Characteristics and phylogenetic analysis of chloroplast genome of a new type of fruit Rubus rosaefolius / 生物工程学报

The genomic DNA of Rubus rosaefolius was extracted and sequenced by Illumina NovaSeq platform to obtain the complete chloroplast genome sequence, and the sequence characteristics and phylogenetic analysis of chloroplast genes were carried out. The results showed that the complete chloroplast genome of the R. rosaefolius was 155 650 bp in length and had a typical tetrad structure, including two reverse repeats (25 748 bp each), a large copy region (85 443 bp) and a small copy region (18 711 bp). A total of 131 genes were identified in the whole genome of R. rosaefolius chloroplast, including 86 protein coding genes, 37 tRNA genes and 8 rRNA genes. The GC content of the whole genome was 36.9%. The genome of R. rosaefolius chloroplast contains 47 scattered repeats and 72 simple sequence repeating (SSR) loci. The codon preference is leucine codon, and the codon at the end of A/U is preferred. Phylogenetic analysis showed that R. rosaefolius had the closest relationship with R. taiwanicola, followed by R. rubraangustifolius and R. glandulosopunctatus. The chloroplast genome characteristics and phylogenetic analysis of R. rosaefolius provide a theoretical basis for its genetic diversity research and chloroplast development and utilization.

Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion

BACKGROUND Evolutionary changes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) include indels in non-structural, structural, and accessory open reading frames (ORFs) or genes. OBJECTIVES We track indels in accessory ORFs to infer evolutionary gene patterns and epidemiological links between outbreaks. METHODS Genomes from Coronavirus disease 2019 (COVID-19) case-patients were Illumina sequenced using ARTIC_V3. The assembled genomes were analysed to detect substitutions and indels. FINDINGS We reported the emergence and spread of a unique 4-nucleotide deletion in the accessory ORF6, an interesting gene with immune modulation activity. The deletion in ORF6 removes one repeat unit of a two 4-nucleotide repeat, which shows that directly repeated sequences in the SARS-CoV-2 genome are associated with indels, even outside the context of extended repeat regions. The 4-nucleotide deletion produces a frameshifting change that results in a protein with two inserted amino acids, increasing the coding information of this accessory ORF. Epidemiological and genomic data indicate that the deletion variant has a single common ancestor and was initially detected in a health care outbreak and later in other COVID-19 cases, establishing a transmission cluster in the Uruguayan population. MAIN CONCLUSIONS Our findings provide evidence for the origin and spread of deletion variants and emphasise indels' importance in epidemiological studies, including differentiating consecutive outbreaks occurring in the same health facility.

Adhesion molecules facilitate host-pathogen interaction & mediate Mycobacterium tuberculosis pathogenesis

Most of the microorganisms display adhesion molecules on their surface which help them to bind and interact with the host cell during infection. Adhesion molecules help mycobacteria to colonize and invade immune system of the host, and also trigger immune response explicated by the host against the infection. Hence, understanding the signalling pathways illustrated by these molecules to enhance our knowledge on mycobacterial survival and persistence inside the host cell is required. Hence, this review was focussed on the role of adhesion molecules and their receptor molecules. The various mechanisms adopted by adhesion molecules to bind with the specific receptors on the host cell and their role in invasion and persistence of mycobacterium inside the host cell are explained.

Contamination and homology of carbapenem-resistant Acinetobacter baumannii from hospital environmental object surface / 中国感染控制杂志

Objective To investigate the contamination of carbapenem-resistant Acinetobacter baumannii (CRAB) from object surface of key departments in a hospital,and identify whether these CRAB were homologous. Methods Environmental hygienic monitoring in intensive care unit (ICU),emergency intensive care unit(EICU), hemodialysis room and operating room was conducted.Acinetobacter baumannii (A.baumannii)isolated from ICU and EICU environmental specimens were amplified and typed by enterobacterial repetitive intergenic consensus-poly-merase chain reaction (ERIC-PCR).Results Except hand hygiene of health care workers in EICU was qualified, bacterial count of object surface of ICU and EICU were all unqualified;detection results of specimens from hemodi-alysis room and operating room were all qualified.A total of 53 specimens were taken from object surface of ICU and EICU,7 (13.21 %)A.baumannii isolates were isolated,and all were CRAB isolates,6 of which were of the same genotype and were identical with A.baumannii from patients’sputum.Conclusion CRAB isolated from object surface in key departments is homologous,cleaning and disinfection of environmental object surface should be inten-sified to reduce the occurrence of healthcare-associated infection.

Comparison of an Automated Repetitive Sequence-based PCR Microbial Typing System with IS6110-Restriction Fragment Length Polymorphism for Epidemiologic Investigation of Clinical Mycobacterium tuberculosis Isolates in Korea / 대한진단검사의학회지

Tuberculosis remains a severe public health problem worldwide. Presently, genotyping is used for conducting epidemiologic and clinical studies on tuberculosis cases. We evaluated the efficacy of the repetitive sequence-based PCR (rep-PCR)-based DiversiLab(TM) system (bioMerieux, France) over the IS6110-restriction fragment length polymorphism analysis for detecting Mycobacterium tuberculosis. In all, 89 clinical M. tuberculosis isolates collected nationwide from Korea were used. The DiversiLab system allocated the 89 isolates to 8 groups with 1 unique isolate when a similarity level of 95% was applied. Seventy-six isolates of the Beijing family and 13 isolates of non-Beijing family strains were irregularly distributed regardless of rep-PCR groups. The DiversiLab system generated a rapid, sensitive, and standardized result. It can be used to conduct molecular epidemiologic studies to identify clinical M. tuberculosis isolates in Korea.

Epidemiological Investigation of an Outbreak of Escherichia coli Infections in Neonatal Intensive Care Unit of a University Hospital / 대한임상미생물학회지

BACKGROUND: In July 2007, three neonates in the neonatal intensive care unit (NICU) of Chosun University Hospital expired due to Escherichia coli sepsis. An E. coli outbreak was suspected. METHODS: To investigate the outbreak, environmental cultures were taken from NICU. We performed repetitive extragenic palindromic (rep)-PCR to compare genotypes of the three isolates from the cases and one environmental strain of E. coli. A case-control study was done in order to identify risk factors for the infection. RESULTS: In July 2007, the attack rate of E. coli was 11.1%, which was higher than the basal rate. All the three E. coli isolates from the cases presented the same antimicrobial susceptibility pattern whereas other E. coli isolated from non-outbreak period presented different patterns. Among environmental cultures, only one specimen collected from the surface of a bathtub for neonates was culture positive for E. coli. Three strains of the cases and one environmental strain of E. coli showed the same rep-PCR pattern, while control strains showed different patterns. No statistically significant difference in risk factors was found between the case and control groups in the case-control study. CONCLUSION: The result of rep-PCR assay showed that the outbreak had originated from a single clone of E. coli. But we could not identify risk factors for the infection. The attack rate of E. coli in NICU returned to the basal level after implement of the infection control measures such as disinfection of NICU environment and equipments, thorough hand washing, and education of health care workers.

The application of TD (Touch-Down) PCR in Diagnosis of leprosy and Detection of MDT-resistant M. leprae / 나학회지

There are several methods for diagnosis of leprosy, including AFB stain, the measurement of PGL-1 (phenolic glycolipid - 1) antigen titer, and DNA-PCR. In this study, we have used the DNA-PCR amplifying the RLEP repetitive sequence. Our result showed that the RLEP primer offered the more sensitive detection and identification of M. leprae DNA in clinical specimens, compared with the other primer, for example, 18-kDa antigen gene. To screen the resistant M. leprae strain of MDT (Multi-Drug Therapy), we have used the TD (Touch-Down) PCR. We arranged and amplified sequences of the genes, folP, rpoB, gyr, 23S rRNA, in M. leprae involved in MDT-resistance, and could obtain the PCR product each gene, simultaneously. This method, based on annealing temperature, was useful to the detection for diagnosis and the screen of MDT-resistant strain of M. leprae, rapidly. Thus, we suggest that the RLEP primer and TD-PCR method are effective in assessing the diagnosis of leprosy and the identification of drug-resistant M. leprae.

Methicillin-Resistant Staphylococcus aureus Infections in Intensive Care Unit (ICU) Patients: Relation to Nasal Carriage of Patients or ICU Personnels / 대한임상미생물학회지

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is the most common nosocomial pathogen, which is particularly prevalent in intensive care units (ICUs). We performed this study to investigate the modes of transmission of MRSA and the role of nasal carriage of MRSA to subsequent MRSA infection in ICU. METHODS: From September to November 1997, all patients admitted for more than two days to the ICU were studied prospectively. Nasal swabs were obtained at admission and weekly during the ICU stay. Surveillance cultures of nares of the ICU personnels were done. Molecular typing was performed with repetitive sequence-based PCR (rep-PCR). RESULTS: At ICU admission 34 patients (21.0%: 19 MSSA, 15 MRSA) were MRSA nasal carrier, while 126 patients were free of nasal colonization. During the ICU stay 12 (9.5%: 3 MSSA, 9 MRSA) of the 126 noncolonized patients became nasal carriers (P <0.05). S. aureus infections (all MRSA) were documented in 14 (15 isolates, 8.6%) of the total 162 patients. S. aureus infections were significantly higher for those patients who were nasal carriers at ICU admission than for those found to be initially negative (P <0.05). Two different type (A, 7 isolate; B, 8 isolates) of rep-PCR patterns were identified. All four nasal and seven clinical isolates from the patients, and four nasal isolates from the ICU personnels were mixed with A and B patterns, respectively. CONCLUSION: Nasal colonization was related to the increased incidence of MRSA infections. Patients or ICU personnels who were nasal colonized with MRSA seemed to be a major source for transmission of MRSA in the ICU.

Clinical and gene study on one pedigree of hereditary spinocerebellar ataxia type 7 / 中华神经科杂志

Objective To summarize the clinical characteristics and make genetic diagnosis in the patients with hereditary spinocerebellar ataxia type 7 (SCA7).Methods Pedigree analysis and clinical examination were performed in one family with SCA7 by clinical findings,of which retinal morphology and visual electrophysiology were available on part numbers.The polymorphic cytosine adenine guanine (CAG) repeats in the encode region of SCA7 gene were detected by combining polymerase chain reaction with deoxyribonucleic acide (DNA) sequencing on 19 familial numbers and 12 controls.Results 6 patients were identified,who manifesting cerebellar ataxia,decreased visual acuity and colour vision defect,as was pigmentary retinopathy on fundoscopy;The 6 patients had not only extinction of the electroretinogram (ERG) but also remarkably reduced amplitudes of oscillatory potentials and flash-visual evoked potentials. On normal alleles CAG repeat size ranges from 8 to 25 repeats,wherease on mutated alleles of the 6 numbers it ranges from 50 to 97 repeats.The 6 numbers were diagnosised as SCA7 patients.One asymptomatic individual of this family,who displayed a normal allele with 18 CAG repeats and another containing abnormal expantion of 56 repeats,was diagnosised as a asymptomatic carrier whose age maybe still below the age of onset.Conclusion The clinical manifestations of SCA7 are heterogeneous,and the detection of CAG repeats can provide an effective way for the gene diagnosis and the prediction of asymptomatic patients.