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Article ; Online: Population genomics implies potential public health risk of two non-toxigenic Vibrio cholerae lineages.

Hao, Tongyu / Zheng, Wei / Wu, Yarong / Yu, Hua / Qian, Xiuwei / Yang, Chao / Zheng, Zhibei / Zhang, Xianglilan / Guo, Yan / Cui, Mengnan / Wang, Haoqiu / Pan, Jingcao / Cui, Yujun

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

2023 Volume 112, Page(s) 105441

Abstract: Diarrheal cases caused by non-toxigenic Vibrio cholerae have been reported globally. Lineages L3b and L9, characterized as ctxAB-negative and tcpA-positive (CNTP), pose the highest risk and have caused long-term epidemics in different regions worldwide. ... ...

Abstract	Diarrheal cases caused by non-toxigenic Vibrio cholerae have been reported globally. Lineages L3b and L9, characterized as ctxAB-negative and tcpA-positive (CNTP), pose the highest risk and have caused long-term epidemics in different regions worldwide. From 2001 to 2018, two waves (2001-2012 and 2013-2018) of epidemic caused by non-toxigenic V. cholerae occurred in the developed city of Hangzhou, China. In this study, through the integrated analysis of 207 genomes of Hangzhou isolates from these two waves (119 and 88) and 1573 publicly available genomes, we showed that L3b and L9 lineages together caused the second wave as had happened in the first wave, but the dominant lineage shifted from L3b (first wave: 69%) to L9 (second wave: 50%). We further found that the genotype of a key virulence gene, tcpF, in the L9 lineage during the second wave shifted to type I, which may have enhanced bacterial colonization in humans and potentially promoted the pathogenic lineage shift. Moreover, we found that 21% of L3b and L9 isolates had changed to predicted cholera toxin producers, providing evidence that gain of complete CTXφ-carrying ctxAB genes, rather than ctxAB gain in pre-CTXφ-carrying isolates, led to the transition. Taken together, our findings highlight the possible public health risk associated with L3b and L9 lineages due to their potential to cause long-term epidemics and turn into high-virulent cholera toxin producers, which necessitates a more comprehensive and unbiased sampling in further disease control efforts.
MeSH term(s)	Humans ; Vibrio cholerae/genetics ; Cholera Toxin/genetics ; Metagenomics ; Public Health ; Virulence ; Cholera/epidemiology ; Cholera/microbiology
Chemical Substances	Cholera Toxin (9012-63-9)
Language	English
Publishing date	2023-05-04
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2037068-4
ISSN	1567-7257 ; 1567-1348
ISSN (online)	1567-7257
ISSN	1567-1348
DOI	10.1016/j.meegid.2023.105441
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Article: Composition and Dynamics of H1N1 and H7N9 Influenza A Virus Quasispecies in a Co-infected Patient Analyzed by Single Molecule Sequencing Technology.

Lin, Peng / Jin, Tao / Yu, Xinfen / Liang, Lifeng / Liu, Guang / Jovic, Dragomirka / Sun, Zhou / Yu, Zhe / Pan, Jingcao / Fan, Guangyi

Frontiers in genetics

2021 Volume 12, Page(s) 754445

Abstract: A human co-infected with H1N1 and H7N9 subtypes influenza A virus (IAV) causes a complex infectious disease. The identification of molecular-level variations in composition and dynamics of IAV quasispecies will help to understand the pathogenesis and ... ...

Abstract	A human co-infected with H1N1 and H7N9 subtypes influenza A virus (IAV) causes a complex infectious disease. The identification of molecular-level variations in composition and dynamics of IAV quasispecies will help to understand the pathogenesis and provide guidance for precision medicine treatment. In this study, using single-molecule real-time sequencing (SMRT) technology, we successfully acquired full-length IAV genomic sequences and quantified their genotypes abundance in serial samples from an 81-year-old male co-infected with H1N1 and H7N9 subtypes IAV. A total of 26 high diversity nucleotide loci was detected, in which the A-G base transversion was the most abundant substitution type (67 and 64%, in H1N1 and H7N9, respectively). Seven significant amino acid variations were detected, such as NA:H275Y and HA: R222K in H1N1 as well as PB2:E627K and NA: K432E in H7N9, which are related to viral drug-resistance or mammalian adaptation. Furtherly, we retrieved 25 H1N1 and 22 H7N9 genomic segment haplotypes from the eight samples based on combining high-diversity nucleotide loci, which provided a more concise overview of viral quasispecies composition and dynamics. Our approach promotes the popularization of viral quasispecies analysis in a complex infectious disease, which will boost the understanding of viral infections, pathogenesis, evolution, and precision medicine.
Language	English
Publishing date	2021-11-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2021.754445
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Article ; Online: Multiple Lineages of Dengue Virus Serotype 2 Cosmopolitan Genotype Caused a Local Dengue Outbreak in Hangzhou, Zhejiang Province, China, in 2017.

Yu, Hua / Kong, Qingxin / Wang, Jing / Qiu, Xiaofeng / Wen, Yuanyuan / Yu, Xinfen / Liu, Muwen / Wang, Haoqiu / Pan, Jingcao / Sun, Zhou

Scientific reports

2019 Volume 9, Issue 1, Page(s) 7345

Abstract: During July to November 2017, a large dengue outbreak involving 1,138 indigenous cases occurred in Hangzhou, Zhejiang Province, China. All patients were clinically diagnosed as mild dengue. Epidemiology investigation and phylogenetic analysis of ... ...

Abstract	During July to November 2017, a large dengue outbreak involving 1,138 indigenous cases occurred in Hangzhou, Zhejiang Province, China. All patients were clinically diagnosed as mild dengue. Epidemiology investigation and phylogenetic analysis of circulating viruses revealed that at least three lineages of dengue virus serotype 2 (DENV-2) Cosmopolitan genotype initiated the outbreak during a short time. The analysis of the time to most recent common ancestor estimated that the putative ancestor of these DENV-2 lineages might rise no later than March, 2017, suggesting independent introductions of these lineages into Hangzhou. We presumed that group travelers visiting dengue-endemic areas gave rise to multiple introductions of these lineages during so short a time. Co-circulating of multiple DENV-2 lineages, emerging of disease in urban areas, hot and humid weather in Hangzhou adequate for mosquito breeding, and limited dengue diagnosis abilities of local hospitals, were the reasons causing the large local outbreak in Hangzhou.
MeSH term(s)	China/epidemiology ; Dengue/epidemiology ; Dengue/virology ; Dengue Virus/genetics ; Dengue Virus/isolation & purification ; Disease Outbreaks ; Female ; Humans ; Male ; Middle Aged ; Phylogeny ; Serogroup
Language	English
Publishing date	2019-05-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-019-43560-5
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Article ; Online: Complete Sequences and Characterization of Two Novel Plasmids Carrying aac(6')-Ib-cr and qnrS Gene in Shigella flexneri.

Pu, Xiao-Ying / Pan, Jing-Cao / Gu, Ya-Ming / Zheng, Wei / Li, Jun / Yu, Hua

Microbial drug resistance (Larchmont, N.Y.)

2016 Volume 22, Issue 2, Page(s) 115–122

Abstract: The complete sequences of two previously reported plasmids carrying plasmid-mediated quinolone resistance genes from Shigella flexneri in China have not been available. The present study using the p5-C3 assembly method revealed that (1) the plasmid ... ...

Abstract	The complete sequences of two previously reported plasmids carrying plasmid-mediated quinolone resistance genes from Shigella flexneri in China have not been available. The present study using the p5-C3 assembly method revealed that (1) the plasmid pSF07201 with aac(6')-Ib-cr had 75,335 bp with antibiotic resistance genes CTX-M-3, TEM-1, and FosA3; (2) seven fragments of pSF07201 had more than 99% homology with the seven corresponding plasmids; (3) the other plasmid pSF07202 with qnrS had 47,669 bp with antibiotic resistance gene TEM-1 and 99.95% homology with a segment of pKF362122, which has the qnrS gene from location 162,490 to 163,146. A conjugation and electrotransformation experiment suggested that these two plasmids might horizontally transfer between and coexist in Escherichia coli J53 and S. flexneri 2a 301. Either the aac(6')-Ib-cr or qnrS gene contributed to, but only the coexistence of the two genes conferred to the resistance to ciprofloxacin in these two strains. To the best of our knowledge, this is the first report of the complete sequences of the aac(6')-Ib-cr- and qnrS-positive plasmids in Shigella isolates. Our findings indicate that two genes probably evolve through horizontal plasmid transfer between the different bacterial types.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Base Sequence ; China ; Ciprofloxacin/pharmacology ; Conjugation, Genetic ; Conserved Sequence ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Dysentery, Bacillary/drug therapy ; Dysentery, Bacillary/microbiology ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Gene Expression ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Plasmids/chemistry ; Plasmids/metabolism ; Shigella flexneri/drug effects ; Shigella flexneri/enzymology ; Shigella flexneri/genetics ; Shigella flexneri/isolation & purification ; beta-Lactamases/genetics ; beta-Lactamases/metabolism
Chemical Substances	Anti-Bacterial Agents ; Bacterial Proteins ; DNA, Bacterial ; Ciprofloxacin (5E8K9I0O4U) ; beta-lactamase CTX-M-3 (EC 3.5.2.-) ; beta-Lactamases (EC 3.5.2.6) ; beta-lactamase TEM-1 (EC 3.5.2.6)
Language	English
Publishing date	2016-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1290490-9
ISSN	1931-8448 ; 1076-6294
ISSN (online)	1931-8448
ISSN	1076-6294
DOI	10.1089/mdr.2015.0082
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Article ; Online: Rapid genomic characterization of SARS-CoV-2 viruses from clinical specimens using nanopore sequencing.

Li, Jun / Wang, Haoqiu / Mao, Lingfeng / Yu, Hua / Yu, Xinfen / Sun, Zhou / Qian, Xin / Cheng, Shi / Chen, Shuchang / Chen, Junfang / Pan, Jingcao / Shi, Jueliang / Wang, Xuchu

Scientific reports

2020 Volume 10, Issue 1, Page(s) 17492

Abstract: The novel SARS-CoV-2 outbreak has swiftly spread worldwide. The rapid genome sequencing of SARS-CoV-2 strains has become a helpful tool for better understanding the genomic characteristics and origin of the virus. To obtain virus whole-genome sequences ... ...

Abstract	The novel SARS-CoV-2 outbreak has swiftly spread worldwide. The rapid genome sequencing of SARS-CoV-2 strains has become a helpful tool for better understanding the genomic characteristics and origin of the virus. To obtain virus whole-genome sequences directly from clinical specimens, we performed nanopore sequencing using a modified ARTIC protocol in a portable nanopore sequencer and validated a routine 8-h workflow and a 5-h rapid pipeline. We conducted some optimization to improve the genome sequencing workflow. The sensitivity of the workflow was also tested by serially diluting RNA from clinical samples. The optimized pipeline was finally applied to obtain the whole genomes of 29 clinical specimens collected in Hangzhou from January to March 2020. In the 29 obtained complete genomes of SARS-CoV-2, 33 variations were identified and analyzed. The genomic variations and phylogenetic analysis hinted at multiple sources and different transmission patterns during the COVID-19 epidemic in Hangzhou, China. In conclusion, the genomic characteristics and origin of the virus can be quickly determined by nanopore sequencing following our workflows.
MeSH term(s)	Adolescent ; Adult ; Betacoronavirus/classification ; Betacoronavirus/genetics ; Betacoronavirus/isolation & purification ; COVID-19 ; Child ; Coronavirus Infections/diagnosis ; Coronavirus Infections/virology ; Female ; Genetic Variation ; Genome, Viral ; Humans ; Male ; Middle Aged ; Mutation, Missense ; Nanopore Sequencing/methods ; Pandemics ; Phylogeny ; Pneumonia, Viral/diagnosis ; Pneumonia, Viral/virology ; SARS-CoV-2 ; Sequence Analysis, DNA ; Young Adult
Keywords	covid19
Language	English
Publishing date	2020-10-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-74656-y
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Article ; Online: Genomic epidemiology of Vibrio cholerae reveals the regional and global spread of two epidemic non-toxigenic lineages.

Wang, Haoqiu / Yang, Chao / Sun, Zhou / Zheng, Wei / Zhang, Wei / Yu, Hua / Wu, Yarong / Didelot, Xavier / Yang, Ruifu / Pan, Jingcao / Cui, Yujun

PLoS neglected tropical diseases

2020 Volume 14, Issue 2, Page(s) e0008046

Abstract: Non-toxigenic Vibrio cholerae isolates have been found associated with diarrheal disease globally, however, the global picture of non-toxigenic infections is largely unknown. Among non-toxigenic V. cholerae, ctxAB negative, tcpA positive (CNTP) isolates ... ...

Abstract	Non-toxigenic Vibrio cholerae isolates have been found associated with diarrheal disease globally, however, the global picture of non-toxigenic infections is largely unknown. Among non-toxigenic V. cholerae, ctxAB negative, tcpA positive (CNTP) isolates have the highest risk of disease. From 2001 to 2012, 71 infectious diarrhea cases were reported in Hangzhou, China, caused by CNTP serogroup O1 isolates. We sequenced 119 V. cholerae genomes isolated from patients, carriers and the environment in Hangzhou between 2001 and 2012, and compared them with 850 publicly available global isolates. We found that CNTP isolates from Hangzhou belonged to two distinctive lineages, named L3b and L9. Both lineages caused disease over a long time period with usually mild or moderate clinical symptoms. Within Hangzhou, the spread route of the L3b lineage was apparently from rural to urban areas, with aquatic food products being the most likely medium. Both lineages had been previously reported as causing local endemic disease in Latin America, but here we show that global spread of them has occurred, with the most likely origin of L3b lineage being in Central Asia. The L3b lineage has spread to China on at least three occasions. Other spread events, including from China to Thailand and to Latin America were also observed. We fill the missing links in the global spread of the two non-toxigenic serogroup O1 V. cholerae lineages that can cause human infection. The results are important for the design of future disease control strategies: surveillance of V. cholerae should not be limited to ctxAB positive strains.
MeSH term(s)	China/epidemiology ; Cholera/epidemiology ; Cholera/microbiology ; Cluster Analysis ; DNA, Bacterial/genetics ; Epidemics ; Gene Expression Regulation, Bacterial ; Genetic Variation ; Genomics ; Global Health ; Humans ; Vibrio cholerae/genetics ; Virulence Factors/genetics ; Virulence Factors/metabolism
Chemical Substances	DNA, Bacterial ; Virulence Factors
Language	English
Publishing date	2020-02-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2429704-5
ISSN	1935-2735 ; 1935-2735
ISSN (online)	1935-2735
ISSN	1935-2735
DOI	10.1371/journal.pntd.0008046
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Control of RNA stability by NrrF, an iron-regulated small RNA in Neisseria gonorrhoeae.

Jackson, Lydgia A / Pan, Jing-Cao / Day, Michael W / Dyer, David W

Journal of bacteriology

2013 Volume 195, Issue 22, Page(s) 5166–5173

Abstract: Regulation of gene expression by small noncoding RNAs (sRNAs) plays a critical role in bacterial response to physiological stresses. NrrF, a trans-acting sRNA in Neisseria meningitidis and Neisseria gonorrhoeae, has been shown in the meningococcus to ... ...

Abstract	Regulation of gene expression by small noncoding RNAs (sRNAs) plays a critical role in bacterial response to physiological stresses. NrrF, a trans-acting sRNA in Neisseria meningitidis and Neisseria gonorrhoeae, has been shown in the meningococcus to control indirectly, in response to iron (Fe) availability, the transcription of genes encoding subunits of succinate dehydrogenase, a Fe-requiring enzyme. Given that in other organisms, sRNAs target multiple mRNAs to control gene expression, we used a global approach to examine the role of NrrF in controlling gonococcal transcription. Three strains, including N. gonorrhoeae FA1090, an nrrF deletion mutant, and a complemented derivative, were examined using a custom CombiMatrix microarray to assess the role of this sRNA in controlling gene expression in response to Fe availability. In the absence of NrrF, the mRNA half-lives for 12 genes under Fe-depleted growth conditions were longer than those in FA1090. The 12 genes controlled by NrrF encoded proteins with biological functions including energy metabolism, oxidative stress, antibiotic resistance, and amino acid synthesis, as well as hypothetical proteins and a regulatory protein whose functions are not fully understood.
MeSH term(s)	Gene Deletion ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Genetic Complementation Test ; Iron/metabolism ; Microarray Analysis ; Neisseria gonorrhoeae/genetics ; Neisseria gonorrhoeae/metabolism ; RNA Stability ; RNA, Bacterial/genetics ; RNA, Bacterial/metabolism ; RNA, Small Untranslated/genetics ; RNA, Small Untranslated/metabolism ; Succinate Dehydrogenase/biosynthesis ; Transcription, Genetic
Chemical Substances	RNA, Bacterial ; RNA, Small Untranslated ; Iron (E1UOL152H7) ; Succinate Dehydrogenase (EC 1.3.99.1)
Language	English
Publishing date	2013-09-13
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2968-3
ISSN	1098-5530 ; 0021-9193
ISSN (online)	1098-5530
ISSN	0021-9193
DOI	10.1128/JB.00839-13
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Article ; Online: Outbreak of coinfection with human metapneumovirus and measles virus resulting in the death of a child at a hospital in China.

Kou, Yu / Sun, Zhou / Li, Feng / Yu, Xinfen / Yang, Xuhui / Li, Jun / Pan, Jingcao

American journal of infection control

2015 Volume 43, Issue 4, Page(s) 365–367

Abstract: Two children with different digestive diseases were admitted to the gastroenterology department of a children's hospital in Hangzhou, Zhejiang Province, China, in May 2010. They manifested successively acute lower respiratory tract infection symptoms ... ...

Abstract	Two children with different digestive diseases were admitted to the gastroenterology department of a children's hospital in Hangzhou, Zhejiang Province, China, in May 2010. They manifested successively acute lower respiratory tract infection symptoms during their stay in the hospital. The epidemiologic and experimental evidence supports that one child acquired nosocomial coinfection with measles virus and human metapneumovirus from another child while they shared the same ward.
MeSH term(s)	Acute Disease ; China/epidemiology ; Coinfection/diagnosis ; Coinfection/virology ; Cross Infection/diagnosis ; Cross Infection/transmission ; Cross Infection/virology ; Cytomegalovirus/isolation & purification ; Cytomegalovirus Infections/diagnosis ; Cytomegalovirus Infections/virology ; Fatal Outcome ; Gastroenterology ; Hospitalization ; Humans ; Infant ; Measles virus/isolation & purification ; Metapneumovirus/isolation & purification ; Respiratory Tract Infections/diagnosis ; Respiratory Tract Infections/transmission ; Respiratory Tract Infections/virology
Keywords	covid19
Language	English
Publishing date	2015-02-14
Publishing country	United States
Document type	Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	392362-9
ISSN	1527-3296 ; 0196-6553
ISSN (online)	1527-3296
ISSN	0196-6553
DOI	10.1016/j.ajic.2015.01.002
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Article ; Online: Quinolone resistance-determining region mutations and the plasmid-mediated quinolone resistance gene qnrS played important roles in decreased susceptibility to fluoroquinolones among Shigella isolates in southeast China between 1998 and 2013.

Pu, Xiao-Ying / Pan, Jing-Cao / Zhang, Wei / Zheng, Wei / Wang, Hao-Qiu / Gu, Ya-Ming

International journal of antimicrobial agents

2015 Volume 45, Issue 4, Page(s) 438–439

MeSH term(s)	Anti-Bacterial Agents/pharmacology ; China ; Drug Resistance, Bacterial ; Dysentery, Bacillary/microbiology ; Fluoroquinolones/pharmacology ; Genes, Bacterial ; Genotype ; Humans ; Microbial Sensitivity Tests ; Mutation ; Plasmids ; Shigella/drug effects ; Shigella/genetics ; Shigella/isolation & purification
Chemical Substances	Anti-Bacterial Agents ; Fluoroquinolones
Language	English
Publishing date	2015-04
Publishing country	Netherlands
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	1093977-5
ISSN	1872-7913 ; 0924-8579
ISSN (online)	1872-7913
ISSN	0924-8579
DOI	10.1016/j.ijantimicag.2014.12.004
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Article: Control of RNA Stability by NrrF, an Iron-Regulated Small RNA in Neisseria gonorrhoeae

Jackson, Lydgia A / Pan, Jing-Cao / Day, Michael W / Dyer, David W

Journal of bacteriology. 2013 Nov. 15, v. 195, no. 22

2013

Abstract	Regulation of gene expression by small noncoding RNAs (sRNAs) plays a critical role in bacterial response to physiological stresses. NrrF, a trans-acting sRNA in Neisseria meningitidis and Neisseria gonorrhoeae, has been shown in the meningococcus to control indirectly, in response to iron (Fe) availability, the transcription of genes encoding subunits of succinate dehydrogenase, a Fe-requiring enzyme. Given that in other organisms, sRNAs target multiple mRNAs to control gene expression, we used a global approach to examine the role of NrrF in controlling gonococcal transcription. Three strains, including N. gonorrhoeae FA1090, an nrrF deletion mutant, and a complemented derivative, were examined using a custom CombiMatrix microarray to assess the role of this sRNA in controlling gene expression in response to Fe availability. In the absence of NrrF, the mRNA half-lives for 12 genes under Fe-depleted growth conditions were longer than those in FA1090. The 12 genes controlled by NrrF encoded proteins with biological functions including energy metabolism, oxidative stress, antibiotic resistance, and amino acid synthesis, as well as hypothetical proteins and a regulatory protein whose functions are not fully understood.
Keywords	Neisseria gonorrhoeae ; Neisseria meningitidis ; amino acids ; antibiotic resistance ; bacteriology ; energy metabolism ; gene expression ; gene expression regulation ; genes ; half life ; iron ; messenger RNA ; microarray technology ; mutants ; non-coding RNA ; oxidative stress ; physiological response ; proteins ; succinate dehydrogenase
Language	English
Dates of publication	2013-1115
Size	p. 5166-5173.
Publishing place	American Society for Microbiology
Document type	Article
ZDB-ID	2968-3
ISSN	1098-5530 ; 0021-9193
ISSN (online)	1098-5530
ISSN	0021-9193
DOI	10.1128/JB.00839-13
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