Challenging the phylogenetic relationships among Echinococcus multilocularis isolates from main endemic areas.

Alveolar echinococcosis (AE) is a rare but severe disease that affects more than 18,000 people worldwide per year. The complete sequencing of the mitochondrial genome of Echinococcus multilocularis has made it possible to study the genetic diversity of the parasite and its spatial and temporal evolution. We amplified the whole mitochondrial genome by PCR, using one uniplex and two multiplex reactions to cover the 13,738 bp of the mitogenome, and then sequenced the amplicons with Illumina technology. In total, 113 samples from Europe, Asia, the Arctic and North America were analyzed. Three major haplogroups were found: HG1, which clustered samples from Alaska (including Saint-Lawrence Island), Yakutia (Russia) and Svalbard; HG2, with samples from Asia, North America and Europe; and HG3, subdivided into three micro-haplogroups. HG3a included samples from North America and Europe, whereas HG3b and HG3c only include samples from Europe. In France, HG3a included samples from patients more recently diagnosed in a region outside the historical endemic area. A fourth putative haplogroup, HG4, was represented by only one isolate from Olkhon Island (Russia). The increased discriminatory power of the complete sequencing of the E. multilocularis mitogenome has made it possible to highlight four distinct geographical clusters, one being divided into three micro-haplogroups in France.

Complete mitochondrial exploration of Echinococcus multilocularis from French alveolar echinococcosis patients.

Alveolar echinococcosis (AE) is a parasitosis that is expanding worldwide, including in Europe. The development of genotypic markers is essential to follow its spatiotemporal evolution. Sequencing of the commonly used mitochondrial genes cob, cox1, and nad2 shows low discriminatory power, and analysis of the microsatellite marker EmsB does not allow nucleotide sequence analysis. We aimed to develop a new method for the genotyping of Echinococcus multilocularis based on whole mitochondrial genome (mitogenome) sequencing, to determine the genetic diversity among 30 human visceral samples from French patients, and compare this method with those currently in use. Sequencing of the whole mitochondrial genome was carried out after amplification by PCR, using one uniplex and two multiplex reactions to cover the 13,738 bp of the mitogenome, combined with Illumina technology. Thirty complete mitogenome sequences were obtained from AE lesions. One showed strong identity with Asian genotypes (99.98% identity) in a patient who had travelled to China. The other 29 mitogenomes could be differentiated into 13 haplotypes, showing higher haplotype and nucleotide diversity than when using the cob, cox1, and nad2 gene sequences alone. The mitochondrial genotyping data and EmsB profiles did not overlap, probably because one method uses the mitochondrial genome and the other the nuclear genome. The pairwise fixation index (Fst) value between individuals living inside and those living outside the endemic area was high (Fst = 0.222, P = 0.002). This is consistent with the hypothesis of an expansion from historical endemic areas to peripheral regions.

Factors associated with late microbiological documentation of prosthetic joint infection.

Purpose: To describe the number of prosthetic joint infections (PJIs) with late documentation and to identify associated factors. Methods: Bacterial PJIs with surgical management between November 2015 and November 2019 in a French center were analyzed. Results of short (72 h) and late culture (at 14 days) were analyzed. Results: A total of 160 PJIs were reported with 215 bacteria. Twenty-nine patients had late documentation (18.1%). The bacteria most involved were coagulase-negative staphylococci and Cutibacterium spp. (60%). In multivariate analysis, late chronic PJI (odds ratio = 2.47) and antibiotic therapy before surgery (odds ratio = 3.13) were associated with late-documented infection. Conclusion: A better knowledge of the factors associated with late-documented infections is essential in order to simplify antibiotic treatment at the appropriate time.

Prosthetic joint infections (PJIs) are rare and occur in around 1% of cases. They are often complex and require multidisciplinary management. The identification of bacteria and the implementation of an effective intravenous antibiotic therapy as soon as the surgery is performed are important points in PJI management. Some bacteria take longer to be cultivated, which is why samples are cultured for at least 14 days after surgery. As soon as the bacteria have been identified, the antibiotic therapy can be taken orally to allow the patient to be discharged early from hospital. The aim of this study was to investigate the factors associated with a positive late culture (day 14 after surgery) compared with an early culture (day 3). We showed that patients who had received antibiotic therapy within 1 month before surgery and patients with chronic PJI (i.e., more than 1 year after surgery) were at greater risk of having long-culture-positive specimens. We also showed that late samples were more often positive for two types of bacteria (Cutibacterium acnes and coagulase-negative staphylococci). In practice, when early samples are positive, oral antibiotics are given rapidly, except for patients who have had prior antibiotic therapy or who have a chronic infection for whom other samples may be positive late (14 days). Moreover, in patients with negative early culture, oral antibiotic therapy active against Cutibacterium acnes and coagulase-negative staphylococci (the two main bacteria in late culture) could be prescribed, waiting for the result of late culture.

COVID-19 patients display distinct SARS-CoV-2 specific T-cell responses according to disease severity.

Adaptive Immune responses generated by SARS-CoV-2 virus in convalescent patients according to disease severity remain poorly characterized. To this end, we designed a prospective study (NCT04365322) that included 60 COVID-19 convalescent patients (1-month post infection) in two cohorts respectively entitled mild illness and severe pneumonia. The monitoring of peripheral immune responses was performed using IFNᵧ ELISpot assay. The serology index of each patient was investigated at the same time. Patients with severe pneumonia were older and had more comorbidities than patients with mild illness. T-cell responses in term of frequency and intensity were clearly distinct between mild illness and severe pneumonia patients. Furthermore, our results demonstrated that recent history of COVID-19 did not hamper viral memory T-cell pool against common viruses (Cytomegalovirus, Epstein-Barr-virus and Flu-virus). The presence of potent adaptive immunity even in patients who underwent severe pneumonia sustain the rationale for the development of protective therapeutics against SARS-CoV-2.