Genetic diversity analysis and fingerprinting of 175 Chimonanthus praecox germplasm based on SSR molecular marker / 生物工程学报

The elucidation of resources pertaining to the Chimonanthus praecox varieties and the establishment of a fingerprint serve as crucial underpinnings for advancing scientific inquiry and industrial progress in relation to C. praecox. Employing the SSR molecular marker technology, an exploration of the genetic diversity of 175 C. praecox varieties (lines) in the Yanling region was conducted, and an analysis of the genetic diversity among these varieties was carried out using the UPDM clustering method in NTSYSpc 2.1 software. We analyzed the genetic structure of 175 germplasm using Structure v2.3.3 software based on a Bayesian model. General linear model (GLM) association was utilized to analyze traits and markers. The genetic diversity analysis revealed a mean number of alleles (Na) of 6.857, a mean expected heterozygosity (He) of 0.496 3, a mean observed heterozygosity (Ho) of 0.503 7, a mean genetic diversity index of Nei՚s of 0.494 9, and a mean Shannon information index of 0.995 8. These results suggest that the C. praecox population in Yanling exhibits a rich genetic diversity. Additionally, the population structure and the UPDM clustering were examined. In the GLM model, a total of fifteen marker loci exhibited significant (P < 0.05) association with eight phenotypic traits, with the explained phenotypic variation ranging from 14.90% to 36.03%. The construction of fingerprints for C. praecox varieties (lines) was accomplished by utilizing eleven primer pairs with the highest polymorphic information content, resulting in the analysis of 175 SSR markers. The present study offers a thorough examination of the genetic diversity and SSR molecular markers of C. praecox in Yanling, and establishes a fundamental germplasm repository of C. praecox, thereby furnishing theoretical underpinnings for the selection and cultivation of novel and superior C. praecox varieties, varietal identification, and resource preservation and exploitation.

Identification and expression analysis of the YABBY gene family in strawberry / 生物工程学报

YABBY proteins are important transcription factors that regulate morphogenesis and organ development in plants. In order to study the YABBY of strawberry, bioinformatic technique were used to identify the YABBY gene families in Fragaria vesca (diploid) and Fragaria×ananassa (octoploid), and then analyze the sequence characters, phylogeny and collinearity of the family members. The RNA-seq data and the quantitative reverse transcription-polymerase chain reaction (qRT-PCR) technique were used to assay the expression patterns of the family members. A green fluorescent protein (GFP) was fused with FvYABBYs and transiently expressed in tobacco leaf cells for the subcellular localization. As the results, six FvYABBY genes and 26 FxaYABBY genes were identified from F. vesca and F.×ananassa, respectively. The FvYABBY genes were grouped into five clades, and five family members were orthologous with AtYABBY genes of Arabidopsis. In F. vesca, all of the FvYABBYs were basically not expressed not expressed in root and receptacle, while FvYABBY1, FvYABBY2, FvYABBY5 and FvYABBY6 were highly expressed in leaf, shoot, flower and achene. In F.×ananassa, FxaYABBY1, FxaYABBY2, FxaYABBY5 and FxaYABBY6 were expressed in achene, and all FxaYABBY were poorly or not expressed in receptacle. Additionally, under the abiotic stresses of low temperature, high salt and drought, the expression of FvYABBY1, FvYABBY3, FvYABBY4 and FvYABBY6 were down-regulated, FvYABBY5 was up-regulated, and FvYABBY2 was up-regulated and then down-regulated. In tobacco leaf cells, the subcellular localization of FvYABBY proteins were in the nucleus. These results provides a foundation for the functional researches of YABBY gene in strawberry.

Progress of Microsatellite (GT/CA)n Repeat Polymorphisms in Non-small Cell Lung Cancer / 肿瘤防治研究

Non-small cell lung cancer (NSCLC) is the most important histological type of lung cancer. This disease affects a large number of patients, and the prognosis of advanced patients is poor. Although great progress has been achieved for existing treatment methods, challenges still exist. Cancer is a genetic disease, and its occurrence is accompanied by substantial genomic-sequence instability. (GT/CA)n repeat sequence is a common microsatellite sequence serving as transcriptional function-related regions, DNA-methylation modification sites, and other functional sites. Its polymorphism is closely related to the expression of EGFR, HO-1, and HIF-1α in NSCLC patients. (GT/CA)n repeat sequence is the breakthrough point to explore the molecular mechanism of NSCLC occurrence and development, develop molecular markers for diagnosis and prognosis and epigenetics research. This paper summarizes the studies on (GT/CA)n repeat polymorphisms in NSCLC with the aim of providing references for relevant NSCLC research.

Isolation and identification of Coxsackievirus A16 strains in Kunming,Yunnan Province in 2019 and analysis of genetic characteristics of VP1 gene / 中国生物制品学杂志

@#Objective To analyze the genetic characteristics of the entire VP1 gene of Coxsackievirus A16(CVA16) strains isolated from the feces of patients with hand,foot and mouth disease(HFMD) in Yunnan Province in 2019.Methods The virus was isolated from human embryonic lung diploid fibroblast(KMB-17) cells and African green monkey kidney(Vero)cells,and the primers for the complete VP1 gene sequence of CVA16 were designed.The target fragment was amplified by RT-PCR and sequenced;the complete VP1 sequence was analyzed by softwares such as MEGA 7.0 and Geneious 9.0.2.Results A total of 26 CVA16 strains were isolated,including eight KMB-17 isolates and 18 Vero isolates.Twenty CVA16isolates were randomly selected for analysis,and three isolates were found to have Bla and 17 B1b genotypes;the nucleotide and amino acid homology of 17 CVA16 B1b isolates were 93.8%—100% and 98.3%—100%,and the nucleotide and amino acid homology with other domestic isolates was 91.1 %—99.2% and 97.3%—99.0%,respectively;the nucleotide and amino acid homology of the three Bla isolates was 98.0%—98.1% and 99.3%,and those with other domestic Bla isolates was 88.7%—98.1% and 98.3%—99.7%,respectively;17 B1b isolates and other three Bla isolates showed the nucleotide and amino acid homology of 87.4%—88.4% and 97.3%—98.7%.Conclusion The CVA16 prevalent in Kunming in 2019 belonged to Bla and B1b genotypes,with B1b as the main strain,and all of them were prevalent strains in the mainland of China.

Serotype distribution and antimicrobial resistance of pediatric Streptococcus pneumoniae isolated from inpatients and outpatients at Beijing Children's Hospital

Abstract Background Understanding the epidemiology of Streptococcus pneumoniae (S. pneumoniae) isolates is important for pneumonia treatment and prevention. This research aimed to explore the epidemiological characteristics of S. pneumoniae isolated from pediatric inpatients and outpatients during the same period. Methods S. pneumoniae were isolated from unsterile samples of inpatients and outpatients younger than five years old between March 2013 and February 2014. The serotypes were determined using diagnostic pneumococcal antisera. The resistance of each strain to 13 antibiotics was tested using either the E-test or the disc diffusion method. The Sequence Types (STs) were analyzed via Multilocus Sequence Typing (MLST). Results The dominant serotypes obtained from inpatients were 19F (32.9 %), 19A (20.7 %), 23F (10.7 %), 6A (10.0 %), and 14 (8.6 %), while those from outpatients were 19F (13.6 %), 23F (12.9 %), 6A (10.0 %), 6B (10.0 %), and 19A (7.9 %). The coverage rates of 13-valent Pneumococcal Conjugate Vaccine (PCV) formulations were high in both groups. The nonsusceptibility to penicillin, cefuroxime, imipenem, erythromycin, and trimethoprim-sulfamethoxazole among the inpatient isolates was 7.1 %, 92.8 %, 65.7 %, 100 %, and 85.0 %, respectively, while that among the outpatient isolates was 0.7 %, 50.0 %, 38.6 %, 96.4 %, and 65.7 %, respectively. There were 45 and 81 STs detected from the pneumococci isolated from inpatients and outpatients, respectively. CC271 was common among both inpatients and outpatients (43.6 % and 14.3 %). Conclusions Pneumococcal vaccine-related serotypes are prevalent among both inpatients and outpatients, especially among inpatients, who exhibit more severe antibiotic resistance. Therefore, universal immunization with PCV13 would decrease the hospitalization rate due to S. pneumoniae and the antibiotic resistance rate of S. pneumoniae.

Comparison of rocuronium priming vs. standard rapid sequence intubation technique in emergency department patients requiring intubation

SUMMARY OBJECTIVE: In our study, we aimed to compare the effect of standard rapid sequence intubation protocol and the application of rocuronium priming technique on the procedure time and hemodynamic profile. METHODS: Patients who applied to the emergency department and needed rapid sequence intubation were included in our study, which we conducted with a randomized controlled design. Randomization in the study was made according to the order of arrival of the cases. Rapid sequence intubation was performed in the standard group. In the priming group, 10% of the rocuronium dose was administered approximately 3 min before the induction agent. Intubation time, amount of drug used, vital signs, and end-tidal CO2 level before and after intubation used to confirm intubation were recorded. RESULTS: A total of 52 patients were included in the study, of which 26 patients were included in the standard group and 26 patients in the priming group. While intubation time was 121.2±21.9 s in the standard group, it was calculated as 68.4±11.6 s in the priming group (p<0.001). While the mean arterial pressure was 58.3±26.6 mmHg in the standard group after intubation, it was 80.6±21.1 mmHg in the priming group (p=0.002). CONCLUSION: It was observed that priming with rocuronium shortened the intubation time and preserved the hemodynamic profile better. Clinical Trial Registration Number: NCT05343702.

Effect of Spatial Contiguity on Learning Sequences of Positions / Efecto de la contigüidad espacial sobre el aprendizaje de secuencias de posiciones

Abstract Four conditions of spatial contiguity of positions were used to assess sequence learning. Two sequences of 16 and 25 positions presented in two matrices of 4x4 and 5x5 respectively were used. Within each matrix, 4 (in the 4x4 matrix) or 6 positions (in the 5x5 matrix) presented spatial contiguity. The place at the sequence in which contiguous positions occurred varied across groups. In this way, spatial contiguity of the 4 or 6 positions was presented at the beginning of the sequence (Group 1), in the middle part (Group 2), at the end of the sequence (Group 3) or it was presented a sequence in which all positions occurred without spatial contiguity (Group 4). 28 undergraduate students participated. Results showed no differences among groups in the number of trials required to reproduce the sequence correctly. Number of errors was lower when contiguous positions were presented at the beginning of the sequence. These findings are explained as a possible effect of accentuation of primacy given by the occurrence of contiguous positions at the beginning of the sequence.

Resumen Cuatro condiciones de contigüidad espacial de posiciones fueron empleadas para evaluar el aprendizaje de secuencias. Se emplearon dos secuencias de 16 y 25 posiciones presentadas en dos matrices de 4x4 y 5x5, respectivamente. Dentro de cada matriz, 4 (en la matriz de 4x4) o 6 posiciones (en la matriz de 5x5) presentaron contigüidad espacial. Entre grupos, se varió el punto de la secuencia en el que se presentaron las posiciones contiguas. De este modo, la contigüidad espacial de las 4 o 6 posiciones se presentó al inicio de la secuencia (Grupo 1), en la parte media (Grupo 2), al final de la secuencia (Grupo 3), o bien, se presentó una secuencia en la que todas las posiciones ocurrieron sin contigüidad espacial (Grupo 4). Participaron 28 estudiantes de licenciatura. Los resultados no mostraron diferencias entre grupos en cuanto al número de ensayos requeridos para reproducir la secuencia correctamente. El número de errores fue menor cuando las posiciones contiguas se presentaron al inicio de la secuencia. Los hallazgos se explican a partir de un posible efecto de acentuación de la primacía, dado por la ocurrencia de posiciones contiguas al inicio de la secuencia.

Review on Applicability of Bioinformatics in Current Research and Database Management

A generation of new science has evolved with the development of bioinformatics and computational biology, which have molecular biology as an integrated part. In the past decade, technological advances have promoted a prominent development in expertise and knowledge in the molecular basis of phenotypes. In Bioinformatics, biological data is evaluated by computational science and processed in a more statistical and meaningful way. It includes the collection classification storage and evaluation of biochemical and organic statistics using computers in particular as implemented in molecular genetics and genomics. Computational Biology and Bioinformatics are emerging branches of science and include the use of techniques and concepts from informatics statistics, mathematics, chemistry, biochemistry, physics and linguistics. Therefore, bioinformatics and computational biology have sought to triumph over many challenges of which a few are listed in this overview. This evaluation intends to provide insight into numerous bioinformatics databases and their uses in the analysis of biological records exploring approaches emerging methodologies strategies tools that can provide scientific meaning to the information generated.

Differential gene expression analysis in germinating and dormant teliospores of Tilletia indica using RNA seq approach

Karnal bunt of wheat is an important quarantine disease that interrupts India’s wheat trade in the international market. The whole transcriptome of germinating and dormant teliospores of Tilletia indica was performed using the RNA Seq approach to identify germination-related genes. Approximately 63 million reads were generated using the RNA sequencing by the Illumina NextSeq500 platform. The high-quality reads were deposited in NCBI SRA database (accession: PRJNA522347). The unigenes from the pooled teliospores were 16,575 having unigenes length of 28,998,753 bases. The high-quality reads of germinating teliospores mapped on to 21,505 predicted CDSs. 9,680 CDSs were common between dormant and germinating teliospores of T. indica. 11,825 CDSs were found to be in germinating teliospores while only 91 were unique in dormant spores of pathogen. The pathway analysis showed the highest number of pathways was found in germinating spores than dormant spores. The highest numbers of CDSs were found to be associated with translation (431 in number), transport and catabolism (340), signal transduction (326), and carbohydrate metabolism (283). The differential expression analysis (DESeq) of germinating and dormant teliospores showed that 686 CDS were up-regulated and 114 CDS were down-regulated in the germinating teliospores. Significant germination-related genes in the spores were validated using qPCR analysis. Ten genes viz. Ti3931, Ti6828, Ti7098, Ti7462, Ti7522, Ti 9289, Ti 8670, Ti 7959, Ti 7809,and Ti10095 were highly up-regulated in germinated teliospores which may have role in germination of spores.Further, these differentially expressed genes provide insights into the molecular events. This first study of transcriptome will be helpful to devise better management strategies to manage Karnal bunt disease.

CONTEXTUAL LEARNING APPROACH FOR SYNDROME DISEASE NAMED ENTITY RECOGNITION

The groundwork for extracting a significant amount of biomedical information from unstructured texts into structured formats is the difficult research area of biological entity recognition from medical documents. The existing work implemented the named entity recognition for diseases using the sequence labelling framework. The performance of this strategy, however, is not always adequate, and it frequently cannot fully exploit the semantic information in the dataset. The Syndrome Diseases Named Entity problem is presented in this work as a sequence labelling with multi-context learning. By using well-designed text/queries, this formulation may incorporate more previous information and to decode it using decoding techniques such conditional random fields (CRF). We performed experiments on three biomedical datasets, and the outcomes show how effective our methodology is on the BC5CDR-Disease, JNLPBA and NCBI-Disease, compared with other techniques our methodology performs with accuracy levels of 96.70%,98.65 and 96.72% respectively.

Perfusão arterial reversa gemelar: revisão da literatura / Twin reverse arterial perfusion: literature review

A perfusão arterial reversa gemelar é uma anormalidade rara que pode ocorrer em gestações gemelares monocoriônicas. Consiste em uma alteração na circulação fetoplacentária, com desvio de sangue de um dos gemelares para o outro, por meio de anastomoses arterioarteriais e venovenosas na superfície placentária e anastomoses arteriovenosas em áreas de circulação placentária compartilhada. O feto bombeador pode desenvolver insuficiência cardíaca devido ao aumento do débito cardíaco, e o feto receptor, perfundido por sangue pobre em oxigênio por meio do fluxo reverso, é severamente malformado, incompatível com a vida extrauterina. Este artigo apresenta o caso de uma gestação gemelar monocoriônica diamniótica, com manejo clínico conservador. O objetivo é relatar um caso de complicação rara de gestações monozigóticas e revisar condutas para diagnóstico e manejo adequado.(AU)

Twin reverse arterial perfusion is a rare abnormality that can occur in monochorionic twin pregnancies. It consists of an alteration in the fetal-placental circulation, with blood diversion from one of the twins to the other, through arterio-arterial and veno- venous anastomosis on the placental surface and arterio-venous anastomosis in areas of shared placental circulation. The pumping fetus may develop heart failure due to increased cardiac output, and the recipient fetus, perfused by oxygen-poor blood through reverse flow, is severely malformed, incompatible with extrauterine life. This article presents the case of a monochorionic diamniotic twin pregnancy, with conservative clinical management. The objective is to report a case of rare complication of monozygotic pregnancies and review procedures for diagnosis and adequate management.(AU)

Molecular epidemiology and antifungal susceptibilities of Aspergillus species isolated from patients with invasive aspergillosis

SUMMARY OBJECTIVE: The aim of this study was to evaluate the demographic data, molecular epidemiology, and in vitro antifungal susceptibility results of patients with Aspergillus isolated from various clinical specimens. METHODS: A total of 44 Aspergillus strains were studied. The definition of invasive aspergillosis in patients was made according to European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG) criteria. Strains were phenotypically and molecularly identified. Demographic characteristics of patients and genotypes of strains were evaluated. Phylogenetic analysis was done by the The Unweighted Pair-Group Method with Arithmetic Mean (UPGMA). Antifungal susceptibility of strains was determined according to The Clinical and Laboratory Standards Institute (CLSI)-M61-Ed2 and The European Committee on Antimicrobial Susceptibility Testing (EUCAST). RESULTS: A total of 11 patients were classified as proven and 33 as probable invasive aspergillosis. There was a statistically significant difference in age groups, subdisease, neutropenic, and receiving chemotherapy between groups. A total of 23 strains were identified as Aspergillus fumigatus, 12 as Aspergillus niger, 6 as Aspergillus flavus, and 3 as Aspergillus terreus. Phylogenetic analysis revealed five different genotypes. No statistical difference was found in the comparisons between patients groups and genotype groups. There was a statistically significant difference between genotype groups and voriconazole, posaconazole, and itraconazole Minimum Inhibition Concentration (MIC). CONCLUSION: Accurate identification of strains and antifungal susceptibility studies should be performed due to azole and amphotericin B resistance. Genotyping studies are important in infection control due to identifying sources of infection and transmission routes.

In vitro transcribed (IVT) mRNA drugs: technical progress and application prospect / 药学学报

The in vitro transcribed (IVT) mRNA technology has progressed rapidly and the application of mRNA vaccines in the COVID-19 pandemic made it become the most talked-about topic. Compared with protein drugs, IVT mRNA has a lower cost; it can be modular produced and its sequence can be modified easily, so it has a broad application prospect. However, due to its short history, mRNA drugs face the problem of lacking sufficient clinical data, and there is no quality control standard for mRNA drugs except mRNA vaccines. We overview the sequence design, delivery vectors, administration, application prospect and safety considerations of mRNA drugs. We also discussed the quality control of mRNA drugs briefly.

Characterization of the complete chloroplast genome of Polygonatum franchetii Hua, a Chinese endemic medicinal species, and phylogenetic relationships of Polygonatum / 药学学报

italic>Polygonatum franchetii Hua is a medicinal plant endemic to China from Polygonatum Mill. The chloroplast genomes of two P. franchetii individuals sampled from two different habitats were sequenced by using the DNBSEQ-T7 high-throughput sequencing platform. After assembly and annotation, the two complete chloroplast genomes were characterized, and then comparative and phylogenetic analyses were performed with other published chloroplast genome sequences from Polygonatum. The whole chloroplast genomes of the two P. franchetii individuals were 155 942 and 155 962 bp in length, with a large single copy region (LSC, 84 670 and 84 722 bp), a small single copy region (SSC, 18 564 and 18 566 bp) and a pair of reverse repeats (IRa/IRb, 26 354 and 26 337 bp), respectively. Both of them contained 113 genes, including 79 protein-coding genes (PCGs), 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Comparative analyses showed that the genome length, the guanine and cytosine (GC) content, genes content and order were highly conserved between the two P. franchetii individuals and among different Polygonatum species. The detected repeat sequences, including dispersed repeats, tandem repeats and simple sequence repeats (SSRs), were also relatively similar in types and positions, though showing a slightly difference in number. No significant expansion or contraction of the inverted repeat regions was found. Sequences variation between the two P. franchetii individuals was lower than that among different Polygonatum species. Besides, coding sequences (CDS) showed less divergence than noncoding sequences, and sequence divergence of IRs regions was lower than that of the LSC and SSC regions, both intraspecifically and interspecifically. Eight sequences with high nucleotide diversity among different species were screened, all of which were found located in the LSC and SSC regions. Phylogenetic inference showed that all Polygonatum species clustered into a monophyletic clade with a 100% bootstrap value, within which, species in section Verticillata formed a distinct group, section Sibirica and section Polygonatum were sister groups. The two P. franchetii individuals grouped together and showed the closest phylogenetic affinity to P. stenophyllum Maxim., belonging to the section Verticillata. The chloroplast genome of P. franchetii and its phylogenetic position in Polygonatum were comprehensively investigated and clearly elucidated in this study, the results may lay a foundation for the resource development and utilization of P. franchetii, as well as further molecular identification and phylogenetic studies of medicinal Polygonatum species.

Phylogenetic analysis of chloroplast genome of Tussilago farfara L / 药学学报

italic>Tussilago farfara L. is a perennial herb of Tussilago genus in the Compositae family. Its dried buds and leaves have good biological activities and have a long history of medicinal use in China and Europe. In this paper, we investigated the whole chloroplast genome characteristics, sequence duplication, structural variation and phylogeny of the Tussilago farfara L. After sequencing the Tussilago farfara L. chloroplast genome using Illumination technology, the complete Tussilago farfara L. chloroplast genome was further obtained by assembly and annotation, followed by a series of inverted repeat-large single copy/small single copy region contraction and expansion analysis, genome sequence variation, etc. The sequences of 13 homologous plants downloaded from NCBI were used to construct a neighbor-joining phylogenetic tree. The results showed that the total GC content of the chloroplast genome was 37.4% and the length was 150 300 bp; 125 genes were annotated, including 82 protein-coding genes, 35 tRNAs and 8 rRNAs; 148 (simple sequence repeats, SSR) loci were detected, and the relative synonymous codon usage showed that 31 codons out of 64 codons had a usage of >1. In the phylogenetic analysis, the chloroplast genomes of the seven species of Asteraceae, including the Yulin Tussilago farfara L., were highly conserved, and the sequence variation of the (large single-copy, LSC) and (small single-copy, SSC) regions was higher than that of the (inverted repeat, IR) region. This is in general agreement with the reported phylogeny of Yulin Tussilago farfara L. In this study, we obtained a high quality chloroplast genome and analyzed its genome characteristics, codon preference, SSR characteristics, SC/IR boundary, sequence variation and phylogeny, which can provide a basis for species identification, genetic diversity analysis and resource development of this medicinal plant.

Identification and biological characterization of pathogen causing black spot of Pseudostellaria heterophylla in Fujian province / 中国中药杂志

In Zherong county, Fujian province, the black spot of Pseudostellaria heterophylla often breaks out in the rainy season from April to June every year. As one of the main leaf diseases of P. heterophylla, black spot seriously affects the yield and quality of the medicinal material. To identify and characterize the pathogens causing black spot, we isolated the pathogens, identified them as a species of Alternaria according to Koch's postulates, and then tested their pathogenicity and biological characteristics. The results showed that the pathogens causing P. heterophylla black spot were A. gaisen, as evidenced by the similar colony morphology, spore characteristics, sporulation phenotype, and the same clade with A. gaisen on the phylogenetic tree(the maximum likelihood support rate of 100% and the Bayesian posterior probability of 1.00) built based on the tandem sequences of ITS, tef1, gapdh, endoPG, Alta1, OPA10-2, and KOG1077. The optimum conditions for mycelial growth of the pathogen were 25 ℃, pH 5-8, and 24 h dark culture. The lethal conditions for mycelia and spores were both treatment at 50 ℃ for 10 min. We reported for the first time the A. gaisen-caused black spot of P. heterophylla. The results could provide a theoretical basis for the diagnosis and control of P. heterophylla leaf spot diseases.

Investigation of a suspected outbreak of carbapenem-resistant Klebsiella pneumonia infection / 上海预防医学

ObjectiveTo investigate a suspected outbreak of healthcare-associated infection （HAI） caused by carbapenem-resistant Klebsiella pneumonia （CRKP） in a secondary grade-A hospital， analyze the infection source and transmission route， and put forward corresponding preventive and control measures. MethodsEpidemiological investigation was conducted on 5 patients with CRKP infection in department of neurosurgery during December 23‒30， 2021. Specimens were collected with the environmental microbiology monitoring procedure. CRKP isolated from the environmental samples were analyzed by multilocus sequence typing （MLST） method. Comprehensive measures were taken to control the CRKP infection. ResultsThe 5 infected patients were located in 3 rooms， and all were diagnosed as HAI. The antimicrobial susceptibility testing results from the specimens of 3 CRKP infected patients were the same. Through environmental microbiology monitoring， CRKP strains were detected from the faucet handle and sink specimens in 3 rooms. The results of MLST analysis showed that the faucet handle and sink specimens in room 2 and 3 were ST11 type. The environmental specimen in room 1 was ST23 type. The suspected outbreak was effectively controlled after comprehensive interventions. ConclusionHAI suspected outbreak might be caused by the environmental contamination from the pathogens of CRKP-infected patients as well as the contaminated hands of medical staff and accompanying family members. Strengthening the publicity， education and management of medical staff and accompanying staff， early identification of infection outbreaks， and timely comprehensive control measures are the keys to controlling multidrug-resistant nosocomial infection outbreaks.

Genetic and evolutionary characteristics of clindamycin-resistant Staphylococcus aureus in Yangzhou / 公共卫生与预防医学

Objective To investigate the drug resistance phenotype, drug resistance genes and molecular characteristics of clinical isolates of Staphylococcus aureus in Yangzhou from 2016 to 2020. Methods A total of 71 strains of clindamycin resistant Staphylococcus aureus were collected. Molecular typing of the strains was performed using multilocus sequence typing (MLST) and SNP. Antimicrobial minimal inhibitory concentrations were detected by the method of microdilution broth. Different resistance genes were detected. Results A total of 71 strains of clindamycin resistant Staphylococcus aureus were collected in this study, of which 42 strains (59.15%) were inherently resistant and 29 strains (40.85%) were induced resistant ; 44 strains (61.97%) were found to be methicillin resistant Staphylococcus aureus (MRSA). Among the 71 strains , 18 ST types were found , and the detection rates of mecA and ermB in ST59 strain were higher than those in other ST types. Among the clustered strains, CC59 was inherently resistant. Conclusion The clinically isolated Staphylococcus aureus in Yangzhou has severe drug resistance, especially the resistance to clindamycin. CC59 clone group carries many drug resistance genes, and all of them are MRSA . This study provides reliable data for clinical selection of appropriate drugs and further investigation of the prevalence of clindamycin-resistant strains.

Genome-sequence, annotation and phylogenetic insights of the lactic acid bacterium Limosilactobacillus fermentum strain LAB1 obtained from the dairy beverage borhani

Limosilactobacillus fermentum is a promising probiotic with several documented health benefits. LAB1 is an antagonistic L. fermentum strain isolated from borhani, a traditional South Asian beverage prepared from dairy and plant ingredients. Here, I present the genome sequence of the L. fermentum LAB1 strain, its annotation, and phylogenetic features. The 2.01 Mb genome with a G+C content of 51.9% was assembled into 221 contigs and predicted to have 1,913 protein-coding genes, 98 pseudo genes, 7 rRNAs, 60 tRNAs, and 1 CRISPR array. As much as 91.1% of the coding sequences could be assigned to known functional genes. Determination of average nucleotide identity (ANI) of the genome sequence revealed 99.37% identity to that of the type strain ATCC 14931. Its 16S rRNA gene sequence extracted from the genome sequence showed close phylogenetic association with several L. fermentum strains. The genome sequence is expected to provide useful insights with regard to the phenotypic, metabolic and beneficial aspects of this lactic acid bacterium.(AU)

Antimicrobial resistance and genomic characteristics of Salmonella enterica serovar Derby isolates from clinical patients and food sources in Hangzhou / 中华微生物学和免疫学杂志

Objective:To analyze the antimicrobial resistance and genomic characteristics of Salmonella enterica serovar Derby strains isolated from human and food sources in Hangzhou. Methods:A total of 60 Salmonella enterica serovar Derby strains isolated in Hangzhou during the period from 2015 to 2020 were subjected to antimicrobial susceptibility testing, pulsed field gel electrophoresis (PFGE) typing and whole-genome sequencing. Multilocus sequence typing (MLST), core genome multilocus sequence typing (cgMLST) and the identification of antimicrobial resistance genes were performed using the sequencing data. Phylogenetic tree based on the single nucleotide polymorphism (SNP) sites in the 60 genomes from Hangzhou and 379 genomes from public databases was constructed. Results:No significant difference was observed in the drug resistance rates between the clinical strains and food strains in Hangzhou. The multidrug resistance (MDR) rate was 76.7% (46/60). All of the 60 Salmonella Derby strains were positive for the antimicrobial resistance genes aac(6′)- Iaa and fosA7. The 60 strains were subtyped into 46 molecular types by PFGE and 53 molecular types by cgMLST(HC2). Except for one strain belonging to ST3220, the other Salmonella Derby strains were ST40. The phylogenetic analysis showed that some strains isolated in Hangzhou were close to the strains in Southeast Asia, suggesting the possibility of cross-border transmission of ST40 strains, with the main food sources being pork and fish; other strains were close to those circulating in Beijing, Guangzhou, Hubei, Chongqing and other provinces, suggesting the possibility of cross-province transmission of the strains, with the main food sources being pork, beef and chicken. Conclusions:The epidemic of Salmonella Derby in Hangzhou was mainly caused by the spread of ST40 strains and MDR was common. Clinical infections might be closely related to the consumption of pork, beef, chicken and fish. There was the possibility of cross-border transmission of Salmonella Derby between Hangzhou and Southeast Asia and cross-province transmission in China.