Spinach genomes reveal migration history and candidate genes for important crop traits.

Spinach (Spinacia oleracea) is an important leafy crop possessing notable economic value and health benefits. Current genomic resources include reference genomes and genome-wide association studies. However, the worldwide genetic relationships and the migration history of the crop remained uncertain, and genome-wide association studies have produced extensive gene lists related to agronomic traits. Here, we re-analysed the sequenced genomes of 305 cultivated and wild spinach accessions to unveil the phylogeny and history of cultivated spinach and to explore genetic variation in relation to phenotypes. In contrast to previous studies, we employed machine learning methods (based on Extreme Gradient Boosting, XGBoost) to detect variants that are collectively associated with agronomic traits. Variant-based cluster analyses revealed three primary spinach groups in the Middle East, Asia and Europe/US. Combining admixture analysis and allele-sharing statistics, migration routes of spinach from the Middle East to Europe and Asia are presented. Using XGBoost machine learning models we predict genomic variants influencing bolting time, flowering time, petiole color, and leaf surface texture and propose candidate genes for each trait. This study enhances our understanding of the history and phylogeny of domesticated spinach and provides valuable information on candidate genes for future genetic improvement of the crop.

Genomic alterations involved in fluoroquinolone resistance development in Staphylococcus aureus.

AIM: Fluoroquinolone (FQ) is a potent antibiotic class. However, resistance to this class emerges quickly which hinders its application. In this study, mechanisms leading to the emergence of multidrug-resistant (MDR) Staphylococcus aureus (S. aureus) strains under FQ exposure were investigated. METHODOLOGY: S. aureus ATCC 29213 was serially exposed to ciprofloxacin (CIP), ofloxacin (OFL), or levofloxacin (LEV) at sub-minimum inhibitory concentrations (sub-MICs) for 12 days to obtain S. aureus -1 strains and antibiotic-free cultured for another 10 days to obtain S. aureus-2 strains. The whole genome (WGS) and target sequencing were applied to analyze genomic alterations; and RT-qPCR was used to access the expressions of efflux-related genes, alternative sigma factors, and genes involved in FQ resistance. RESULTS: A strong and irreversible increase of MICs was observed in all applied FQs (32 to 128 times) in all S. aureus-1 and remained 16 to 32 times in all S. aureus-2. WGS indicated 10 noticeable mutations occurring in all FQ-exposed S. aureus including 2 insdel mutations in SACOL0573 and rimI; a synonymous mutation in hslO; and 7 missense mutations located in an untranslated region. GrlA, was found mutated (R570H) in all S. aureus-1 and -2. Genes encoding for efflux pumps and their regulator (norA, norB, norC, and mgrA); alternative sigma factors (sigB and sigS); acetyltransferase (rimI); methicillin resistance (fmtB); and hypothetical protein BJI72_0645 were overexpressed in FQ-exposed strains. CONCLUSION: The emergence of MDR S. aureus was associated with the mutations in the FQ-target sequences and the overexpression of efflux pump systems and their regulators.

Factors influencing adverse events following immunization with AZD1222 in Vietnamese adults during first half of 2021.

BACKGROUND: COVID-19 vaccines have been speedily developed and deployed. The more vaccine doses are delivered to users, the more common adverse events following immunization (AEFI) are reported. This study aimed to identify factors affecting AEFI in Vietnamese people receiving the COVID-19 vaccine AZD1222 developed by AstraZeneca and Oxford University. METHODS: In July 2021, an online cross-sectional survey was conducted among Vietnamese who have been vaccinated with COVID-19 vaccines. The questionnaire collected demographic characteristics, medical history, types of injected vaccines, common AEFI, and post-vaccination activities from respondents. The effects of host-related factors on AEFI including 24 specific symptoms were also explored. RESULTS: After screening, 1028 participants who were Vietnamese, over 18 years old and received at least one dose of AZD1222, were included in the study. Only 40/1028 (3.9%) participants reported not having any AEFI, whereas 25/1028 (2.4%) reported to have severe symptoms. The most common AEFI were moderate fever (69.4%), muscle aches (68.6%), followed by fatigue/ sleepiness (62.5%), body aches (59.4%), headache (58.5%), pain at injection site (58.3%) and chills (45.7%). Data analysis showed that females complained about AEFI particularly gastrointestinal symptoms more frequently than males. Age of participants and number of doses were also important factors affecting AEFI as the increase of age or number of vaccine doses was associated with the decrease of self-reported AEFI frequency. CONCLUSIONS: This study provides a detailed assessment of risk factors associated with AEFI in Vietnamese people vaccinated with AZD1222. It seems that gender, age and vaccine doses are important factors affecting AEFI.

Analysis of drug-resistant strains of Mycobacterium leprae in an endemic area of Vietnam.

BACKGROUND: Multidrug therapy has effectively reduced the number of leprosy cases in the world. However, the rate of reduction has decelerated over the years, giving early detection of Mycobacterium leprae and epidemiological study of relapse renewed relevance in attempts to eliminate the disease. METHODS: A molecular epidemiological survey for drug-resistant M. leprae was conducted in the central and highland regions of Vietnam. A total of 423 samples taken from patients, including 83 patients with new cases, 321 patients receiving treatment, and 19 patients with relapse, were studied for detection of M. leprae with mutations relating to drug resistance by sequencing the drug resistance determining region of the folP1, rpoB, and gyrA genes, which are responsible for dapsone, rifampicin, and ofloxacin resistance, respectively. RESULTS: Nineteen mutations were found in the folP1 gene samples, and no mutations relating to drug resistance were found in either the rpoB or gyrA genes. Samples from patients with relapse showed folP1 mutation rates as high as 57%, and the mutation rates in samples from new and recent cases were <10%. Patients with relapse who had histories of treatment with dapsone monotherapy showed high mutation rates (78%), compared with patients with relapse who had previously only received multidrug therapy (33%). CONCLUSIONS: Our study indicated high rates of dapsone resistance in patients with relapse, compared with patients with new and recent cases of leprosy. Moreover, it was observed that many of the patients with relapse who had dapsone-resistant mutations had histories of treatment with dapsone monotherapy.