Whole-genome sequencing of strains of Vibrio spp. from China reveals different genetic contexts of blaCTX-M-14 among diverse lineages

2021 ◽  
Author(s):  
Zhiwei Zheng ◽  
Lianwei Ye ◽  
Ruichao Li ◽  
Sheng Chen
Keyword(s):  
Vibrio Parahaemolyticus ◽  
Southern Blotting ◽  
Upstream Region ◽  
Whole Genome ◽  
The Novel ◽  
Whole Genome Analysis ◽  
Integrative Conjugative Element ◽  
Chromosome I ◽  
Vibrio Spp ◽  
M 14

Abstract Objectives To investigate the prevalence and genetic contexts of the blaCTX-M-14 gene harboured by foodborne isolates of Vibrio spp. in China. Methods A total of 1856 Vibrio spp. isolates collected from raw meat and shrimp samples in Guangdong Province of China were screened for blaCTX-M-14 by PCR. The blaCTX-M-14-positive isolates were characterized by MIC, PFGE, MLST, conjugation, S1-PFGE and Southern blotting and WGS using Illumina and Nanopore platforms. Results A total of 35 (1.9%) Vibrio isolates were positive for blaCTX-M-14, including 33 Vibrio parahaemolyticus strains and two Vibrio alginolyticus strains. MLST showed that most of the blaCTX-M-14-bearing isolates could be assigned into two major STs, with ST163 being more prevalent (n = 23), followed by ST180 (n = 6). Whole-genome analysis of these 35 isolates revealed that the blaCTX-M-14 gene was associated with ISEcp1 in the upstream region, of which 32 blaCTX-M-14 genes were located in the same loci of chromosome I, 1 blaCTX-M-14 gene was located in a novel chromosomal integrative conjugative element (ICE) belonging to the SXT/R391 family and 2 blaCTX-M-14 genes were located in the same type of plasmid, which belonged to the IncP-1 group. Conjugation experiments showed that only the plasmid-borne blaCTX-M-14 gene could be transferred to the recipient strain Escherichia coli J53. Conclusions The emergence of the novel ICE and IncP-1 plasmids has contributed to the variable genetic contexts of blaCTX-M-14 among strains of Vibrio spp. and facilitated the horizontal transfer of such genes between Vibrio spp. and other zoonotic pathogens, resulting in a rapid increase in the prevalence of blaCTX-M-14-bearing bacterial pathogens worldwide.

scholarly journals Phylogenomic analysis of Pseudomonas nitroreducens strains FY43 and FY47

2022 ◽  
pp. 1-11
Author(s):  
Xue Li Tan ◽  
Wei Yee Wee ◽  
Boon Chin Tan ◽  
Chee How Teo
Keyword(s):  
Genome Analysis ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
The Novel ◽  
Species Classification ◽  
Whole Genome Analysis ◽  
Pseudomonas Nitroreducens ◽  
High Level ◽  
Next Generation Sequencing Ngs ◽  
Diversity Studies

Proper identification of strain is essential in understanding the ecology of a bacteria species. The classification of Pseudomonas nitroreducens is still being questioned and revised until now. The novel P. nitroreducens strains FY43 and FY47 used in this study have been reported to show a high level of tolerance to glyphosate. In this study, next-generation sequencing (NGS) and whole genome analysis were used to clarify the delineation of the species. Whole genome analysis showed that P. nitroreducens strains FY43 and FY47 shared high homology to five reference genomes of P. nitroreducens: strain B, Aramco J, NBRC 12694, DF05, and TX01. Phylogenomic and phylogenetic analysis (average nucleotide identity based on BLAST (ANIb), genome-to-genome distance (GGDC) analysis) showed that both P. nitroreducens strains FY43 and FY47 are Pseudomonas nitroreducens members. However, strains DF05 and TX01 were not correctly assigned at the species level for all the analyses. The P. nitroreducens strain DF05 and TX01 should be further investigated for their classification as the correct species classification is the prerequisite for future diversity studies.

scholarly journals Prevalence and Characteristics of Ceftriaxone-Resistant Salmonella in Children’s Hospital in Hangzhou, China

2021 ◽  
Vol 12 ◽  
Author(s):  
Qiucheng Shi ◽  
Yihua Ye ◽  
Peng Lan ◽  
Xinhong Han ◽  
Jingjing Quan ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Resistance Mechanism ◽  
Resistance Rate ◽  
High Rate ◽  
Whole Genome ◽  
Older Children ◽  
Whole Genome Analysis ◽  
Antimicrobial Resistance Genes ◽  
Resistance Rates ◽  
M 14

The non-Typhi Salmonella (NTS) infection is critical to children’s health, and the ceftriaxone is the important empirical treatment choice. With the increase resistance rate of ceftriaxone in Salmonella, the molecular epidemiology and resistance mechanism of ceftriaxone-resistant Salmonella needs to be studied. From July 2019 to July 2020, a total of 205 NTS isolates were collected, 195 of which (95.1%) were cultured from stool, but 10 isolates were isolated from an extraintestinal site. Serogroup B accounted for the vast majority (137/205) among the isolates. Fifty-three isolates were resistant to ceftriaxone, and 50 were isolated from children younger than 4years of age. The resistance rates for ceftriaxone, ciprofloxacin, and levofloxacin were significantly higher in younger children than the older children. The resistance genes in the ceftriaxone-susceptible isolates were detected by PCR, and ceftriaxone-resistant Salmonella were selected for further whole-genome sequencing. Whole-genome analysis showed that serotype Typhimurium and its monophasic variant was the most prevalent in ceftriaxone-resistant isolates (37/53), which comprised ST34 (33/53), ST19 (2/53), and ST99 (2/53), and they were close related in the phylogenetic tree. However, the other isolates were diverse, which included one Enteritidis (ST11), one Indiana (ST17), one Derby (ST40), four Kentucky (ST198), two Goldcoast (ST2529, ST358), one Muenster (ST321), one Virchow (ST359), one Rissen (ST469), one Kedougou (ST1543), two Uganda (ST684), and one Kottbus (ST8839). Moreover, CTX-M-55 ESBLs production (33/53) was found to be mainly responsible for ceftriaxone resistance, followed by blaCTX-M-65 (12/53), blaCTX-M-14 (4/53), blaCTX-M-9 (2/53), blaCTX-M-64 (1/53), blaCTX-M-130 (1/53), and blaCMY-2 (1/53). ISEcp1, IS903B, IS Kpn26, IS1F, and IS26 were connected to antimicrobial resistance genes transfer. In conclusion, the dissemination of ESBL-producing Salmonella isolates resulted in an increased prevalence of ceftriaxone resistance in young children. The high rate of multidrug resistance should be given additional attention.

Whole-genome analysis of EC129, an NDM-5-, CTX-M-14-, OXA-10- and MCR-1-co-producing Escherichia coli ST167 strain isolated from Japan

2019 ◽  
Vol 18 ◽  
pp. 148-150 ◽  
Author(s):  
Yoko Nukui ◽  
Alafate Ayibieke ◽  
Makoto Taniguchi ◽  
Yoshibumi Aiso ◽  
Yuka Shibuya ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genome Analysis ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
M 14

scholarly journals First whole genome analysis of the novel coronavirus (SARS-CoV-2) obtained from COVID-19 patients from five districts in Western Serbia

2021 ◽  
pp. 1-31
Author(s):  
Dejan Vidanović ◽  
Bojana Tešović ◽  
Jeremy D Volkening ◽  
Claudio L Afonso ◽  
Joshua Quick ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Whole Genome ◽  
The Novel ◽  
Whole Genome Analysis ◽  
Novel Coronavirus

NGHIÊN CỨU ĐẶC ĐIỂM GÂY BỆNH VÀ DỊCH TỄ CỦA BỆNH TÔM CHẾT SỚM (EMS) TẠI TỈNH QUẢNG BÌNH NHẰM ĐỀ XUẤT QUY TRÌNH CHẨN ĐOÁN VÀ PHÒNG TRỊNGHIÊN CỨU ĐẶC ĐIỂM DỊCH TỄ CỦA BỆNH TÔM CHẾT SỚM (EMS) TẠI TỈNH QUẢNG BÌNH NHẰM ĐỀ XUẤT QUY TRÌNH CHẨN ĐOÁN VÀ PHÒNG TRỊ

2015 ◽  
Vol 104 (5) ◽  
Author(s):  
Trần Thị Linh Giang ◽  
Dương Viết Phương Tuấn
Keyword(s):  
Bile Salt ◽  
Vibrio Parahaemolyticus ◽  
Vibrio Spp

Nghiên cứu về Hội chứng chết sớm ở tôm thực hiện ở Quảng Bình với mục đích tìm hiểu đặc điểm gây bệnh của vi khuẩn Vibrio paraheamolyticus và đặc điểm dịch tể để khuyến cao cách phòng trị và có dự báo sớm làm giảm rủi roc ho nghề nuôi tôm. Có 120 phiếu và 91 mẫu tôm nghi bệnh được thu và nuôi cấy, tìm hiểu đặc điểm vi khuẩn này và phân tích gen để xác định độc tố, đồng thời nghiên cứu về đặc điểm dịch tễ của bệnh EMS ở 4 huyện, thành phố . Kết quả cho thấy rằng hơn 70% số mẫu nghi bệnh có kết quả dương tính, tần suất nhiễm bệnh cao 10 – 60,6 % và khác nhau ở các tháng và vụ nuôi, cao nhất vào tháng 4 – 7 DL, X2 = 1.60 (df = 4), với P < 0,05. Tôm nhiễm bệnh EMS có các biểu hiện các triệu chứng điển hình gan tuỵ và tỷ lệ chết cao đến 100% nếu không can thiệp kịp thời. Đặc điểm chung các loài vi khuẩn thuộc giống Vibrio: Gram âm, hình que thẳng hoặc hơi uốn cong, kích thước 0,3-0,5 x 1,4-2,6 μm, không hình thành bào tử và chuyển động nhờ một tiên mao hoặc nhiều tiên mao mảnh và yếm khí, hầu hết là oxy hoá và lên men trong môi trường O/F Glucose. Thiosulphate citrate bile salt agar (TCBS) là môi trường chọn lọc của Vibrio spp. Chúng mẫn cảm với Vibriostat 2,4 diamino-6,7 diisopropyl pteridine phosphate (0/129). Tỷ lệ V. parahaemolyticus gây bệnh tôm chết sớm.Vi khuẩn V. parahaemolyticus gây bệnh có đặc điểm cấu trúc gen khác biệt, nhiễm sắc thể tự điều chỉnh nằm ở vị trí 01. Từ những kết quả hình ảnh trên ta thấy được sự sai khác về trình tự gen DNA của mẫu W1, trình tự gen của mẫu này trùng hợp với trình tự gen DNA của Vibrio parahaemolyticus dùng đối chứng trên và sự sai khác về trình tự gen cũng đã thể hiện được khả năng gây bệnh của vi khuẩn V. parahaemolyticus. Các phản ứng với các loại kháng sinh có hiệu quả từ 8 – 45%, đều làm giảm số lượng tôm chết khi nhiễm, cao nhất là Baymet và Osamet, Olimos. Sử dụng chế phẩm Bokashi trầu với hiệu quả tốt nếu dùng từ đầu vụ và đến cuối vụ, với thành phần Eugenol, chavicol và chavibetol đã hạn chế sự phát triển của bệnh, kể cả những ao có mật độ V. parahaemolyticus cao nhưng ít có nguy cơ gây bệnh.

scholarly journals Detection of SARS-CoV-2 from patient fecal samples by whole genome sequencing

Gut Pathogens ◽  
2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Andreas Papoutsis ◽  
Thomas Borody ◽  
Siba Dolai ◽  
Jordan Daniels ◽  
Skylar Steinberg ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Nasopharyngeal Swab ◽  
Whole Genome ◽  
Rt Pcr ◽  
Whole Genome Analysis ◽  
Fecal Samples ◽  
Oral Transmission ◽  
Study Participants ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Background SARS-CoV-2 has been detected not only in respiratory secretions, but also in stool collections. Here were sought to identify SARS-CoV-2 by enrichment next-generation sequencing (NGS) from fecal samples, and to utilize whole genome analysis to characterize SARS-CoV-2 mutational variations in COVID-19 patients. Results Study participants underwent testing for SARS-CoV-2 from fecal samples by whole genome enrichment NGS (n = 14), and RT-PCR nasopharyngeal swab analysis (n = 12). The concordance of SARS-CoV-2 detection by enrichment NGS from stools with RT-PCR nasopharyngeal analysis was 100%. Unique variants were identified in four patients, with a total of 33 different mutations among those in which SARS-CoV-2 was detected by whole genome enrichment NGS. Conclusion These results highlight the potential viability of SARS-CoV-2 in feces, its ongoing mutational accumulation, and its possible role in fecal–oral transmission. This study also elucidates the advantages of SARS-CoV-2 enrichment NGS, which may be a key methodology to document complete viral eradication. Trial registration ClinicalTrials.gov, NCT04359836, Registered 24 April 2020, https://clinicaltrials.gov/ct2/show/NCT04359836?term=NCT04359836&draw=2&rank=1).

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