Microevolution, reinfection and highly complex genomic diversity in patients with sequential isolates of Mycobacterium abscessus

Mycobacterium abscessus is an opportunistic, extensively drug-resistant non-tuberculous mycobacterium. Few genomic studies consider its diversity in persistent infections. Our aim was to characterize microevolution/reinfection events in persistent infections. Fifty-three sequential isolates from 14 patients were sequenced to determine SNV-based distances, assign resistance mutations and characterize plasmids. Genomic analysis revealed 12 persistent cases (0-13 differential SNVs), one reinfection (15,956 SNVs) and one very complex case (23 sequential isolates over 192 months), in which a first period of persistence (58 months) involving the same genotype 1 was followed by identification of a genotype 2 (76 SNVs) in 6 additional alternating isolates; additionally, ten transient genotypes (88-243 SNVs) were found. A macrolide resistance mutation was identified from the second isolate. Despite high diversity, the genotypes shared a common phylogenetic ancestor and some coexisted in the same specimens. Genomic analysis is required to access the true intra-patient complexity behind persistent infections involving M. abscessus.This work was supported by the Instituto de Salud Carlos III [AC16/00057, FIS15/01554, PI21/01823, PI19/00331, FI20/00129, PI21/01738], co-financed by European Regional Development Funds of the European Commission: “A way of making Europe”; a Miguel Servet Contract (ISCIII) CPII20/00001 to LPL. FI22/00145 contract from a PFIS (ISCIII) to SBS and Ministerio de Ciencia (MCIN/AEI/10.13039/501100011033, grant PID2020-112865RB-I00).Peer reviewe

A Prospective Study of the Serological, Clinical, and Epidemiological Features of a SARS-CoV-2 Positive Pediatric Cohort

Background: SARS-CoV-2 was a global pandemic. Children develop a mild disease and may have a different rate of seroconversion compared to adults. The objective was to determine the number of seronegative patients in a pediatric cohort. We also reviewed the clinical–epidemiological features associated with seroconversion. Methods: A multicenter prospective observational study during September–November 2020, of COVID-19, confirmed by reverse transcription-polymerase chain reaction. Data were obtained 4–8 weeks after diagnosis. Blood samples were collected to investigate the humoral response, using three different serological methods. Results: A total of 111 patients were included (98 symptomatic), 8 were admitted to hospital, none required an Intensive Care Unit visit. Median age: 88 months (IQR: 24–149). Median time between diagnosis and serological test: 37 days (IQR: 34–44). A total of 19 patients were non-seroconverters when using three serological techniques (17.1%; 95% CI: 10.6–25.4); most were aged 2–10 years (35%, p < 0.05). Univariate analysis yielded a lower rate of seroconversion when COVID-19 confirmation was not present amongst household contacts (51.7%; p < 0.05). Conclusions: There was a high proportion of non-seroconverters. This is more commonly encountered in childhood than in adults. Most seronegative patients were in the group aged 2–10 years, and when COVID-19 was not documented in household contacts. Most developed a mild disease. Frequently, children were not the index case within the family