A #MDR #Plasmid pIMP26, Carrying blaIMP-26, fosA5, blaDHA-1, and qnrB4 in #Enterobacter cloacae (Sci Rep., abstract)

[Source: Scientific Reports, full page: (LINK). Abstract, edited.]

Article | OPEN | Published: 15 July 2019

A Multidrug Resistance Plasmid pIMP26, Carrying blaIMP-26, fosA5, blaDHA-1, and qnrB4 in Enterobacter cloacae

Su Wang,  Kaixin Zhou, Shuzhen Xiao, Lianyan Xie, Feifei Gu, Xinxin Li, Yuxing Ni, Jingyong Sun & Lizhong Han

Scientific Reports, volume 9, Article number: 10212 (2019)



IMP-26 was a rare IMP variant with more carbapenem-hydrolyzing activities, which was increasingly reported now in China. This study characterized a transferable multidrug resistance plasmid harboring blaIMP-26 from one Enterobacter cloacae bloodstream isolate in Shanghai and investigated the genetic environment of resistance genes. The isolate was subjected to antimicrobial susceptibility testing and multilocus sequence typing using broth microdilution method, Etest and PCR. The plasmid was analyzed through conjugation experiments, S1-nuclease pulsed-field gel electrophoresis and hybridization. Whole genome sequencing and sequence analysis was conducted for further investigation of the plasmid. E. cloacae RJ702, belonging to ST528 and carrying blaIMP-26, blaDHA-1, qnrB4 and fosA5, was resistant to almost all β-lactams, but susceptible to quinolones and tigecycline. The transconjugant inherited the multidrug resistance. The resistance genes were located on a 329,420-bp IncHI2 conjugative plasmid pIMP26 (ST1 subtype), which contained trhK/trhV, tra, parA and stbA family operon. The blaIMP-26 was arranged following intI1. The blaDHA-1 and qnrB4cluster was the downstream of ISCR1, same as that in p505108-MDR. The fosA5 cassette was mediated by IS4. This was the first report on complete nucleotide of a blaIMP-26-carrying plasmid in E. cloacae in China. Plasmid pIMP26 hosted high phylogenetic mosaicism, transferability and plasticity.

Keywords: Antibiotics; Drugs Resistance; Carbapenem; Beta-lactams; Enterobacter cloacae; Shanghai; China; Quinolones; Tigecycline.


Isolation of #H8N4 #avian #influenza virus from #wildbirds in #Shanghai, #China (Acta Virol., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Acta Virol. 2019;63(1):121-125. doi: 10.4149/av_2019_116.

Isolation of H8N4 avian influenza virus from wild birds in Shanghai, China.

Tang W, Li X, Hu CH, Zhu C, Li Z, Wu D, Wang T, He G.



The H8 subtype viruses are rarely isolated from wild ducks. Shanghai is one of the important wintering or stopover sites on the East Asia-Australia Migration Flyway. An influenza virus, subtype H8N4, was firstly isolated from a common teal (Anas crecca) in Shanghai during 2017-2018 in this study. To clarify the genetic characteristics of the H8N4 virus, the whole genome sequences were analyzed. Phylogenetic analysis of the hemagglutinin and neuraminidase genes showed that they shared highest nucleotide identity (99.19%-99.64%) with the Japan duck-origin H8N4 virus collected in 2016 (A/duck/Aichi/231003/2016) and belonged to the Eurasian-like avian lineage. Six other genes of the H8N4 isolated virus were all highly similar to the corresponding genes of a wide range of AIV subtypes including H9N2, H5N7, H3N8, H1N2, H4N6 and H1N1. The results indicated that the H8N4 virus was a multiple reassortant virus. The study emphasized that the continuous surveillance of influenza virus in wild birds should be strengthened.

Keywords: avian influenza virus; H8N4; phylogenetic analysis; Shanghai.

PMID: 30879322 DOI: 10.4149/av_2019_116

Keywords: Avian Influenza; H8N4; Reassortant strain; Wild Birds; Shanghai; China.


New #strains of Japanese #encephalitis virus circulating in #Shanghai, #China after a ten-year hiatus in local #mosquito #surveillance (Parasit Vectors, abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Parasit Vectors. 2019 Jan 9;12(1):22. doi: 10.1186/s13071-018-3267-9.

New strains of Japanese encephalitis virus circulating in Shanghai, China after a ten-year hiatus in local mosquito surveillance.

Fang Y1, Zhang Y2, Zhou ZB1, Xia S1, Shi WQ1, Xue JB1, Li YY1, Wu JT1.

Author information: 1 National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, 20025, People’s Republic of China. 2 National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, 20025, People’s Republic of China. zhang1972003@163.com.




Continuous vector pathogen surveillance is essential for preventing outbreaks of mosquito-borne diseases. Several mosquito species acting as vectors of Japanese encephalitis virus (JEV), dengue virus, Zika virus, malaria parasites and other pathogens are primary mosquito species in Shanghai, China. However, few surveys of human pathogenic arboviruses in mosquitoes in Shanghai have been reported in the last ten years. Therefore, in this study, we evaluated mosquito activity in Shanghai, China during 2016 and tested for the presence of alphaviruses, flaviviruses, orthobunyaviruses and several parasitic pathogens.


Five pooled samples were JEV-positive [4/255 pools of Culex tritaeniorhynchus and 1/256 pools of Cx. pipiens (s.l.)] based on analysis of the NS5 gene. Alphaviruses, orthobunyaviruses, Plasmodium and filariasis were not found in this study. Phylogenetic and molecular analyses revealed that the JEV strains belonged to genotype I. Moreover, newly detected Shanghai JEV strains were genetically close to previously isolated Shandong strains responsible for transmission during the 2013 Japanese encephalitis (JE) outbreak in Shandong Province, China but were more distantly related to other Shanghai strains detected in the early 2000s. The E proteins of the newly detected Shanghai JEV strains differed from that in the live attenuated vaccine SA14-14-2-derived strain at six amino residues: E130 (Ile→Val), E222 (Ala→Ser), E327 (Ser→Thr), E366 (Arg→Ser/Pro), E393 (Asn→Ser) and E433 (Val→Ile). However, no differences were observed in key amino acid sites related to antigenicity. Minimum JEV infection rates were 1.01 and 0.65 per 1000 Cx. tritaeniorhynchus and Cx. pipiens (s.l.), respectively.


Five new Shanghai JEV genotype I strains, detected after a ten-year hiatus in local mosquito surveillance, were genetically close to strains involved in the 2013 Shandong JE outbreak. Because JEV is still circulating, vaccination in children should be extensively and continuously promoted. Moreover, JEV mosquito surveillance programmes should document the genotype variation, intensity and distribution of circulating viruses for use in the development and implementation of disease prevention and control strategies.

KEYWORDS: Culex pipiens; Culex tritaeniorhynchus; Japanese encephalitis; Mosquito-borne diseases; SA14-14-2

PMID: 30626442 DOI: 10.1186/s13071-018-3267-9

Keywords: Japanese Encephalitis; Arbovirus; Mosquitoes; China; Shanghai; Culex spp.


#Epidemiological and molecular analysis of #avian #influenza A(#H7N9) virus in #Shanghai, #China, 2013-2017 (Infect Drug Resist., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Infect Drug Resist. 2018 Nov 22;11:2411-2424. doi: 10.2147/IDR.S179517. eCollection 2018.

Epidemiological and molecular analysis of avian influenza A(H7N9) virus in Shanghai, China, 2013-2017.

Wang SJ1,2,3, Liu XW1, Shen X1,2, Hua XG1,2, Cui L1,2.

Author information: 1 Department of Animal Science, Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China, lcui@sjtu.edu.cn. 2 Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China, lcui@sjtu.edu.cn. 3 Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea.




Human infections with a novel avian influenza A virus (H7N9) were reported in Shanghai municipality, China, at the beginning of 2013. High-pathogenic avian influenza (HPAI) H7N9 virus emerged in late February 2017 along with existing low-pathogenic avian influenza (LPAI) H7N9 virus, and this has the potential to develop into a pandemic that could be harmful to humans.


To elucidate the epidemiological characteristics of H7N9-infected cases from 2013 to 2017 in Shanghai, data on the 59 laboratory-confirmed human cases and 26 bird and environmental contamination cases were collected from the WHO website and Food and Agriculture Organization Emergency Prevention System for Animal Health (FAO EMPRES-AH). Full-length sequences of H7N9 viruses that emerged in Shanghai were collected from the Global Initiative on Sharing Avian Influenza Data to analyze the evolutionary and genetic features.


We found that genetically different strains emerged in every epidemic in Shanghai, and most of the circulating H7N9 strains had affinity to human-type receptors, with the characteristics of high-virulence and low-pathogenic influenza viruses. Furthermore, our findings suggest that the Shanghai chicken strains are closely related to the HPAI H7N9 virus A/Guangdong/17SF003/2016, indicating that this viral strain is of avian origin and generated from the LPAI H7N9 viruses in Shanghai. The gradual decrease in H7N9 human infection in Shanghai was probably due to the control measures taken by the Shanghai government and the enhanced public awareness leading to a reduced risk of H7N9 virus infection. However, LPAI H7N9 viruses from poultry and environmental samples were continually detected in Shanghai across the epidemics, increasing the risk of new emerging H7N9 outbreaks.


It is important to consistently obtain sufficient surveillance data and implement prevention measures against H7N9 viruses in Shanghai municipality.

KEYWORDS: H7N9 virus; epidemiology; molecular evolutionary study; phylogenetic tree

PMID: 30538508 PMCID: PMC6254586 DOI: 10.2147/IDR.S179517

Keywords: Avian Influenza; H7N9; Human; Poultry; China; Shanghai.


Internal #migration and #transmission dynamics of #tuberculosis in #Shanghai, #China: an epidemiological, spatial, genomic analysis (Lancet Infect Dis., abstract)

[Source: The Lancet Infectious Diseases, full page: (LINK). Abstract, edited.]

Internal migration and transmission dynamics of tuberculosis in Shanghai, China: an epidemiological, spatial, genomic analysis

Chongguang Yang, PhD, Liping Lu, MPH, Joshua L Warren, PhD, Jie Wu, MPH, Qi Jiang, BSc, Tianyu Zuo, BSc, Mingyu Gan, BSc, Mei Liu, MSc, Qingyun Liu, PhD, Kathryn DeRiemer, PhD, Jianjun Hong, BSc, Xin Shen, PhD, Caroline Colijn, PhD, Xiaoqin Guo, MD†, Qian Gao, PhD†, Ted Cohen, DPH†

† These authors contributed equally

Published: 19 April 2018 / DOI: https://doi.org/10.1016/S1473-3099(18)30218-4

© 2018 Elsevier Ltd. All rights reserved.




Massive internal migration from rural to urban areas poses new challenges for tuberculosis control in China. We aimed to combine genomic, spatial, and epidemiological data to describe the dynamics of tuberculosis in an urban setting with large numbers of migrants.


We did a population-based study of culture-positive Mycobacterium tuberculosis isolates in Songjiang, Shanghai. We used whole-genome sequencing to discriminate apparent genetic clusters of M tuberculosis sharing identical variable-number-tandem-repeat (VNTR) patterns, and analysed the relations between proximity of residence and the risk of genomically clustered M tuberculosis. Finally, we used genomic, spatial, and epidemiological data to estimate time of infection and transmission links among migrants and residents.


Between Jan 1, 2009, and Dec 31, 2015, 1620 cases of culture-positive tuberculosis were recorded, 1211 (75%) of which occurred among internal migrants. 150 (69%) of 218 people sharing identical VNTR patterns had isolates within ten single-nucleotide polymorphisms (SNPs) of at least one other strain, consistent with recent transmission of M tuberculosis. Pairs of strains collected from individuals living in close proximity were more likely to be genetically similar than those from individuals who lived far away—for every additional km of distance between patients’ homes, the odds that genotypically matched strains were within ten SNPs of each other decreased by about 10% (OR 0·89 [95% CI 0·87–0·91]; p<0·0001). We inferred that transmission from residents to migrants occurs as commonly as transmission from migrants to residents, and we estimated that more than two-thirds of migrants in genomic clusters were infected locally after migration.


The primary mechanism driving local incidence of tuberculosis in urban centres is local transmission between both migrants and residents. Combined analysis of epidemiological, genomic, and spatial data contributes to a richer understanding of local transmission dynamics and should inform the design of more effective interventions.


National Natural Science Foundation of China, National Science and Technology Major Project of China, and US National Institutes of Health.

Keywords: China; Society; Tuberculosis; Shanghai.


Molecular #epidemiological study of #human #coronavirus OC43 in #Shanghai from 2009-2016 (Zhonghua Yu Fang Yi Xue Za Zhi, abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Zhonghua Yu Fang Yi Xue Za Zhi. 2018 Jan 6;52(1):55-61. doi: 10.3760/cma.j.issn.0253-9624.2018.01.011.

[Molecular epidemiological study of human coronavirus OC43 in Shanghai from 2009-2016].

[Article in Chinese; Abstract available in Chinese from the publisher]

Yang YJ1, Hu YW2.

Author information: 1 School of Laboratory Medicine and Life Science of Wenzhou Medical University, Wenzhou 325035, China (Department of Pathogen Diagnosis and Biosafety, Shanghai Public Health Clinical Center, Shanghai 201508, China). 2 School of Laboratory Medicine and Life Science of Wenzhou Medical University, Wenzhou 325035, China.


Abstract in English, Chinese


To understand the epidemiological characteristics of Human coronavirus (HCoV), the patterns of emergence and circulation, and the genotype distribution of human coronavirus OC43 (HCoV-OC43) from November, 2009 to April, 2016 in Shanghai.


A total of 6 059 respiratory specimens, including pharyngeal swab, sputum, nasopharyngeal aspirates and alveolar lavage fluid, as well as relative clinical data were collected from patients with acute respiratory infections from seven sentinel hospitals during November, 2009 to April, 2016 in Shanghai. Respiratory specimens were tested by RT-PCR with HCoV-conserved primers and subsequently genotyped by DNA sequencing. Using specific primers to amplify and sequence full-length Spike (S), RNA-dependent RNA polymerase (RDRP) and nucleocapsid (N) gene from HCoV-OC43 positive samples. Further genotype and phylogenetic analysis of HCoV-OC43 were performed by conducting phylogenetic trees.


Among 6 059 patients, the total frequency of HCoV was 63 (1.04%), in which HCoV-OC43 was the most frequently detected species with 34 positive samples, followed by human coronavirus 229E (HCoV-229E) and human coronavirus HKU1 (HCoV-HKU1) with 18 and 10 positive sample respectively. However, other HCoV like human coronavirus NL63 (HCoV-NL63), severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle-East Respiratory Syndrome Coronavirus (MERS-CoV), were not been detected, which illustrated that HCoV-OC43 was the dominant subtype. The full-length of S, RDRP and N gene were obtained from 29 HCoV-OC43 positive samples. According to the sequence-analysis, 27 of which was genotype D, 2 of which was genotype B and others genotype, including genotype E, F and G, were not detected. The result indicated that the genotype D may be the dominant genotype. Further analysis of S protein that help HCoV-OC43 to entry host cell and stimulate the host immune system to produce neutralizing antibody found that two important functional domains in S protein, N-terminal domain (NTD) and receptor-binding domain (RBD) contained more amino acid substitution and positive selection sites, accompanied with amino acid insertion/deletion. 13 positive selection sites were all located in the NTD or RBD, 10 of which were located in the NTD and 3 in the RBD.


Human coronavirus OC43 was the major circulation human coronaviurs in Shanghai from 2009 to 2016, in which genotype D was the dominant genotype. NTD and RBD regions of the S protein were hypervariable region during HCoV-OC43 evolution, and had amino acid substitutions as well as amino acid insertion/deletion.

KEYWORDS: Coronavirus OC43, human; Genotype; Molecular epidemiology

PMID: 29334709

Keywords: Coronavirus; Shanghai; China.


#Antimicrobial susceptibility and molecular epidemiology of clinical #Enterobacter cloacae #bloodstream isolates in #Shanghai, China (PLoS One, abstract)

[Source: PLoS One, full page: (LINK). Abstract, edited.]

Open Access / Peer-reviewed / Research Article

Antimicrobial susceptibility and molecular epidemiology of clinical Enterobacter cloacae bloodstream isolates in Shanghai, China

Su Wang , Shu-Zhen Xiao , Fei-Fei Gu, Jin Tang, Xiao-Kui Guo, Yu-Xing Ni, Jie-Ming Qu , Li-Zhong Han

Published: December 15, 2017 / DOI: https://doi.org/10.1371/journal.pone.0189713




Enterobacter cloacae is a major nosocomial pathogen causing bloodstream infections. We retrospectively conducted a study to assess antimicrobial susceptibility and phylogenetic relationships of E. cloacae bloodstream isolates in two tertiary university-affiliated hospitals in Shanghai, in order to facilitate managements of E. cloacae bloodstream infections and highlight some unknowns for future prevention.


Fifty-three non-duplicate E. cloacae bloodstream isolates were consecutively collected from 2013 to 2016. Antimicrobial susceptibility was determined by disk diffusion. PCR was performed to detect extended-spectrum β-lactamase (ESBL), carbapenemase and colistin resistance (MCR-1) gene. Plasmid-mediated AmpC β-lactamase (pAmpC) genes were detected using a multiplex PCR assay targeting MIR/ACT gene (closely related to chromosomal EBC family gene) and other plasmid-mediated genes, including DHA, MOX, CMY, ACC, and FOX. eBURST was applied to analyze multi-locus sequence typing (MLST).


The rates of resistance to all tested antibiotics were <40%. Among 53 E. cloacae isolates, 8(15.1%) were ESBL producers, 3(5.7%) were carbapenemase producers and 18(34.0%) were pAmpC producers. ESBL producers bear significantly higher resistance to cefotaxime (100.0%), ceftazidime (100.0%), aztreonam (100.0%), piperacillin (87.5%), tetracycline (75.0%), and trimethoprim-sulfamethoxazole (62.5%) than non-producers (p<0.05). PAmpC- and non-producers both presented low resistance rates (<40%) to all antibiotics (p>0.05). SHV (6/8, 75.0%) and MIR/ACT (15/18, 83.3%) predominated in ESBL and pAmpC producers respectively. Moreover, 2 isolates co-carried TEM-1, SHV-12, IMP-26 and DHA-1. MLST analysis distinguished the 53 isolates into 51 STs and only ST414 and ST520 were assigned two isolates of each (2/53).


The antimicrobial resistance rates were low among 53 E. cloacae bloodstream isolates in the two hospitals. Multiclonality disclosed no evidence on spread of these isolates in Shanghai. The simultaneous presence of ESBL, carbapenemase and pAmpC detected in 2 isolates was firstly reported in Shanghai, which necessitated active ongoing surveillances and consistent prevention and control of E. cloacae.


Citation: Wang S, Xiao S-Z, Gu F-F, Tang J, Guo X-K, Ni Y-X, et al. (2017) Antimicrobial susceptibility and molecular epidemiology of clinical Enterobacter cloacae bloodstream isolates in Shanghai, China. PLoS ONE 12(12): e0189713. https://doi.org/10.1371/journal.pone.0189713

Editor: Massimiliano Galdiero, Seconda Universita degli Studi di Napoli, ITALY

Received: August 22, 2017; Accepted: November 30, 2017; Published: December 15, 2017

Copyright: © 2017 Wang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All relevant data are within the paper and its Supporting Information files.

Funding: This work was supported by the Special Fund for Health-scientific Research in the Public Interest of China Program (201002021) to Yu-Xing Ni, the National Natural Science Foundation of China (81472010) to Yu-Xing Ni and the Shanghai Three-Year Plan of the Key Subjects Construction in Public Health-Infectious Diseases and Pathogenic Microorganism (15GWZK0102). The funders had no role in study design, data collection and analysis, preparation of the manuscript or decision for publication.

Competing interests: The authors have declared that no competing interests exist.

Keywords: Enterobacter Cloacae; Bacteremia; China; Antibiotics; Drugs Resistance.