained by digestions with these three enzymes. Partial and multiple digestions of genomic DNA in conjunction with Southern hybridization were used to map SfiI, BssHII, and SmaI fragments. All restriction fragments were arranged in a unique circular chromosome. Southern hybridization analysis with specific probes allowed 23 genetic markers to be located on the restriction map. Among them, six rrn loci were precisely located. The area of the chromosome containing the ribosomal operons was further detailed by mapping some of the ApaI and SgrAI sites. Comparison of macrorestriction patterns from three clones derived from strain A054 revealed two variable regions in the chromosome. One was associated with the tandem rrnD and rrnE loci, and the other was mapped in the region of the lactose operon.

Strain characterization, genome size and plasmid content in the Lactobacillus acidophilus group (Hansen and Mocquot)

Chromosomal DNA of nine strains of the Lactobacillus acidophilus (Hansen and Mocquot) group in which heterogeneity had previously been revealed by biochemical characteristics and DNA-DNA hybridization studies were further investigated by restriction analysis, Southern hybridization, conventional and pulsed-field gel electrophoresis (PFGE) analyses. Industrial strains were characterized and identified as Lact. acidophilus. For this species, the number of rRNA gene clusters was estimated to be at least four from analyses of rRNA gene restriction patterns. The chromosome size of type-strains of Lact. acidophilus and Lact. gasseri was estimated from PFGE analysis to be 1.85 and 2.02 Mb respectively and Lact. gasseri strains were found to contain large-sized linear plasmids.