Incidental diagnosis of mpox virus infection in patients undergoing sexually transmitted infection screening-findings from a study in France

OBJECTIVES

This study aimed to investigate the prevalence of mpox virus (MPXV) infections in the general population consulting for routine sexually transmitted infections (STIs) in our Marseille public hospital. In fact, the recent worldwide MPXV outbreak mainly impacted men who have sex with men and the prevalence of MPXV infections in the general population remains poorly defined.

METHODS

All samples addressed routinely to our microbiological laboratory for STIs between July 1 and October 15, 2022 were screened with MPXV-specific quantitative polymerase chain reaction.

RESULTS

A total of 2688 samples from 1896 patients suspected of having STIs were tested and eight (0.4%) patients were incidentally diagnosed with MPXV infection, including six men and two women. MPXV was detected in rectal swabs (n = 2), urine (n = 2), vaginal swabs (n = 2), a urethral swab (n = 1), and a skin swab (n = 1).

CONCLUSIONS

This study suggests that some MPXV infections are likely to be underdiagnosed because of their non-specific clinical presentation and/or insufficient clinical knowledge of the disease. Our data showed that systematic screening was particularly useful for detecting MPXV in patients without classic lesions or cases of asymptomatic carriage in patients reporting recent high-risk exposure and in patients presenting no obvious risk factor.

Molecular detection and MST genotyping of Coxiella burnetii in ruminants and stray dogs and cats in Northern Algeria

Aiming at identifying the reservoir and contamination sources of Coxiella burnetii in Northern Algeria, we investigated the molecular presence of the bacterium in 599 samples (blood, placenta, liver, spleen, and uterus) collected from cattle, sheep, dogs and cats. Our qPCR results showed that 15/344 (4.36%) blood samples and six/255 (2.35%) organ specimens were positive for C. burnetii. In cattle, three (4%) blood and liver samples were positive. In sheep, one blood (1.19%) and 3 (8.57%) placenta samples were positive. At the Algiers dog pound, 8 (10%) and 3 (5%) blood samples were qPCR positivein dogs and cats, respectively. In addition, MST genotyping showed that MST 33 was present in cattle and sheep, MST 20 in cattle,andMST 21 in dogs and cats.

Judicial Opinion 129

Opinion 129 addresses the status of Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980). The name has the category 'division' and was included in the Approved Lists of Bacterial Names, although that category had previously been removed from the International Code of Nomenclature of Bacteria (1975 revision onwards). When the category 'phylum' was introduced into the International Code of Nomenclature of Prokaryotes (ICNP) in 2021, equivalence between 'phylum' and 'division' was not stipulated. Since the definition of the taxonomic categories and their relative order is one of the principal tasks of every code of nomenclature, the inclusion of Firmicutes corrig. Gibbons and Murray 1978 in the Approved Lists was an error. The name is either not validly published or illegitimate because its category is not covered by the ICNP. If Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980) was a validly published phylum name, it would be illegitimate because it would contravene Rule 8, which does not permit any deviation from the requirement to derive a phylum name from the name of the type genus. Since Firmicutes corrig. Gibbons and Murray 1978 is also part of a 'misfitting megaclassification' recognized in Opinion 128, the name is rejected, without any pre-emption regarding a hypothetically validly published name Firmicutes at the rank of phylum. Gracilicutes Gibbons and Murray 1978 (Approved Lists 1980) and Anoxyphotobacteriae Gibbons and Murray 1978 (Approved Lists 1980) are also rejected. The validly published phylum names have a variety of advantages over their not validly published counterparts and cannot be replaced with ad hoc names suggested in the literature. To ease the transition, it is recommended to mention the not validly published phylum names which strongly deviate in spelling from their validly published counterparts along with the latter in publications during the next years.

Hidden Burden of Bartonella quintana on the African Continent: Should the Bacterial Infection Be Considered a Neglected Tropical Disease?

Bartonella quintana is a louse-borne gram-negative bacillus that remains a poorly characterized cause of bacteremia, fever, and infective endocarditis. Due to the link with pediculosis, B quintana transmission is tied to poverty, conflict, overcrowding, and inadequate water access to maintain personal hygiene. Although these risk factors may be present globally, we argue that a substantial burden of undocumented B quintana infection occurs in Africa due to the high prevalence of these risk factors. Here, we describe the neglected burden of B quintana infection, endocarditis, and vector positivity in Africa and evaluate whether B quintana meets criteria to be considered a neglected tropical disease according to the World Health Organization.

COVID-19 in 16 West African Countries: An Assessment of the Epidemiology and Genetic Diversity of SARS-CoV-2 after Four Epidemic Waves

West Africa faced the COVID-19 pandemic in early March 2020 and, as of March 31, 2022, had more than 900,000 confirmed cases and more than 12,000 deaths. During this period, SARS-CoV-2 genomes evolved genetically, resulting in the emergence of distinct lineages. This review was conducted to provide the epidemiological profile of COVID-19, the mutational profile of SARS-CoV-2, and the dynamics of its lineages in the 16 west African countries by analyzing data from 33 studies and seven situation reports. For a more complete representation of the epidemiology and genetic diversity of SARS-CoV-2, we used reliable public data in addition to eligible studies. As of March 31, 2022, the 16 west African countries experienced four epidemic waves with variable intensities. Higher mortality was noted during the third wave with a case fatality rate (CFR) of 1.9%. After these four epidemic waves, Liberia recorded the highest CFR (4.0%), whereas Benin had the lowest CFR (0.6%). Through mutational analysis, a high genetic heterogeneity of the genomes was observed, with a predominance of mutations in the spike protein. From this high mutational rate, different lineages emerged. Our analysis of the evolutionary diversity allowed us to count 205 lineages circulating in west Africa. This study has provided a good representation of the mutational profile and the prevalence of SARS CoV-2 lineages beyond the knowledge of the global epidemiology of the 16 African countries.

Case series of 12 Bartonella quintana endocarditis from the Southwest Indian Ocean

BACKGROUND

Bartonella spp. are fastidious bacteria frequently identified as the cause of blood culture-negative (BCN) endocarditis. However, Bartonella infections are difficult to diagnose in routine laboratory testing and their incidence is probably underestimated. We investigated the epidemiological and clinical features of Bartonella endocarditis cases diagnosed between 2009 and 2021 on Reunion Island (Southwest Indian Ocean).

METHOD

We retrospectively included all patients diagnosed with Bartonella endocarditis at Reunion Island University Hospital during this period. Endocarditis was diagnosed on the basis of microbiological findings, including serological tests (IFA) and PCR on cardiac valves, and the modified Duke criteria. We used then the multispacer typing (MST) method to genotype the available Bartonella strains.

FINDINGS

We report 12 cases of B. quintana endocarditis on Reunion Island (83.3% in men, median patient age: 32 years). All the patients originated from the Comoros archipelago. The traditional risk factors for B. quintana infection (homelessness, alcoholism, exposure to body lice) were absent in all but two of the patients, who reported head louse infestations in childhood. Previous heart disease leading to valve dysfunction was recorded in 50% of patients. All patients underwent cardiac valve surgery and antimicrobial therapy with a regimen including doxycycline. All patients presented high C-reactive protein concentrations, anemia and negative blood cultures. The titer of IgG antibodies against Bartonella sp. exceeded 1:800 in 42% of patients. Specific PCR on cardiac valves confirmed the diagnosis of B. quintana endocarditis in all patients. Genotyping by the MST method was performed on four strains detected in preserved excised valves and was contributive for three, which displayed the MST6 genotype.

CONCLUSIONS

Bartonella quintana is an important cause of infective endocarditis in the Comoros archipelago and should be suspected in patients with mitral valve dysfunction and BCN from this area.

Coxiella burnetii Femoro-Popliteal Bypass Infection: A Case Report

Cardiovascular infections are the most severe and potentially lethal among the persistent focalized Coxiella burnetii infections. While aortic infections on aneurysms or prostheses are well-known, with specific complications (risk of fatal rupture), new non-aortic vascular infections are increasingly being described thanks to the emerging use of 18-fluorodeoxyglucose positron emission tomography (18F-FDG PET-scan). Here, we describe an infection of a femoro-popliteal bypass that would not have been diagnosed without the use of PET-scan. It is well-known that vascular prosthetic material is a site favorable for bacterial persistence, but the description of unusual anatomical sites, outside the heart or aorta, should raise the clinicians' awareness and generalize the indications for PET-scan, with careful inclusion of the upper and lower limbs (not included in PET-scan for cancer), particularly in the presence of vascular prostheses. Future studies will be needed to precisely determine their optimal management.

Description of Streptococcus thalassemiae sp. nov., a Bacterium Isolated from Human Blood

Blood is a precious biological liquid that is normally sterile. Therefore, bacteria in the bloodstream are shown a priori anomaly. A blood culture is systematically performed to diagnose the cause of the bacteremia. Indeed, a patient received in our service had a thalassemia major and underwent a genoidentical transplant. Then, a blood test was performed to diagnose a four-day fever. In this context, we have isolated strain Marseille-Q2617 from the blood sample. It revealed a new bacterial strain that belongs to the genus Streptococcus. It is a Gram-positive coccus, nonmotile, and nonspore forming. The major fatty acid found is hexadecanoic acid, with 49.5%. A taxonomic method was used to characterize the strain by studying their phenotypic, phylogenetic, and genomic characteristics. In addition, sequence analysis of the 16S rRNA gene shows that the strain Marseille-Q2617 has 99.94% sequence similarity to Streptococcus mitis. Average nucleotide identity (ANI) analysis for strain Marseille-Q2617T showed the highest similarity of 92.9% with S. mitis. The DNA-DNA hybridization value obtained (50.2%) between strain Marseille-Q2607 and S. mitis, its closest related species, was below the recommended threshold (<70%). Strain Marseille-Q2617T has a genome size of 2.02 Mbp with 40.5 mol% of G + C content. Based on these results, we propose a new species of the genus Streptococcus, for which the name Streptococcus thalassemiae sp. nov., Marseille-Q2617T (=CSUR Q2617 = CECT 30109) was proposed.

Taxonogenomics of Culturomica massiliensis gen. nov., sp. nov., and Emergencia timonensis gen. nov., sp. nov. new bacteria isolated from human stool microbiota

Two new bacterial strains, Marseille-P2698^T (CSUR P2698 = DSM 103,121) and Marseille-P2260^T (CSUR P2260 = DSM 101,844 = SN18), were isolated from human stools by the culturomic method. We used the taxonogenomic approach to fully describe these two new bacterial strains. The Marseille-P2698^T strain was a Gram-negative, motile, non-spore-forming, rod-shaped bacterium. The Marseille-P2260^T strain was a Gram-positive, motile, spore-forming rod-shaped bacterium. Major fatty acids found in Marseille-P2698^T were C_{15:0 iso} (63%), C_{15:0 anteiso} (11%), and C_{17:0 3-OH iso} (8%). Those found in Marseille-P2260^T strain were C_16:00 (39%), C_18:1n9 (16%) and C_18:1n7 (14%). Strains Marseille-P2698^T and Marseille-P2260^T had 16S rRNA gene sequence similarities of 91.50% with Odoribacter laneus^T, and of 90.98% and 95.07% with Odoribacter splanchnicus^T and Eubacterium sulci^T, respectively. The exhibited digital DNA-DNA Hybridization values lower than 20.7%, and Orthologous Average Nucleotide Identity values lower than 73% compared to their closest related bacterial species O. splanchnicus^T and E. sulci^T respectively. Phenotypic, biochemical, phylogenetic, and genomic results obtained by comparative analyses provided sufficient evidence that both of the two studied strains Marseille-P2698^T and Marseille-P2260^T are two new bacterial species and new bacterial genera for which the names Culturomica massiliensis gen. nov., sp. nov., and Emergencia timonensis gen. nov., sp. nov. were proposed, respectively.

Genomic Epidemiology of SARS-CoV-2 in Urban Settings in Senegal

We used whole genome sequencing to identify and analyze mutations in SARS-CoV-2 in urban settings during the deadliest wave of the COVID-19 epidemic-from March to April 2021-in Senegal. Nasopharyngeal samples testing positive for SARS-CoV-2 were sequenced on the Illumina NovaSeq 6000 sequencing system using the COVIDSeq protocol. A total of 291 genotypable consensus genome sequences were obtained. Phylogenetic analyses grouped the genomes into 16 distinct PANGOLIN lineages. The major lineage was B.1.1.420, despite circulation of the Alpha variant of concern (VOC). A total of 1125 different SNPs, identified relative to the Wuhan reference genome, were detected. These included 13 SNPs in non-coding regions. An average density of 37.2 SNPs per 1000 nucleotides was found, with the highest density occurring in ORF10. This analysis allowed, for the first time, the detection of a Senegalese SARS-CoV-2 strain belonging to the P.1.14 (GR/20J, Gamma V3) sublineage of the Brazilian P.1 lineage (or Gamma VOC). Overall, our results highlight substantial SARS-CoV-2 diversification in Senegal during the study period.

Maliibacterium massiliense gen. nov. sp. nov., Isolated from Human Feces and Proposal of Maliibacteriaceae fam. nov

Bacterial strain Marseille-P3954 was isolated from a stool sample of a 35-year-old male patient living in France. It was a gram-positive, rod-shaped anaerobic, non-motile, and non-spore-forming bacterium. C_16:0 and C_18:1n9 were the major fatty acid, while its genome measured 2,422,126 bp with 60.8 mol% of G+C content. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain Marseille-P3954 had 85.51% of similarity with Christensenella minuta, its closest related species with standing in nomenclature. As this value is very low compared to the recommended threshold, it suggested that the Marseille-P3954 strain belongs to a new bacterial genus, classified in a new family. On the basis of these genomic, phenotypic, and phylogenetic evidences, we propose that strain Marseille-P3954 should be classified as a new genus and species, Maliibacterium massiliense gen. nov., sp. nov. The type strain of M. massiliense sp. nov. is Marseille-P3954 (CSUR P3954 = CECT 9568).

New Genotype of Coxiella burnetii Causing Epizootic Q Fever Outbreak in Rodents, Northern Senegal

In Senegal, Coxiella burnetii, which causes Q fever, has often been identified in ticks and humans near livestock, which are considered to be reservoirs and main sources of infection. We describe the emergence of C. burnetii in rodents, not previously known to carry this pathogen, and describe 2 new genotypes.

Tracking the Source of Human Q Fever from a Southern French Village: Sentinel Animals and Environmental Reservoir

Coxiella burnetii, also known as the causal agent of Q fever, is a zoonotic pathogen infecting humans and several animal species. Here, we investigated the epidemiological context of C. burnetii from an area in the Hérault department in southern France, using the One Health paradigm. In total, 13 human cases of Q fever were diagnosed over the last three years in an area comprising four villages. Serological and molecular investigations conducted on the representative animal population, as well as wind data, indicated that some of the recent cases are likely to have originated from a sheepfold, which revealed bacterial contamination and a seroprevalence of 47.6%. However, the clear-cut origin of human cases cannot be ruled out in the absence of molecular data from the patients. Multi-spacer typing based on dual barcoding nanopore sequencing highlighted the occurrence of a new genotype of C. burnetii. In addition, the environmental contamination appeared to be widespread across a perimeter of 6 km due to local wind activity, according to the seroprevalence detected in dogs (12.6%) and horses (8.49%) in the surrounding populations. These findings were helpful in describing the extent of the exposed area and thus supporting the use of dogs and horses as valuable sentinel indicators for monitoring Q fever. The present data clearly highlighted that the epidemiological surveillance of Q fever should be reinforced and improved.

Bacterial Agents Detected in 418 Ticks Removed from Humans during 2014-2021, France

Monitoring of tickborne diseases is critical for prevention and management. We analyzed 418 ticks removed from 359 patients during 2014-2021 in Marseille, France, for identification and bacteria detection. Using morphology, molecular methods, or matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, we identified 197 (47%) Ixodes, 136 (33%) Dermacentor, 67 (16%) Rhipicephalus, 8 (2%) Hyalomma, 6 (1%) Amblyomma, 2 (0.5%) Argas, and 2 (0.5%) Haemaphysalis tick species. We also detected bacterial DNA in 241 (58%) ticks. The most frequent bacterial pathogens were Rickettsia raoultii (17%) and R. slovaca (13%) in Dermacentor ticks, Borrelia spp. (9%) in Ixodes ticks, and R. massiliae (16%) in Rhipicephalus ticks. Among patients who were bitten, 107 had symptoms, and tickborne diseases were diagnosed in 26, including scalp eschar and neck lymphadenopathy after tick bite and Lyme borrelioses. Rapid tick and bacteria identification using a combination of methods can substantially contribute to clinical diagnosis, treatment, and surveillance of tickborne diseases.

Clinical and biological diagnosis and follow-up of patients treated for endovascular infections due to Coxiellaburnetii

The objective of this study was to evaluate the effectiveness of the recommended treatment for endovascular infections due to Coxiella burnetii. This single-center retrospective study was conducted in 13 patients with endovascular infection due to C. burnetii between January 2001 and December 2020 for a definite or possible endovascular infection due to C. burnetii with a minimum follow-up of 18 months post-infection. Clinical and biological data, including serology, blood and tissue PCR results, doxycycline and hydroxychloroquine assays were collected. Among the 13 patients, 11 had endocarditis (8 definite and 3 possible) and 2 had a vascular infection. At the time of diagnosis, fever was present in only 46% of cases. In case of endocarditis, 73% of patients had a pathological echocardiography. Biologically, the CRP level was low (52 mg/l ± 44). Autoimmune antibodies (antinuclear factor, neutrophil anticytoplasm) were present in 23% of patients. At the time of diagnosis, tissue PCR was very sensitive (100%) unlike blood or serum (29%). Blood levels of doxycycline and hydroxychloroquine were within expected values. Only one patient experienced treatment failure at two years, requiring surgery. For the 7 patients whose phase I IgG titres fell below 1/800, a minimum of 18 months of treatment was necessary. In the long term, the clinical and biological cure was 100% and 92% respectively, underlining the importance of monitoring the serum dosages of doxycycline and hydroxychloroquine. Given its sensitivity, tissue PCR could be added to the major Duke criteria.

Judicial Opinion 128

Judicial Opinion 128 addresses nomenclatural issues related to the names of classes validly published under the International Code of Nomenclature of Prokaryotes. It is confirmed that the common ending -proteobacteria of some class names is not indicative of a joint taxonomic or phylogenetic placement; that the nomenclatural type of Mollicutes Edward and Freundt 1967 (Approved Lists 1980) is Mycoplasmatales Freundt 1955 (Approved Lists 1980); and that the placement of a name on the list of rejected names does not imply that another name with the same spelling but a distinct rank is also placed on that list. The names at the rank of class Anoxyphotobacteria (Gibbons and Murray 1978) Murray 1988, Archaeobacteria Murray 1988, Bacteria Haeckel 1894 (Approved Lists 1980), Firmibacteria Murray 1988, Microtatobiotes Philip 1956 (Approved Lists 1980), Oxyphotobacteria (ex Gibbons and Murray 1978) Murray 1988, Photobacteria Gibbons and Murray 1978 (Approved Lists 1980), Proteobacteria Stackebrandt et al. 1988, Schizomycetes Nägeli 1857 (Approved Lists 1980), Scotobacteria Gibbons and Murray 1978 (Approved Lists 1980) are placed on the list of rejected names. For three common nominative singular suffixes of genus names their genitive singular and nominative plural forms are confirmed: -bacter (-bacteris, -bacteres); -fex (-ficis, -fices); and -genes (-genis, -genes). The class names Aquificae Reysenbach 2002, Chrysiogenetes Garrity and Holt 2002, Chthonomonadetes Lee et al. 2011, Gemmatimonadetes Zhang et al. 2003, Opitutae Choo et al. 2007 and Verrucomicrobiae Hedlund et al. 1998 are orthographically corrected to Aquificia, Chrysiogenia, Chthonomonadia, Gemmatimonadia, Opitutia and Verrucomicrobiia, respectively.

Guidelines for interpreting the International Code of Nomenclature of Prokaryotes and for preparing a Request for an Opinion

In this paper the Judicial Commission provides general guidance for interpreting the International Code of Nomenclature of Prokaryotes (ICNP) and specific assistance to authors, reviewers and editors of a Request for an Opinion, or of other suggestions related to the ICNP. The role of the Judicial Commission is recapitulated, particularly with respect to the processing of such Requests. Selected kinds of nomenclature-related proposals are discussed that are unsuitable as the basis for a Request. Particular emphasis is put on Requests for placing names or epithets on the list of nomina rejicienda, and a dichotomous identification key is provided to guide potential authors of a Request that targets the name of a species or subspecies because of issues with its type strain. To this end, the criteria for the valid publication of such names under the ICNP are revisited. Aspects of other kinds of Requests are also addressed. The study is based on a comprehensive review of all Judicial Opinions issued since the publication of the Approved Lists in 1980. One goal of this paper is to assist potential authors in deciding whether their concern should be the subject of a Request, and if so, in composing it with the greatest chance of success. It is also clarified how to obtain additional help regarding nomenclature-related issues.

Mycoplasma haemohominis as a cause of fever of unknown origin in a traveller

Candidatus mycoplasma haemohominis (cMh) is the most human-adapted and lethal haemoplasma. Bats are the common reservoir worldwide. cMh should be suspected in fever of unknown origin associated with splenomegaly, and haemolytic anaemia or haemophagocytic lymphohistiocytosis, above all in Asia Pacific travellers. Doxycycline should  be started preemptively as diagnosis can be retrospectively confirmed.

Carbonyl Cyanide 3-Chloro Phenyl Hydrazone (CCCP) Restores the Colistin Sensitivity in Brucella intermedia

Brucella intermedia (formerly Ochrobactrum intermedium), a non-fermentative bacterium, has been isolated from animals and human clinical specimens. It is naturally resistant to polymyxins, including colistin (CO), and may cause opportunistic infections in humans. We isolated six Brucella intermedia strains from Senegalese monkey stool. In order to determine whether an efflux pump mechanism was involved in CO resistance in B. intermedia, we evaluated the effects of verapamil (VRP), reserpine (RSP), phe-arg β-naphthylamide dihydrochloride (PAβN) and carbonyl cyanide 3-chloro phenyl hydrazone (CCCP), four efflux pump inhibitors, on these colistin-resistant strains. Using the broth microdilution method, a CO and CCCP combination of 2 µg/mL and 10 µg/mL, respectively, significantly reduced the CO minimal inhibitory concentration (MIC) of B. intermedia, supporting an efflux pump mechanism. In contrast, VRP, PAβN and RSP did not restore CO susceptibility. A time kill assay showed a bactericidal effect of the CO-CCCP combination. Genomic analysis revealed a potential implication in the CO resistance mechanism of some conserved efflux pumps, such as YejABEF, NorM and EmrAB, as previously reported in other bacteria. An inhibitory effect of the CO-CCCP combination was observed on biofilm formation using the crystal violet method. These results suggest that the intrinsic CO resistance in Brucella intermedia is linked to an efflux pump mechanism and that the synergistic effect of CO-CCCP may open a new field to identify new treatments to restore antibiotic efficacy in humans.

Observational Cohort Study of Evolving Epidemiologic, Clinical, and Virologic Features of Monkeypox in Southern France

We enrolled 136 patients with laboratory-confirmed monkeypox during June 4-August 31, 2022, at the University Hospital Institute Méditerranée Infection in Marseille, France. The median patient age was 36 years (interquartile range 31-42 years). Of 136 patients, 125 (92%) were men who have sex with men, 15 (11%) reported previous smallpox vaccinations, and 21 (15.5%) were HIV-positive. The most frequent lesion locations were the genitals (68 patients, 53%), perianal region (65 patients, 49%), and oral/perioral area (22 patients, 17%). Lesion locations largely corresponded with the route of contamination. Most (68%) patients had isolated anal, genital, or oral lesions when they were first seen, including 56 (61%) who had >1 positive site without a visible lesion. Concurrent sexually transmitted infections were diagnosed in 19 (15%) patients, and 7 patients (5%) were asymptomatic. We recommend vaccination campaigns, intensified testing for sexually transmitted infections, and increased contact tracing to control the ongoing monkeypox outbreak.

Judicial Opinions 123-127

Opinion 123 places the epithet of the name Aeromonas punctata on the list of rejected epithets and clarifies the citation of authors of selected names within the genus Aeromonas. Opinion 124 denies the request to place Borreliella on the list of rejected names because the request is based on a misinterpretation of the Code, which is clarified. There are alternative ways to solve the perceived problem. Opinion 125 denies the request to place Lactobacillus fornicalis on the list of rejected names because the provided information does not yield a reason for rejection. Opinion 126 denies the request to place Prolinoborus and Prolinoborus fasciculus on the list of rejected names because a relevant type strain deposit was not examined. Opinion 127 grants the request to assign the strain deposited as ATCC 4720 as the type strain of Agrobacterium tumefaciens, thereby correcting the Approved Lists. These Opinions were ratified by the voting members of the International Committee on Systematics of Prokaryotes.

Pangenomic analysis of Coxiella burnetii unveils new traits in genome architecture

Coxiella burnetii is the etiological agent of Q fever, a worldwide zoonosis able to cause large outbreaks. The disease is polymorphic. Symptomatic primary infection is named acute Q fever and is associated with hepatitis, pneumonia, fever, and auto-immune complications while persistent focalized infections, mainly endocarditis, and vascular infections, occur in a minority of patients but are potentially lethal. In order to evaluate the genomic features, genetic diversity, evolution, as well as genetic determinants of antibiotic resistance, pathogenicity, and ability to cause outbreaks of Q fever, we performed a pangenomic analysis and genomic comparison of 75 C. burnetii strains including 63 newly sequenced genomes. Our analysis demonstrated that C. burnetii has an open pangenome, unique genes being found in many strains. In addition, pathogenicity islands were detected in all genomes. In consequence C. burnetii has a high genomic plasticity, higher than that of other intracellular bacteria. The core- and pan-genomes are made of 1,211 and 4,501 genes, respectively (ratio 0.27). The core gene-based phylogenetic analysis matched that obtained from multi-spacer typing and the distribution of plasmid types. Genomic characteristics were associated to clinical and epidemiological features. Some genotypes were associated to specific clinical forms and countries. MST1 genotype strains were associated to acute Q fever. A significant association was also found between clinical forms and plasmids. Strains harboring the QpRS plasmid were never found in acute Q fever and were only associated to persistent focalized infections. The QpDV and QpH1 plasmids were associated to acute Q fever. In addition, the Guyanese strain CB175, the most virulent strain to date, exhibited a unique MST genotype, a distinct COG profile and an important variation in gene number that may explain its unique pathogenesis. Therefore, strain-specific factors play an important role in determining the epidemiological and clinical manifestations of Q fever alongside with host-specific factors (valvular and vascular defects notably).

SARS-CoV-2 quasi-species analysis from patients with persistent nasopharyngeal shedding

At the time of a new and unprecedented viral pandemic, many questions are being asked about the genomic evolution of SARS-CoV-2 and the emergence of different variants, leading to therapeutic and immune evasion and survival of this genetically highly labile RNA virus. The nasopharyngeal persistence of infectious virus beyond 17 days proves its constant interaction with the human immune system and increases the intra-individual mutational possibilities. We performed a prospective high-throughput sequencing study (ARTIC Nanopore) of SARS-CoV-2 from so-called "persistent" patients, comparing them with a non-persistent population, and analyzing the quasi-species present in a single sample at time t. Global intra-individual variability in persistent patients was found to be higher than in controls (mean 5.3%, Standard deviation 0.9 versus 4.6% SD 0.3, respectively, p < 0.001). In the detailed analysis, we found a greater difference between persistent and non-persistent patients with non-severe COVID 19, and between the two groups infected with clade 20A. Furthermore, we found minority N501Y and P681H mutation clouds in all patients, with no significant differences found both groups. The question of the SARS-CoV-2 viral variants' genesis remains to be further investigated, with the need to prevent new viral propagations and their consequences, and quasi-species analysis could be an important key to watch out.

A 21L/BA.2-21K/BA.1 "MixOmicron" SARS-CoV-2 hybrid undetected by qPCR that screen for variant in routine diagnosis

Among the multiple SARS-CoV-2 variants identified since summer 2020, several have co-circulated, creating opportunities for coinfections and potentially genetic recombinations that are common in coronaviruses. Viral recombinants are indeed beginning to be reported more frequently. Here, we describe a new SARS-CoV-2 recombinant genome that is mostly that of a Omicron 21L/BA.2 variant but with a 3' tip originating from a Omicron 21K/BA.1 variant. Two such genomes were obtained in our institute from adults sampled in February 2022 in university hospitals of Marseille, southern France, by next-generation sequencing carried out with the Illumina or Nanopore technologies. The recombination site was located between nucleotides 26,858-27,382. In the two genomic assemblies, mean sequencing depth at mutation-harboring positions was 271 and 1362 reads and mean prevalence of the majoritary nucleotide was 99.3 ± 2.2% and 98.8 ± 1.6%, respectively. Phylogeny generated trees with slightly different topologies according to whether genomes analyzed were depleted or not of the 3' tip. This 3' terminal end brought in the Omicron 21L/BA.2 genome a short transposable element of 41 nucleotides named S2m that is present in most SARS-CoV-2 except a few variants among which the Omicron 21L/BA.2 variant and may be involved in virulence. Importantly, this recombinant is not detected by currently used qPCR that screen for variants in routine diagnosis. The present observation emphasizes the need to survey closely the genetic pathways of SARS-CoV-2 variability by whole genome sequencing, and it could contribute to gain a better understanding of factors that lead to observed differences between epidemic potentials of the different variants.

Renewed Risk for Epidemic Typhus Related to War and Massive Population Displacement, Ukraine

Epidemic typhus, caused by Rickettsia prowazekii bacteria and transmitted through body lice (Pediculus humanus corporis), was a major public health threat in Eastern Europe as a consequence of World War II. In 2022, war and the resulting population displacement in Ukraine risks the return of this serious disease.

Real-time metagenomics-based diagnosis of community-acquired meningitis: A prospective series, southern France

BACKGROUND

Point-Of-Care (POC) diagnosis of life-threatening community-acquired meningitis currently relies on multiplexed RT-PCR assays, that lack genotyping and antibiotic susceptibility profiling. We assessed the usefulness of real-time metagenomics (RTM) directly applied to the cerebrospinal fluid (CSF) for the identification, typing and susceptibility profiling of pathogens responsible for community-acquired meningitis.

METHODS

A series of 52 CSF samples from patients suspected of having community-acquired meningitis, were investigated at POC by direct RTM in parallel to routine real-time multiplex PCR (RT-PCR) and bacterial culture, for the detection of pathogens. RTM-generated sequences were blasted in real-time against an in-house database incorporating the panel of 12 most prevalent pathogens and against NCBI using EPI2ME online software, for pathogen identification. In-silico antibiogram and genotype prediction were determined using the ResFinder bio-tool and MLST online software.

FINDINGS

Over eight months, routine multiplex RT-PCR yielded 49/52 positive CSFs, including 21 Streptococcus pneumoniae, nine Neisseria meningitidis, eight Haemophilus influenzae, three Streptococcus agalactiae, three Herpesvirus-1, two Listeria monocytogenes, and one each of Escherichia coli, Staphylococcus aureus and Varicella-Zoster Virus. Parallel RTM agreed with the results of 47/52 CSFs and revealed two discordant multiplex RT-PCR false positives, one H. influenzae and one S. pneumoniae. Both multiplex RT-PCR and RTM agreed on the negativity of three CSFs. While multiplex RT-PCR routinely took 90 min, RTM took 120 min, although the pipeline analysis detected the pathogen genome after 20 min of sequencing in 33 CSF samples; and after two hours in 14 additional CSFs; yielding > 50% genome coverage in 19 CSFs. RTM identified 14 pathogen genotypes, including a majority of H. influenzae b, N. meningitidis B and S. pneumoniae 11A and 3A. In all 16 susceptible cultured bacteria, the in-silico antibiogram agreed with the in-vitro antibiogram in 10 cases, available within 48 h in routine bacteriology.

INTERPRETATION

In addition to pathogen detection, RTM applied to CSF samples offered supplementary information on bacterial profiling and genotyping. These data provide the proof-of-concept that RTM could be implemented in a POC laboratory for one-shot diagnostic and genomic surveillance of pathogens responsible for life-threatening meningitis.

FUNDING

This work was supported by the French Government under the Investments in the Future programme managed by the National Agency for Research reference: Méditerranée Infection 10-IAHU-03.

Ottowia massiliensis sp. nov., a new bacterium isolated from a fresh, healthy human fecal sample

The culturomics method enabled isolation of a new member of the Ottowia genus from the stool sample of a healthy volunteer. Strain Marseille-P4747T exhibited a 96.18% 16S rRNA sequence identity with Ottowia beijingensis strain GCS-AN-3 (NR_133803.1), the closest species with standing in nomenclature. It is a Gram-stain-negative, non-motile, aerobic bacterium. It does not possess catalase and oxidase activities. Its genome has a size of 2830 447 bp and a G + C content of 63.5 mol%. Based on the phylogenic, phenotypic and genomic analyses, we conclude that Ottowia massiliensis sp. nov. is a new species, represented by Marseille-P4747T ( = CSUR P4747 = CECT 30348) as type strain.

Prevotella merdae sp. nov., a new bacterial species isolated from human faeces

Strain Marseille-P4119T was isolated from a faecal sample of a healthy 32-year-old faecal transplant donor. The bacterium was anaerobic, Gram-negative, rod-shaped, non-motile and did not produce spores. We studied its phenotypic characteristics and sequenced its whole genome. The major fatty acids were C15:0 anteiso and C15:0 iso. The final genome assembly was 3912 650 bp long with a 44.4 mol% G + C content, 3094 protein-coding genes and 74 RNA genes. Strain Marseille-P4119T exhibited a 97.10% 16S rRNA sequence identity and a 29.0% dDDH with Prevotella stercorea CB35T, OrthoANI values ranged from 68.5% with Prevotella enoeca to 77.4% with Prevotella stercorea, the phylogenetically closest bacterial species with standing in nomenclature. Based on the phylogenetic, phenotypic and genomic analyses, we propose the creation of the novel species Prevotella merdae sp. nov. The type strain is Marseille-P4119T ( = CSUR P4119T = CECT 9566T).

Rickettsial infections are an unlikely cause of peripheral facial palsy in Southern Jutland, Denmark

INTRODUCTION

Several infectious aetiologies have been associated with peripheral facial palsy, among others Herpes viridae and Borrelia burgdorferi and, rarely, cases of rickettsiosis. In this study, we prospectively included 19 patients with peripheral facial palsy from the Department of Neurology, University Hospital of Southern Denmark, and 29 healthy controls to examine infectious causes and risk factors of peripheral facial palsy.

METHODS

Patients and controls completed a questionnaire regarding exposures, and the patients' medical files were examined. Serum from patients and controls were tested for antibodies against B. burgdorferi, Rickettsia felis and Rickettsia helvetica. Cerebrospinal fluids were tested using polymerase chain reaction for the presence of herpes simplex virus 1 and 2, herpes zoster virus and spotted fever group rickettsial DNA and for intrathecal production of antibodies against B. burgdorferi with an antibody index test.

RESULTS

One patient was diagnosed with peripheral facial palsy associated with neuroborreliosis with a positive antibody index test but had a negative serological analysis. No patients had evidence of herpes or rickettsial infection. Fourteen out of the 19 patients had symptom onset in the winter months. Preceding myalgia was the only significant difference in symptoms between patients and controls (p = 0.011).

CONCLUSION

Rickettsiosis is unlikely as a common cause of facial palsy in Southern Jutland, Denmark.

FUNDING

The study was supported financially by the Knud and Edith Eriksen Mindefond and the Region of Southern Denmark.

TRIAL REGISTRATION

The study population and the control group were approved by the Regional Committees on Health Research Ethics for Southern Denmark (S-20170136 and S-20170049) and by the Danish Data Protection Agency (17/31901 and 18/28928). All participants provided informed consent before their enrollment in the study.

Peptoniphilus coli sp. nov. and Peptoniphilus urinae sp. nov., isolated from humans

Strains Marseille-P3761 and Marseille-P3195 are representatives of two bacterial species isolated from human specimens. Strain Marseille-P3761 was isolated from the stool of a healthy volunteer, while strain Marseille-P3915 was cultivated from the urine of a kidney transplant recipient. Both strains are anaerobic Gram-positive coccoid bacteria. Both are catalase-negative and oxidase-negative and grow optimally at 37 °C in anaerobic conditions. They also metabolize carbohydrates, such as galactose, glucose, fructose, and glycerol. The major fatty acids were hexadecanoic acid for both strains. The highest digital DNA–DNA hybridization (dDDH) values of Marseille-P3761 and Marseille-P3195 strains when compared to their closest phylogenetic relatives were 52.3% and 56.4%, respectively. Strains Marseille-P3761 and Marseille-P3195 shared an OrthoANI value of 83.5% which was the highest value found with Peptoniphilus species studied here. The morphological, biochemical, phenotypic and genomic characteristics strongly support that these strains are new members of the Peptoniphilus genus. Thus, we suggest that Peptoniphilus coli sp. nov., and Peptoniphilus urinae sp. nov., are new species for which strains Marseille-P3761 (CSUR P3761 = CCUG 71,569) and Marseille-P3195 (CSUR P3195 = DSM 103,468) are their type strains, respectively of two new Peptoniphilus species, for which we propose the names Peptoniphilus coli sp. nov. and Peptoniphilus urinae sp. nov., respectively.

Sequential Appearance and Isolation of a SARS-CoV-2 Recombinant between Two Major SARS-CoV-2 Variants in a Chronically Infected Immunocompromised Patient

Genetic recombination is a major evolutionary mechanism among RNA viruses, and it is common in coronaviruses, including those infecting humans. A few SARS-CoV-2 recombinants have been reported to date whose genome harbored combinations of mutations from different mutants or variants, but only a single patient's sample was analyzed, and the virus was not isolated. Here, we report the gradual emergence of a hybrid genome of B.1.160 and Alpha variants in a lymphoma patient chronically infected for 14 months, and we isolated the recombinant virus. The hybrid genome was obtained by next-generation sequencing, and the recombination sites were confirmed by PCR. This consisted of a parental B.1.160 backbone interspersed with two fragments, including the spike gene, from an Alpha variant. An analysis of seven sequential samples from the patient decoded the recombination steps, including the initial infection with a B.1.160 variant, then a concurrent infection with this variant and an Alpha variant, the generation of hybrid genomes, and eventually the emergence of a predominant recombinant virus isolated at the end of the patient's follow-up. This case exemplifies the recombination process of SARS-CoV-2 in real life, and it calls for intensifying the genomic surveillance in patients coinfected with different SARS-CoV-2 variants, and more generally with several RNA viruses, as this may lead to the appearance of new viruses.

Screening and Whole Genome Sequencing of SARS-CoV-2 Circulating During the First Three Waves of the COVID-19 Pandemic in Libreville and the Haut-Ogooué Province in Gabon

Since the onset of the COVID-19 pandemic, the SARS-CoV-2 viral dynamics in Africa have been less documented than on other continents. In Gabon, a Central African country, a total number of 37,511 cases of COVID-19 and 281 deaths have been reported as of December 8, 2021. After the first COVID-19 case was reported on March 12, 2020, in the capital Libreville, the country experienced two successive waves. The first one, occurred in March 2020 to August 2020, and the second one in January 2021 to May 2021. The third wave began in September 2021 and ended in November 2021. In order to reduce the data gap regarding the dynamics of SARS-CoV-2 in Central Africa, we performed a retrospective genotyping study using 1,006 samples collected from COVID-19 patients in Gabon from 2020 to 2021. Using SARS-CoV-2 variant screening by Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) and whole genome sequencing (WGS), we genotyped 809 SARS-CoV-2 samples through qRT-PCR and identified to generated 291 new genomes. It allowed us to describe specific mutations and changes in the SARS-CoV-2 variants in Gabon. The qRT-PCR screening of 809 positive samples from March 2020 to September 2021 showed that 119 SARS-CoV-2 samples (14.7%) were classified as VOC Alpha (Pangolin lineage B.1.1.7), one (0.1%) was a VOC Beta (B.1.351), and 198 (24.5 %) were VOC Delta (B.1.617.2), while 491 samples (60.7%) remained negative for the variants sought. The B1.1 variant was predominant during the first wave while the VOC Alpha dominated the second wave. The B1.617.2 Delta variant is currently the dominant variant of the third wave. Similarly, the analysis of the 291 genome sequences indicated that the dominant variant during the first wave was lineage B.1.1, while the dominant variants of the second wave were lineages B.1.1.7 (50.6%) and B.1.1.318 (36.4%). The third wave started with the circulation of the Delta variant (B.1.617). Finally, we compared these results to the SARS-CoV-2 sequences reported in other African, European, American and Asian countries. Sequences of Gabonese SARS-CoV-2 strains presented the highest similarities with those of France, Belgium and neighboring countries of Central Africa, as well as West Africa.

Culture-negative endocarditis caused by Stenotrophomonas maltophilia: a report of two cases

Stenotrophomonas maltophilia, an aerobic, non-fermenting, Gram-negative bacterium, is an emerging nosocomial pathogen. It is considered to be a low-grade pathogen, and infections due to S. maltophilia are uncommon. However, in the recent past, S. maltophilia infections have been on the rise, particularly in patients who are either immunocompromised, aged or on long-term antibiotic therapy. Endocarditis due to S. maltophilia is extremely rare. This is a report of two patients with S. maltophilia endocarditis who were diagnosed by 16S rRNA gene sequencing.

Outcomes of 2111 COVID-19 Hospitalized Patients Treated with Hydroxychloroquine/Azithromycin and Other Regimens in Marseille, France, 2020: A Monocentric Retrospective Analysis

Objectives

We evaluated the 6-week mortality of SARS-CoV-2 hospitalized patients treated using a standardized protocol in 2020 in Marseille, France.

Methods

A retrospective monocentric cohort study was conducted in the standard hospital wards at the Institut Hospitalo-Universitaire Méditerranée Infection, between March and December 2020 in adults with SARS-CoV-2 PCR-proven infection.

Results

Of the 2111 hospitalized patients (median age, 67 [IQR 55-79] years; 1154 [54.7%] men), 271 were transferred to the intensive care unit (12.8%) and 239 died (11.3%; the mean age of patients who died was 81.2 (±9.9)). Treatment with hydroxychloroquine plus azithromycin (HCQ-AZ), used in 1270 patients, was an independent protective factor against death (0.68 [0.52 - 0.88]). This effect was consistent for all subgroups of age, comorbidities, severity of the disease and comedications with zinc or corticosteroids. Zinc was independently protective against death (0.39 [0.23 - 0.67]), in a subgroup analysis of patients treated with HCQ-AZ without dexamethasone. The use of high-flow oxygen therapy in elderly patients who were not eligible for intensive care unit transfer saved 19 patients (33.9%).

Conclusions

In our 2020 cohort, treating COVID-19 with HCQ-AZ was associated with lower mortality. These results need to be analyzed in the context of academic discussions about observational studies versus randomized clinical trials. More data will deserve to be analyzed in the SARS-Cov 2 variants, vaccination and post-vaccination era.

Description of Acinetobacter ihumii sp. nov., Microbacterium ihumii sp. nov., and Gulosibacter massiliensis sp. nov., three new bacteria isolated from human blood

Blood is precious tissue that is normally sterile. With the aim of diagnosing the cause of bacteremia, three bacterial strains were isolated from three different individuals. Strains Marseille-P7157^T and Marseille-Q2854^T are Gram-stain positive, non-spore-forming rod-shaped bacteria, while strain Marseille-P8049^T is a Gram-stain negative, motile, non-spore-forming and rod-shaped bacterium. The major fatty acids found (>30%) were hexadecanoic acid for strain Marseille-P8049^T and 12-methyl tetradecanoic acid for both strains Marseille-P7157^T and Marseille-Q2854^T. The 16S rRNA gene sequence analysis shows that strains Marseille-P8049 and Marseille-Q2854^T have sequence similarity of 96.8%, 99.04%, and 98.3% with Acinetobacter ursingii strain LUH3792 (NR_025392.1), Gulosibacter faecalis strain B187 (NR_041812.1), and Schaalia canis strain CCUG 41706 (NR_025366.1), respectively. In addition, strains Marseille-Q2854^T, Marseille-P8049^T and Marseille-P7157^T shared with their closely related species cited above the following DDH values: 19.5%, 24.4%, and 20.2%, respectively. Based on these phenotypic and genomic findings, we consider that strains Marseille-P8049^T (= CSUR P8049 = CECT 30350), Marseille-P2854^T ( = CSUR Q2854 = CECT 30120) and Marseille-P7157^T ( = CSUR P7157 = CECT 30048) are new bacterial species, for which the names Acinetobacter ihumii sp. nov., Microbacterium ihumii sp. nov., and Gulosibacter massiliensis sp. nov., are proposed.

Tick borne relapsing fever after travelling to a Greek island

A 23-year-old man presented to the emergency department with recurrent fever after returning from a camping trip on the Greek island of Tilos in the Aegean sea. In the last 2 months, four distinct episodes of fever, chills and myalgia occurred. A peripheral-blood smear revealed an unexpected guest.

SARS-CoV-2 reinfection and COVID-19 severity

SARS-CoV-2 reinfection rate is low. The relative severity of the first and second episodes of infection remains poorly studied. In this study, we aimed at assessing the frequency of SARS-CoV-2 reinfections and comparing the severity of the first and second episodes of infection. We retrospectively included patients with SARS-CoV-2 positive RT-PCR at least 90 days after clinical recovery from a COVID-19 episode and with at least one negative RT-PCR after the first infection. Whole genome sequencing and variant-specific RT-PCR were performed and clinical symptoms and severity of infection were retrospectively documented from medical files. A total of 209 COVID-19 reinfected patients were identified, accounting for 0.4% of positive cases diagnosed from 19 March 2020 to 24 August 2021. Serology was performed in 64 patients, of whom 39 (60.1%) had antibodies against SARS-CoV-2 when sampled at the early stage of their second infection. Only seven patients (3.4%) were infected twice with the same variant. We observed no differences in clinical presentation, hospitalization rate, and transfer to ICU when comparing the two episodes of infections. Our results suggest that the severity of the second episode of COVID-19 is in the same range as that of the first infection, including patients with antibodies.

First cases of infection with the 21L/BA.2 Omicron variant in Marseille, France

The SARS‐CoV‐2 21K/BA.1, 21L/BA.2, and BA.3 Omicron variants have recently emerged worldwide. To date, the 21L/BA.2 Omicron variant has remained very minority globally but became predominant in Denmark instead of the 21K/BA.1 variant. Here, we describe the first cases diagnosed with this variant in south‐eastern France. We identified 13 cases using variant‐specific qPCR and next‐generation sequencing between 28/11/2021 and 31/01/2022, the first two cases being diagnosed in travelers returning from Tanzania. Overall, viral genomes displayed a mean (±standard deviation) number of 65.9 ± 2.5 (range, 61–69) nucleotide substitutions and 31.0 ± 8.3 (27–50) nucleotide deletions, resulting in 49.6 ± 2.2 (45–52) amino acid substitutions (including 28 in the spike protein) and 12.4 ± 1.1 (12–15) amino acid deletions. Phylogeny showed the distribution in three different clusters of these genomes, which were most closely related to genomes from England and South Africa, from Singapore and Nepal, or from France and Denmark. Structural predictions highlighted a significant enlargement and flattening of the surface of the 21L/BA.2 N‐terminal domain of the spike protein compared to that of the 21K/BA.1 Omicron variant, which may facilitate initial viral interactions with lipid rafts. Close surveillance is needed at global, country, and center scales to monitor the incidence and clinical outcome of the 21L/BA.2 Omicron variant.

Analysis of SARS-CoV-2 Variants From 24,181 Patients Exemplifies the Role of Globalization and Zoonosis in Pandemics

After the end of the first epidemic episode of SARS-CoV-2 infections, as cases began to rise again during the summer of 2020, we at IHU Méditerranée Infection in Marseille, France, intensified the genomic surveillance of SARS-CoV-2, and described the first viral variants. In this study, we compared the incidence curves of SARS-CoV-2-associated deaths in different countries and reported the classification of SARS-CoV-2 variants detected in our institute, as well as the kinetics and sources of the infections. We used mortality collected from a COVID-19 data repository for 221 countries. Viral variants were defined based on ≥5 hallmark mutations along the whole genome shared by ≥30 genomes. SARS-CoV-2 genotype was determined for 24,181 patients using next-generation genome and gene sequencing (in 47 and 11% of cases, respectively) or variant-specific qPCR (in 42% of cases). Sixteen variants were identified by analyzing viral genomes from 9,788 SARS-CoV-2-diagnosed patients. Our data show that since the first SARS-CoV-2 epidemic episode in Marseille, importation through travel from abroad was documented for seven of the new variants. In addition, for the B.1.160 variant of Pangolin classification (a.k.a. Marseille-4), we suspect transmission from farm minks. In conclusion, we observed that the successive epidemic peaks of SARS-CoV-2 infections are not linked to rebounds of viral genotypes that are already present but to newly introduced variants. We thus suggest that border control is the best mean of combating this type of introduction, and that intensive control of mink farms is also necessary to prevent the emergence of new variants generated in this animal reservoir.

Limited spread of a rare spike E484K-harboring SARS-CoV-2 in Marseille, France

We detected SARS-CoV-2 of PANGO lineage R.1 with the spike substitution E484K in three patients. Eleven other sequences in France and 8,831 worldwide were available from GISAID, 92% originating from Japan. The three genome sequences from our institute were phylogenetically closest to another from Guinea-Conakry, where one of the patients had travelled. These viruses did not exhibit any unusual features in cell culture. Spike structural predictions indicated a 1.3-time higher transmissibility index than for the globally spread B.1.1.7 variant but also an affinity loss for gangliosides that might have slowed dissemination. The spread of new SARS-CoV-2 mutants/variants is still not well understood and therefore difficult to predict, and this hinders implementation of effective preventive measures, including adapted vaccines.

Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France

Great concerns have been raised about SARS-CoV-2 variants over the past six months. At the end of 2020, an increasing incidence of spike substitutions Q677H/P was described in the USA, which involved six independent lineages. We searched for changes to this amino acid in the sequence database of SARS-CoV-2 genomes obtained at the IHU Méditerranée Infection (Marseille, France) from 3634 patients sampled between February 2020 and April 2021. In seven genomes (0.2%), we found a deletion of five amino acids at spike positions 675-679 (QTQTN) including Q677, and in 76 genomes (2.3%) we found a Q677H substitution. The 83 genomes were classified in ten different Pangolin lineages. Genomes with a spike Q677 deletion were obtained from respiratory samples collected in six cases between 28 March 2020 and 12 October 2020 and in one case on 1 February 2021. The Q677H substitution was found in genomes all obtained from respiratory samples collected from 19 January 2021 and were classified in seven different lineages. Most of these genomes (41 cases) were of UK variant. Two others were classified in the B.1.160 Pangolin lineage (Marseille-4 variant) which was first detected in July 2020 in our institute but was devoid of this substitution until 19 January 2021. Also, eight genomes were classified in the A.27/Marseille-501 lineage which was first detected in our institute in January 2021 and which either harboured or did not harbour the Q677H substitution. Thus, the spike Q677H substitution should be considered as another example of convergent evolution, as it is the case of spike substitutions L18F, E484K, L452R, and N501Y which also independently appeared in various lineages.

Human galectin-1 and galectin-3 promote Tropheryma whipplei infection

Tropheryma whipplei, is an actinobacterium that causes different infections in humans, including Whipple's disease. The bacterium infects and replicates in macrophages, leading to a Th2-biased immune response. Previous studies have shown that T. whipplei harbors complex surface glycoproteins with evidence of sialylation. However, the exact contribution of these glycoproteins for infection and survival remains obscure. To address this, we characterized the bacterial glycoprofile and evaluated the involvement of human β-galactoside-binding lectins, Galectin-1 (Gal-1) and Galectin-3 (Gal-3) which are highly expressed by macrophages as receptors for bacterial glycans. Tropheryma whipplei glycoproteins harbor different sugars including glucose, mannose, fucose, β-galactose and sialic acid. Mass spectrometry identification revealed that these glycoproteins were membrane- and virulence-associated glycoproteins. Most of these glycoproteins are highly sialylated and N-glycosylated while some of them are rich in poly-N-acetyllactosamine (Poly-LAcNAc) and bind Gal-1 and Gal-3. In vitro, T. whipplei modulates the expression and cellular distribution of Gal-1 and Gal-3. Although both galectins promote T. whipplei infection by enhancing bacterial cell entry, only Gal-3 is required for optimal bacterial uptake. Finally, we found that serum levels of Gal-1 and Gal-3 were altered in patients with T. whipplei infections as compared to healthy individuals, suggesting that galectins are also involved in vivo. Among T. whipplei membrane-associated proteins, poly-LacNAc rich-glycoproteins promote infection through interaction with galectins. T. whipplei modulates the expression of Gal-1 and Gal-3 both in vitro and in vivo. Drugs interfering with galectin-glycan interactions may provide new avenues for the treatment and diagnosis of T. whipplei infections.