Publications by authors named "Anthony Levasseur"

133 Publications

SARS-CoV-2 European resurgence foretold: interplay of introductions and persistence by leveraging genomic and mobility data.

Res Sq 2021 Feb 10. Epub 2021 Feb 10.

Following the first wave of SARS-CoV-2 infections in spring 2020, Europe experienced a resurgence of the virus starting late summer that was deadlier and more difficult to contain. Relaxed intervention measures and summer travel have been implicated as drivers of the second wave. Here, we build a phylogeographic model to evaluate how newly introduced lineages, as opposed to the rekindling of persistent lineages, contributed to the COVID-19 resurgence in Europe. We inform this model using genomic, mobility and epidemiological data from 10 West European countries and estimate that in many countries more than 50% of the lineages circulating in late summer resulted from new introductions since June 15th. The success in onwards transmission of these lineages is predicted by SARS-CoV-2 incidence during this period. Relatively early introductions from Spain into the United Kingdom contributed to the successful spread of the 20A.EU1/B.1.177 variant. The pervasive spread of variants that have not been associated with an advantage in transmissibility highlights the threat of novel variants of concern that emerged more recently and have been disseminated by holiday travel. Our findings indicate that more effective and coordinated measures are required to contain spread through cross-border travel.
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http://dx.doi.org/10.21203/rs.3.rs-208849/v1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7885927PMC
February 2021

Draft Genome Sequence of Comamonas jiangduensis Strain YW1.

Microbiol Resour Announc 2021 Feb 11;10(6). Epub 2021 Feb 11.

Aix-Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France

Here, we report the draft genome sequence of strain YW1 (= DSM 100319 = CSUR Q1714 = CCTCC AB 2012033  =  KACC 16697). is a new species that was isolated from agricultural soil. The genome sequence from strain YW1 has been assembled into 322 contigs for a total size of 2,758,586 bp with a G+C content of 59.1%.
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http://dx.doi.org/10.1128/MRA.00513-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7883839PMC
February 2021

Draft Genome Sequence of Vogesella oryzae L3B39, Isolated from the Rhizosphere of Saline-Tolerant Pokkali Rice.

Microbiol Resour Announc 2021 Feb 4;10(5). Epub 2021 Feb 4.

Aix-Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France

Here, we report the draft genome sequence of L3B39 (CSUR Q2602 = DSM 28780), which is a species isolated from the rhizosphere of saline-tolerant pokkali rice. The genome sequence was assembled into 58 contigs for a total size of 3,415,129 bp, with a G+C content of 62.3%.
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http://dx.doi.org/10.1128/MRA.00515-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7862949PMC
February 2021

Draft Genome Sequence of Comamonas aquatilis Strain LK (= CSUR P6418 = CECT 9772), Isolated from the Planarian Schmidtea mediterranea.

Microbiol Resour Announc 2021 Feb 4;10(5). Epub 2021 Feb 4.

Aix-Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France

was defined as a new species based on its 16S rRNA sequence, but the genome from the type strain SB30-Cr27-3 (= CIP 111491 = CCM 8815) is not available. We have cultivated from the planarian a strain, LK (= CSUR P6418 = CECT 9772), that exhibits 100% 16S rRNA sequence similarity to strain SB30-Cr27-3 We have sequenced the genome of strain LK and obtained a chromosome of 4,899,818 bp, with a G+C content of 61.75%, assembled into two contigs.
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http://dx.doi.org/10.1128/MRA.00297-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7862948PMC
February 2021

Introduction into the Marseille geographical area of a mild SARS-CoV-2 variant originating from sub-Saharan Africa: An investigational study.

Travel Med Infect Dis 2021 Jan 31;40:101980. Epub 2021 Jan 31.

IHU Méditerranée Infection, Marseille, France; Aix-Marseille Univ, Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France. Electronic address:

Background: In Marseille, France, the COVID-19 incidence evolved unusually with several successive epidemic phases. The second outbreak started in July, was associated with North Africa, and involved travelers and an outbreak on passenger ships. This suggested the involvement of a new viral variant.

Methods: We sequenced the genomes from 916 SARS-CoV-2 strains from COVID-19 patients in our institute. The patients' demographic and clinical features were compared according to the infecting viral variant.

Results: From June 26th to August 14th, we identified a new viral variant (Marseille-1). Based on genome sequences (n = 89) or specific qPCR (n = 53), 142 patients infected with this variant were detected. It is characterized by a combination of 10 mutations located in the nsp2, nsp3, nsp12, S, ORF3a, ORF8 and N/ORF14 genes. We identified Senegal and Gambia, where the virus had been transferred from China and Europe in February-April as the sources of the Marseille-1 variant, which then most likely reached Marseille through Maghreb when French borders reopened. In France, this variant apparently remained almost limited to Marseille. In addition, it was significantly associated with a milder disease compared to clade 20A ancestor strains, in univariate analysis.

Conclusion: Our results demonstrate that SARS-CoV-2 can genetically diversify rapidly, its variants can diffuse internationally and cause successive outbreaks.
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http://dx.doi.org/10.1016/j.tmaid.2021.101980DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7847701PMC
January 2021

Anaerococcus urinimassiliensis sp. nov., a new bacterium isolated from human urine.

Sci Rep 2021 Jan 29;11(1):2684. Epub 2021 Jan 29.

Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.

To date there are thirteen species validly assigned to the genus Anaerococcus. Most of the species in this genus are anaerobic and of human origin. Anaerococcus urinimassiliensis sp. nov., strain Marseille-P2143 is member of family Peptoniphilaceae, which was isolated from the urine of a 17-year-old boy affected by autoimmune hepatitis and membranoproliferative glomerulonephritis using the culturomic approach. In the current study, a taxono-genomics method was employed to describe this new species. The strain Marseille-P2143 was gram positive cocci with translucent colonies on blood agar. Its genome was 2,189,509 bp long with a 33.5 mol% G + C content and exhibited 98.48% 16S rRNA similarity with Anaerococcus provencensis strain 9,402,080. When Anaerococcus urinomassiliensis strain Marseill-P2143 is compared with closely related species, the values ranged from 71.23% with A. hydrogenalis strain DSM 7454 (NZ_ABXA01000052.1) to 90.64% with A. provencensis strain 9402080 (NZ_HG003688.1). This strain has implemented the repertoire of known bacteria of the human urinary tract.
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http://dx.doi.org/10.1038/s41598-021-82420-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7846727PMC
January 2021

Rapid Scanning Electron Microscopy Detection and Sequencing of Severe Acute Respiratory Syndrome Coronavirus 2 and Other Respiratory Viruses.

Front Microbiol 2020 19;11:596180. Epub 2020 Nov 19.

Aix-Marseille Université, Institut de Recherche pour le Développement(IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.

There is an urgent need for accurate and rapid testing methods to quickly identify infected patients as well as asymptomatic carriers, in order to prevent the spread of emerging viruses. Here, we developed a rapid testing strategy by scanning electron microscopy capable of detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses directly from patients. We evaluated our results by comparing them to real-time reverse transcription-polymerase chain reaction (RT-PCR) and metagenomic sequencing results. We correlated the presence of the SARS-CoV-2 to the viral load, where samples with Ct values lower than 18 were all detected by scanning electron microscopy (SEM). The sensitivity deacresed progressively with higher Ct values. In addition, we found a correlation with metagenomic sequencing, where all samples detected by SEM were sequenced and viral sequences were easily recovered. Following this study, SEM proved its efficiency as a frontline method for directly detecting previously unknown microorganisms that cannot be targeted by molecular methods and can cause potential outbreaks.
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http://dx.doi.org/10.3389/fmicb.2020.596180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7711091PMC
November 2020

Enteroviruses from Humans and Great Apes in the Republic of Congo: Recombination within Enterovirus C Serotypes.

Microorganisms 2020 Nov 13;8(11). Epub 2020 Nov 13.

IHU Méditerranée Infection, CEDEX 05, 13005 Marseille, France.

Enteroviruses (EVs) are viruses of the family Picornaviridae that cause mild to severe infections in humans and in several animal species, including non-human primates (NHPs). We conducted a survey and characterization of enteroviruses circulating between humans and great apes in the Congo. Fecal samples (N = 24) of gorillas and chimpanzees living close to or distant from humans in three Congolese parks were collected, as well as from healthy humans (N = 38) living around and within these parks. Enteroviruses were detected in 29.4% of gorilla and 13.15% of human feces, including wild and human-habituated gorillas, local humans and eco-guards. Two identical strains were isolated from two humans coming from two remote regions. Their genomes were similar and all genes showed their close similarity to coxsackieviruses, except for the 3C, 3D and 5'-UTR regions, where they were most similar to poliovirus 1 and 2, suggesting recombination. Recombination events were found between these strains, poliovirus 1 and 2 and EV-C99. It is possible that the same EV-C species circulated in both humans and apes in different regions in the Congo, which must be confirmed in other investigations. In addition, other studies are needed to further investigate the circulation and genetic diversity of enteroviruses in the great ape population, to draw a definitive conclusion on the different species and types of enteroviruses circulating in the Republic of Congo.
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http://dx.doi.org/10.3390/microorganisms8111779DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7709013PMC
November 2020

An Earliest Endosymbiont, sp. nov., Strain PL13 from the Bed Bug (), Type Strain of a New Supergroup T.

Int J Mol Sci 2020 Oct 29;21(21). Epub 2020 Oct 29.

Aix Marseille Univ, IRD, AP-HM, MEPHI, 13385 Marseille, France.

The symbiotic are the most sophisticated mutualistic bacterium among all insect-associated microbiota. -insect relationship fluctuates from the simple facultative/parasitic to an obligate nutritional-mutualistic association as it was the case of the bedbug- from . Understanding this association may help in the control of associated arthropods. Genomic data have proven to be reliable tools in resolving some aspects of these symbiotic associations. Although, appear to be fastidious or uncultivated bacteria which strongly limited their study. Here we proposed S2 cell line for the isolation and culture model to study strains. We therefore isolated and characterized a novel strain associated with the bedbug , designated as strain PL13, and proposed sp. nov. strain -PL13 a type strain of this new species from new supergroup T. Phylogenetically, T-supergroup was close to F and S-supergroups from insects and D-supergroup from filarial nematodes. We determined the 1,291,339-bp genome of -PL13, which was the smallest insect-associated genomes. Overall, the genome shared 50% of protein coding genes with the other insect-associated facultative strains. These findings highlight the diversity of genotypes as well as the -host relationship among Cimicinae subfamily. The provides folate and riboflavin vitamins on which the host depends, while the bacteria had a limited translation mechanism suggesting its strong dependence to its hosts. However, the clear-cut distinction between mutualism and parasitism of the in . cannot be yet ruled out.
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http://dx.doi.org/10.3390/ijms21218064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7662661PMC
October 2020

Draft Genome Sequence of Streptomyces mexicanus Strain Q0842, Isolated from Human Skin.

Microbiol Resour Announc 2020 Oct 29;9(44). Epub 2020 Oct 29.

Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France

In 2003, was reported as a novel xylanolytic bacterial species isolated from soil; a partial genome sequence was determined. In 2019, a strain from the same species was isolated from a hand skin swab sample from a healthy French woman. Genome sequencing revealed an 8,011,832-bp sequence with a GC content of 72.5%.
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http://dx.doi.org/10.1128/MRA.01527-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7595954PMC
October 2020

Flying fox haemolytic fever, description of a new zoonosis caused by "Candidatus Mycoplasma haemohominis".

Clin Infect Dis 2020 Oct 29. Epub 2020 Oct 29.

Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.

Background: Hemotropic mycoplasmas, previously classified in the genus Eperythrozoon, have been reported as causing human infections in Brazil, China, Japan and Spain.

Methods: In 2017, we detected DNA from "Candidatus Mycoplasma haemohominis" in the blood of a Melanesian patient from New Caledonia presenting with febrile splenomegaly,weight loss, life-threatening autoimmune haemolytic anemia and hemophagocytosis. The full genome of the bacterium was sequenced from a blood isolate. Subsequently, we tested retrospectively (2011-2017) and prospectively (2018-2019) patients who had been hospitalized with a similar clinico-biological picture. In addition, as these patients had been in contact with frugivorous bats (authorized under conditions for hunting and eating in New Caledonia) we investigated the role of these animals and their biting flies by testing them for hemotropic mycoplasmas.

Results: Fifteen patients were found to be infected by this hemotropic mycoplasma. Among them, four (27%) died following splenectomy performed for spontaneous spleen rupture, or to cure refractory autoimmune haemolytic anemia. The bacterium was cultivated from the patient's blood. The full genome of the Neocaledonian "Candidatus M. haemohominis" strain differed from that of a recently identified Japanese strain. Forty-six percent of 40 tested Pteropus bats and 100% of collected bat flies Cyclopodia horsfieldi (Nycteribiidae, Diptera) were positive. Human,bat and dipteran strains were highly similar.

Conclusions: The bacterium being widely distributed in bats, "Candidatus M. haemohominis" should be regarded as a potential cause of severe infections in humans.
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http://dx.doi.org/10.1093/cid/ciaa1648DOI Listing
October 2020

Host-virus interactions and defense mechanisms for giant viruses.

Ann N Y Acad Sci 2020 Oct 8. Epub 2020 Oct 8.

Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.

Giant viruses, with virions larger than 200 nm and genomes larger than 340 kilobase pairs, modified the now outdated perception of the virosphere. With virions now reported reaching up to 1.5 μm in size and genomes of up to 2.5 Mb encoding components shared with cellular life forms, giant viruses exhibit a complexity similar to microbes, such as bacteria and archaea. Here, we review interactions of giant viruses with their hosts and defense strategies of giant viruses against their hosts and coinfecting microorganisms or virophages. We also searched by comparative genomics for homologies with proteins described or suspected to be involved in defense mechanisms. Our search reveals that natural immunity and apoptosis seem to be crucial components of the host defense against giant virus infection. Conversely, giant viruses possess methods of hijacking host functions to counteract cellular antiviral responses. In addition, giant viruses may encode other unique and complex pathways to manipulate the host machinery and eliminate other competing microorganisms. Notably, giant viruses have evolved defense mechanisms against their virophages and they might trigger defense systems against other viruses through sequence integration. We anticipate that comparative genomics may help identifying genes involved in defense strategies of both giant viruses and their hosts.
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http://dx.doi.org/10.1111/nyas.14469DOI Listing
October 2020

Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates.

Microorganisms 2020 Oct 3;8(10). Epub 2020 Oct 3.

Aix Marseille Université, IRD, AP-HM, MEPHI, 13005 Marseille, France.

Long considered to be a consequence of human antibiotics use by deduction, antibiotic resistance mechanisms appear to be in fact a much older phenomenon as antibiotic resistance genes have previously been detected from millions of year-old permafrost samples. As these specimens guarantee the viability of archaic bacteria, we herein propose to apply the culturomics approach to recover the bacterial content of a Siberian permafrost sample dated, using the in situ-produced cosmogenic nuclide chlorine36 (Cl), at 2.7 million years to study the dynamics of bacterial evolution in an evolutionary perspective. As a result, we cultured and sequenced the genomes of 28 ancient bacterial species including one new species. To perform genome comparison between permafrost strains and modern isolates we selected 7 of these species (i.e., and ). We observed a high level of variability in genomic content with a percentage of shared genes in the core genomes ranging from 21.23% to 55.59%. In addition, the Single Nucleotide Polymorphism (SNP) comparison between permafrost and modern strains for the same species did not allow a dating of ancient strains based on genomic content. There were no significant differences in antibiotic resistance profiles between modern and ancient isolates of each species. Acquired resistance to antibiotics was phenotypically detected in all gram-negative bacterial species recovered from permafrost, with a significant number of genes coding for antibiotic resistance detected. Taken together, these findings confirm previously obtained data that antibiotic resistance predates humanity as most of antimicrobial agents are natural weapons used in inter-microbial conflicts within the biosphere.
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http://dx.doi.org/10.3390/microorganisms8101522DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7600834PMC
October 2020

Publisher Correction: Dramatic HIV DNA degradation associated with spontaneous HIV suppression and disease-free outcome in a young seropositive woman following her infection.

Sci Rep 2020 Sep 4;10(1):14829. Epub 2020 Sep 4.

IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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http://dx.doi.org/10.1038/s41598-020-70050-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7474091PMC
September 2020

How Tupanvirus Degrades the Ribosomal RNA of Its Amoebal Host? The Ribonuclease T2 Track.

Front Microbiol 2020 28;11:1691. Epub 2020 Jul 28.

Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, France.

Tupanviruses are giant viruses recently discovered in Brazil from extreme environments: (TPV-SL) and (TPV-DO). Unexpected features in Tupanviruses is the cytotoxic effect observed during infection, where the virus degrades the ribosomal RNA (rRNA) of its amoebal host. Interestingly, only TPV-SL causes this rRNA shutdown. We performed a genomic comparison of the two strains to determine potential modifications explaining the absence of rRNA degradation by TPV-DO. Whole genome comparisons were performed as well as more in-depth analysis at the gene level. We also calculated selective pressure on the orthologous genes between the two viruses. Our computational and evolutionary investigations revealed a potential target: a ribonuclease T2. These enzymes are known to be involved in cellular RNA catabolism such as in lysosomal degradation of rRNA. Our results suggest a functional ribonuclease localized in acid compartment closely related to ribonuclease T2 from eukaryotes. Silencing of the RNAse T2 gene of TPV-SL abolished its rRNA shutdown ability thereby correlating assumption to the experimental evidence. In conclusion, all our results pointed to RNAse T2 as a target for explaining the difference for rRNA degradation ability between both strains.
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http://dx.doi.org/10.3389/fmicb.2020.01691DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7399046PMC
July 2020

New Molecular Data on Filaria and its from Red Howler Monkeys () in French Guiana-A Preliminary Study.

Pathogens 2020 Jul 31;9(8). Epub 2020 Jul 31.

IRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix Marseille Univ, 19-21, Bd Jean Moulin, 13005 Marseille, France.

Previous studies have reported filarial parasites of the genus and from French Guiana monkeys, based on morphological taxonomy. In this study, we screened blood samples from nine howler monkeys () for the presence of filaria and DNA. The infection rates were 88.9% for filaria and 55.6% for wolbachiae. The molecular characterization, based on the gene of filariids, revealed that are infected with at least three species ( sp., sp. and an unidentified Onchocercidae species.). Since the and generic primers are not very effective at resolving co-infections, we developed ITS genus-specific PCRs for and genus. The results revealed coinfections in 75% of positives. The presence of sp. and sp. was also confirmed by the phylogenetic analysis of their associated . sp., which close to the species from the subgenus encountered in New World Monkeys, while sp. was identical to the strain circulating in French Guiana dogs. We propose a novel genus-specific qPCR. We applied it to screen for infection in howler monkeys and 66.7% were found to be positive. Our finding highlights the need for further studies to clarify the species diversity of neotropics monkeys by combining molecular and morphological features. The novel genus-specific qPCR assays could be an effective tool for the surveillance and characterization of this potential zoonosis.
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http://dx.doi.org/10.3390/pathogens9080626DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7460519PMC
July 2020

Methanobrevibacter smithii archaemia in febrile patients with bacteremia, including those with endocarditis.

Clin Infect Dis 2020 Jul 15. Epub 2020 Jul 15.

Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France.

Background: The spectrum of infections caused by the emerging opportunistic pathogens methanogens which escape routine detection remains to be described. To determine the prevalence of archaemia, we searched for methanogens in the blood of febrile patients using specific tools.

Methods: We conducted a prospective study at Institut Hospitalier Universitaire Méditerranée Infection, Marseille, France, September 2018 - April 2020, enrolling 7,716 blood culture samples routinely collected in patients with fever. Blood samples were screened by specific PCR assays for the presence of methanogens. Positive samples were observed by autofluorescence and electron microscopy, analyzed by metagenomics and cultured using previously developed methods. Blood culture bottles experimentally inoculated were used as controls. The presence of methanogens in vascular and cardiac tissues was assessed by indirect immunofluorescence, fluorescent in situ hybridization and PCR-based investigations.

Results: PCR detection attempted in 7,716 blood samples, was negative in all 1,312 aerobic bottles and 810 bacterial culture-negative anaerobic bottles. PCRs were positive in 27/5,594 (0.5%) bacterial culture-positive anaerobic bottles that contained cultures collected from 26 patients. Sequencing confirmed Methanobrevibacter smithii associated with staphylococci in 14 patients, fermentative Enterobacteriaceae in nine patients and streptococci in three patients. Metagenomics confirmed M. smithii in five blood samples, and M. smithii was isolated via culture in broth from two samples; the genomes of these two isolates were sequenced. Blood cultures experimentally inoculated with Enterobacteriaceae, Staphylococcus epidermidis or Staphylococcus hominis yielded hydrogen, but no methane, authentifying observational data.Three patients, all diagnosed with infectious mitral endocarditis, were diagnosed by microscopy, PCR-based detections and culture: we showed M. smithii microscopically and by a specific PCR followed by sequencing method in two of three cardiovascular tissues.

Conclusions: Using appropriate methods of detection, M. smithii is demonstrated as causing archaemia and endocarditis in febrile patients who are coinfected by bacteria.
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http://dx.doi.org/10.1093/cid/ciaa998DOI Listing
July 2020

Parasitic Infections in African Humans and Non-Human Primates.

Pathogens 2020 Jul 11;9(7). Epub 2020 Jul 11.

Aix Marseille Univ, IRD, AP-HM, MEPHI, 13385 Marseille, France.

Different protozoa and metazoa have been detected in great apes, monkeys and humans with possible interspecies exchanges. Some are either nonpathogenic or their detrimental effects on the host are not yet known. Others lead to serious diseases that can even be fatal. Their survey remains of great importance for public health and animal conservation. Fecal samples from gorillas () and humans living in same area in the Republic of Congo, chimpanzees () from Senegal and one other from the Republic of Congo, Guinea baboons ( from Senegal, hamadryas baboons () from Djibouti and Barbary macaques ) from Algeria, were collected. DNA was extracted and screened using specific qPCR assays for the presence of a large number of helminths and protozoa. Positive samples were then amplified in standard PCRs and sequenced when possible. Overall, infection rate was 36.5% in all non-human primates (NHPs) and 31.6% in humans. Great apes were more often infected (63.6%) than monkeys (7.3%). At least twelve parasite species, including ten nematodes and two protozoa were discovered in NHPs and five species, including four nematodes and a protozoan in humans. The prevalences of , were similar between gorillas and human community co-habiting the same forest ecosystem in the Republic of Congo. In addition, human specific (5.1%) and other spp. (5.1%) detected in these gorillas suggest a possible cross-species exchange. Low prevalence (2%) of were observed in chimpanzees, as well as a high prevalence of (57.1%), which should be considered carefully as this parasite can affect other NHPs, animals and humans. The Barbary macaques were less infected (7.2%) and was the main parasite detected (5.8%). Finally, we report the presence of sp. and an environmental Nematoda DNAs in chimpanzee feces, sp. and sp. in gorillas, as well as DNA of uncharacterized Nematoda in apes and humans, but with a relatively lower prevalence in humans. Prevalence of extraintestinal parasites remains underestimated since feces are not the suitable sampling methods. Using non-invasive sampling (feces) we provide important information on helminths and protozoa that can infect African NHPs and human communities living around them. Public health and animal conservation authorities need to be aware of these infections, as parasites detected in African NHPs could affect both human and other animals' health.
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http://dx.doi.org/10.3390/pathogens9070561DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7400533PMC
July 2020

Yaravirus: A novel 80-nm virus infecting .

Proc Natl Acad Sci U S A 2020 07 29;117(28):16579-16586. Epub 2020 Jun 29.

Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil;

Here we report the discovery of Yaravirus, a lineage of amoebal virus with a puzzling origin and evolution. Yaravirus presents 80-nm-sized particles and a 44,924-bp dsDNA genome encoding for 74 predicted proteins. Yaravirus genome annotation showed that none of its genes matched with sequences of known organisms at the nucleotide level; at the amino acid level, six predicted proteins had distant matches in the nr database. Complimentary prediction of three-dimensional structures indicated possible function of 17 proteins in total. Furthermore, we were not able to retrieve viral genomes closely related to Yaravirus in 8,535 publicly available metagenomes spanning diverse habitats around the globe. The Yaravirus genome also contained six types of tRNAs that did not match commonly used codons. Proteomics revealed that Yaravirus particles contain 26 viral proteins, one of which potentially representing a divergent major capsid protein (MCP) with a predicted double jelly-roll domain. Structure-guided phylogeny of MCP suggests that Yaravirus groups together with the MCPs of endemic viruses. Yaravirus expands our knowledge of the diversity of DNA viruses. The phylogenetic distance between Yaravirus and all other viruses highlights our still preliminary assessment of the genomic diversity of eukaryotic viruses, reinforcing the need for the isolation of new viruses of protists.
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http://dx.doi.org/10.1073/pnas.2001637117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368276PMC
July 2020

Klenkia terrae resistant to DNA extraction in germ-free mice stools illustrates the extraction pitfall faced by metagenomics.

Sci Rep 2020 06 23;10(1):10228. Epub 2020 Jun 23.

Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France, Marseille, France.

Over the past decade, metagenomics has become the preferred method for exploring complex microbiota such as human gut microbiota. However, several bias affecting the results of microbiota composition, such as those due to DNA extraction, have been reported. These bias have been confirmed with the development of culturomics technique. In the present study, we report the contamination of a gnotobiotic mice unit with a bacterium first detected by gram staining. Scanning electron microscopy and transmission electron microscopy permitted to detect a bacterium with a thick cell wall. However, in parallel, the first attempt to identify and culture this bacterium by gene amplification and metagenomics of universal 16S rRNA failed. Finally, the isolation in culture of a fastidious bacterium not detected by using universal PCR was successfully achieved by using a BCYE agar plate with CO atmosphere at 30 °C. We performed genome sequencing of this bacterium using a strong extraction procedure. The genomic comparison allowed us to classify this bacterium as Klenkia terrae. And finally, it was also detected in the stool and kibble that caused the contamination by using specific qPCR against this bacterium. The elucidation of this contamination provides additional evidence that DNA extraction could be a bias for the study of the microbiota. Currently, most studies that strive to analyze and compare the gut microbiota are based on metagenomics. In a gnotobiotic mice unit contaminated with the fastidious Actinobacteria Klenkia terrae, standard culture, 16S rRNA gene amplification and metagenomics failed to identify the micro-organism observed in stools by gram-staining. Only a procedure based on culturomics allowed us to identify this bacterium and to elucidate the mode of contamination of the gnotobiotic mice unit through diet.
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http://dx.doi.org/10.1038/s41598-020-66627-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7311423PMC
June 2020

Adenovirus Infections in African Humans and Wild Non-Human Primates: Great Diversity and Cross-Species Transmission.

Viruses 2020 06 18;12(6). Epub 2020 Jun 18.

IHU Méditerranée Infection, 13385 Marseille CEDEX 05, France.

Non-human primates (NHPs) are known hosts for adenoviruses (AdVs), so there is the possibility of the zoonotic or cross-species transmission of AdVs. As with humans, AdV infections in animals can cause diseases that range from asymptomatic to fatal. The aim of this study was to investigate the occurrence and diversity of AdVs in: (i) fecal samples of apes and monkeys from different African countries (Republic of Congo, Senegal, Djibouti and Algeria), (ii) stool of humans living near gorillas in the Republic of Congo, in order to explore the potential zoonotic risks. Samples were screened by real-time and standard PCRs, followed by the sequencing of the partial DNA polymerase gene in order to identify the AdV species. The prevalence was 3.3 folds higher in NHPs than in humans. More than 1/3 (35.8%) of the NHPs and 1/10 (10.5%) of the humans excreted AdVs in their feces. The positive rate was high in great apes (46%), with a maximum of 54.2% in chimpanzees () and 35.9% in gorillas (), followed by monkeys (25.6%), with 27.5% in Barbary macaques () and 23.1% in baboons (seven and six ). No green monkeys () were found to be positive for AdVs. The AdVs detected in NHPs were members of (HAdV-E), HAdV-C or HAdV-B, and those in the humans belonged to HAdV-C or HAdV-D. HAdV-C members were detected in both gorillas and humans, with evidence of zoonotic transmission since phylogenetic analysis revealed that gorilla AdVs belonging to HAdV-C were genetically identical to strains detected in humans who had been living around gorillas, and, inversely, a HAdV-C member HAdV type was detected in gorillas. This confirms the gorilla-to-human transmission of adenovirus. which has been reported previously. In addition, HAdV-E members, the most often detected here, are widely distributed among NHP species regardless of their origin, i.e., HAdV-E members seem to lack host specificity. Virus isolation was successful from a human sample and the strain of the Mbo024 genome, of 35 kb, that was identified as belonging to HAdV-D, exhibited close identity to HAdV-D members for all genes. This study provides information on the AdVs that infect African NHPs and the human populations living nearby, with an evident zoonotic transmission. It is likely that AdVs crossed the species barrier between different NHP species (especially HAdV-E members), between NHPs and humans (especially HAdV-C), but also between humans, NHPs and other animal species.
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http://dx.doi.org/10.3390/v12060657DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7354429PMC
June 2020

Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus.

DNA Res 2020 Apr;27(2)

INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.

White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here, we combined comparative genomics, transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood-decaying activity within the Basidiomycota genus Pycnoporus. We observed a strong conservation in the genome structures and the repertoires of protein-coding genes across the four Pycnoporus species described to date, despite the species having distinct geographic distributions. We further analysed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin. The co-occurrence in the exo-proteomes of H2O2-producing enzymes with H2O2-consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 lytic polysaccharide monooxygenase gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood-decaying process.
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http://dx.doi.org/10.1093/dnares/dsaa011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7406137PMC
April 2020

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

Travel Med Infect Dis 2020 May - Jun;35:101738. Epub 2020 May 5.

IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ., IRD, AP-HM, MEPHI, Marseille, France. Electronic address:

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.
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http://dx.doi.org/10.1016/j.tmaid.2020.101738DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7199729PMC
July 2020

Vermamoeba vermiformis CDC-19 draft genome sequence reveals considerable gene trafficking including with candidate phyla radiation and giant viruses.

Sci Rep 2020 04 3;10(1):5928. Epub 2020 Apr 3.

Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEPHI); Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 27 boulevard Jean Moulin, 13005, Marseille, France.

Vermamoeba vermiformis is a predominant free-living amoeba in human environments and amongst the most common amoebae that can cause severe infections in humans. It is a niche for numerous amoeba-resisting microorganisms such as bacteria and giant viruses. Differences in the susceptibility to these giant viruses have been observed. V. vermiformis and amoeba-resisting microorganisms share a sympatric lifestyle that can promote exchanges of genetic material. This work analyzed the first draft genome sequence of a V. vermiformis strain (CDC-19) through comparative genomic, transcriptomic and phylogenetic analyses. The genome of V. vermiformis is 59.5 megabase pairs in size, and 22,483 genes were predicted. A high proportion (10% (n = 2,295)) of putative genes encoded proteins showed the highest sequence homology with a bacterial sequence. The expression of these genes was demonstrated for some bacterial homologous genes. In addition, for 30 genes, we detected best BLAST hits with members of the Candidate Phyla Radiation. Moreover, 185 genes (0.8%) best matched with giant viruses, mostly those related to the subfamily Klosneuvirinae (101 genes), in particular Bodo saltans virus (69 genes). Lateral sequence transfers between V. vermiformis and amoeba-resisting microorganisms were strengthened by Sanger sequencing, transcriptomic and phylogenetic analyses. This work provides important insights and genetic data for further studies about this amoeba and its interactions with microorganisms.
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http://dx.doi.org/10.1038/s41598-020-62836-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7125106PMC
April 2020

Case Report: Biliary Tract Infections in Two North Africans in France.

Am J Trop Med Hyg 2020 06;102(6):1306-1308

IHU-Méditerranée Infection, Marseille, France.

The origin of a cholera outbreak may be unclear, as recently in Algeria. In two patients from North Africa, was isolated in the context of hepatobiliary tract infections without any known outbreak. Gallbladder and asymptomatic long-term carriers might play a role in the emergence of cholera.
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http://dx.doi.org/10.4269/ajtmh.19-0884DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7253139PMC
June 2020

Full-length title: Dramatic HIV DNA degradation associated with spontaneous HIV suppression and disease-free outcome in a young seropositive woman following her infection.

Sci Rep 2020 02 13;10(1):2548. Epub 2020 Feb 13.

IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.

Strategies to cure HIV-infected patients by virus-targeting drugs have failed to date. We identified a HIV-1-seropositive woman who spontaneously suppressed HIV replication and had normal CD4-cell counts, no HIV-disease, no replication-competent virus and no cell HIV DNA detected with a routine assay. We suspected that dramatic HIV DNA degradation occurred post-infection. We performed multiple nested-PCRs followed by Sanger sequencing and applied a multiplex-PCR approach. Furthermore, we implemented a new technique based on two hybridization steps on beads prior to next-generation sequencing that removed human DNA then retrieved integrated HIV sequences with HIV-specific probes. We assembled ≈45% of the HIV genome and further analyzed the G-to-A mutations putatively generated by cellular APOBEC3 enzymes that can change tryptophan codons into stop codons. We found more G-to-A mutations in the HIV DNA from the woman than in that of her transmitting partner. Moreover, 74% of the tryptophan codons were changed to stop codons (25%) or were deleted as a possible consequence of gene inactivation. Finally, we found that this woman's cells remained HIV-susceptible in vitro. Our findings show that she does not exhibit innate HIV-resistance but may have been cured of it by extrinsic factors, a plausible candidate for which is the gut microbiota.
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http://dx.doi.org/10.1038/s41598-020-58969-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7018955PMC
February 2020

Isolation and genomic characterization of a new mimivirus of lineage B from a Brazilian river.

Arch Virol 2020 Apr 12;165(4):853-863. Epub 2020 Feb 12.

Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.

Since its discovery, the first identified giant virus associated with amoebae, Acanthamoeba polyphaga mimivirus (APMV), has been rigorously studied to understand the structural and genomic complexity of this virus. In this work, we report the isolation and genomic characterization of a new mimivirus of lineage B, named "Borely moumouvirus". This new virus exhibits a structure and replicative cycle similar to those of other members of the family Mimiviridae. The genome of the new isolate is a linear double-strand DNA molecule of ~1.0 Mb, containing over 900 open reading frames. Genome annotation highlighted different translation system components encoded in the DNA of Borely moumouvirus, including aminoacyl-tRNA synthetases, translation factors, and tRNA molecules, in a distribution similar to that in other lineage B mimiviruses. Pan-genome analysis indicated an increase in the genetic arsenal of this group of viruses, showing that the family Mimiviridae is still expanding. Furthermore, phylogenetic analysis has shown that Borely moumouvirus is closely related to moumouvirus australiensis. This is the first mimivirus lineage B isolated from Brazilian territory to be characterized. Further prospecting studies are necessary for us to better understand the diversity of these viruses so a better classification system can be established.
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http://dx.doi.org/10.1007/s00705-020-04542-5DOI Listing
April 2020

Core gene-based molecular detection and identification of Acanthamoeba species.

Sci Rep 2020 01 31;10(1):1583. Epub 2020 Jan 31.

Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 19-21 boulevard Jean Moulin, 13005, Marseille, France.

Acanthamoeba spp. are predominant free-living amoebae of water and soil. They have been used as tools for the isolation and culture of microbes that resist after their phagocytosis, such as Legionella-like bacteria, and, more recently giant viruses for which differences in permissiveness have been reported. However, problems have been reported regarding their identification at the species level. The present work implemented specific PCR systems for the detection and identification of Acanthamoeba species through comparison of sequences and phylogenetic analyses. Thirty-three Acanthamoeba isolates were studied, including 20 reference strains and 13 isolates retrieved from water, soil or clinical samples. Previous delineation of a core genome encompassing 826 genes based on draft genome sequences from 14 Acanthamoeba species allowed designing PCR systems for one of these core genes that encodes an alanine-tRNA ligase. These primers allowed an efficient and specific screening to detect Acanthamoeba presence. In addition, they identified all 20 reference strains, while partial and complete sequences coding for 18S ribosomal RNA identified only 11 (55%). We found that four isolates may be considered as new Acanthamoeba species. Consistent with previous studies, we demonstrated that some Acanthamoeba isolates were incorrectly assigned to species using the 18S rDNA sequences. Our implemented tool may help determining which Acanthamoeba strains are the most efficient for the isolation of associated microorganisms.
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http://dx.doi.org/10.1038/s41598-020-57998-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6994504PMC
January 2020

Culture of Methanogenic Archaea from Human Colostrum and Milk.

Sci Rep 2019 12 9;9(1):18653. Epub 2019 Dec 9.

IHU-Méditerranée Infection, Marseille, France.

Archaeal sequences have been detected in human colostrum and milk, but no studies have determined whether living archaea are present in either of these fluids. Methanogenic archaea are neglected since they are not detected by usual molecular and culture methods. By using improved DNA detection protocols and microbial culture techniques associated with antioxidants previously developed in our center, we investigated the presence of methanogenic archaea using culture and specific Methanobrevibacter smithii and Methanobrevibacter oralis real-time PCR in human colostrum and milk. M. smithii was isolated from 3 colostrum and 5 milk (day 10) samples. M. oralis was isolated from 1 milk sample. For 2 strains, the genome was sequenced, and the rhizome was similar to that of strains previously isolated from the human mouth and gut. M. smithii was detected in the colostrum or milk of 5/13 (38%) and 37/127 (29%) mothers by culture and qPCR, respectively. The different distribution of maternal body mass index according to the detection of M. smithii suggested an association with maternal metabolic phenotype. M. oralis was not detected by molecular methods. Our results suggest that breastfeeding may contribute to the vertical transmission of these microorganisms and may be essential to seed the infant's microbiota with these neglected critical commensals from the first hour of life.
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http://dx.doi.org/10.1038/s41598-019-54759-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6901439PMC
December 2019

Extensive culturomics of 8 healthy samples enhances metagenomics efficiency.

PLoS One 2019 21;14(10):e0223543. Epub 2019 Oct 21.

Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France.

Molecular approaches have long led to the assumption that the human gut microbiota is dominated by uncultivable bacteria. The recent advent of large-scale culturing methods, and in particular that of culturomics have demonstrated that these prokaryotes can in fact be cultured. This is increasing in a dramatic manner the repertoire of commensal microbes inhabiting the human gut. Following eight years of culturomics approach applied on more than 900 samples, we propose herein a remake of the pioneering study applying a dual approach including culturomics and metagenomics on a cohort of 8 healthy specimen. Here we show that culturomics enable a 20% higher richness when compared to molecular approaches by culturing 1 archaeal species and 494 bacterial species of which 19 were new taxa. Species discovered as a part of previous culturomics studies represent 30% of the cultivated isolates, while sequences derived from these new taxa enabled to increase by 22% the bacterial richness retrieved by metagenomics. Overall, 67% of the total reads generated were covered by cultured isolates, significantly reducing the hidden content of sequencing methods compared to the pioneering study. By redefining culture conditions to recover microbes previously considered fastidious, there are greater opportunities than ever to eradicate metagenomics dark matter.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223543PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6802823PMC
March 2020