Publications by authors named "Hongbin Song"

154 Publications

Association between coronavirus disease 2019 (COVID-19) and long-term exposure to air pollution: Evidence from the first epidemic wave in China.

Environ Pollut 2021 May 8;276:116682. Epub 2021 Feb 8.

Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, China. Electronic address:

People with chronic obstructive pulmonary disease, cardiovascular disease, or hypertension have a high risk of developing severe coronavirus disease 2019 (COVID-19) and of COVID-19 mortality. However, the association between long-term exposure to air pollutants, which increases cardiopulmonary damage, and vulnerability to COVID-19 has not yet been fully established. We collected data of confirmed COVID-19 cases during the first wave of the epidemic in mainland China. We fitted a generalized linear model using city-level COVID-19 cases and severe cases as the outcome, and long-term average air pollutant levels as the exposure. Our analysis was adjusted using several variables, including a mobile phone dataset, covering human movement from Wuhan before the travel ban and movements within each city during the period of the emergency response. Other variables included smoking prevalence, climate data, socioeconomic data, education level, and number of hospital beds for 324 cities in China. After adjusting for human mobility and socioeconomic factors, we found an increase of 37.8% (95% confidence interval [CI]: 23.8%-52.0%), 32.3% (95% CI: 22.5%-42.4%), and 14.2% (7.9%-20.5%) in the number of COVID-19 cases for every 10-μg/m increase in long-term exposure to NO, PM, and PM, respectively. However, when stratifying the data according to population size, the association became non-significant. The present results are derived from a large, newly compiled and geocoded repository of population and epidemiological data relevant to COVID-19. The findings suggested that air pollution may be related to population vulnerability to COVID-19 infection, although the extent to which this relationship is confounded by city population density needs further exploration.
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http://dx.doi.org/10.1016/j.envpol.2021.116682DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7868737PMC
May 2021

Plasmid-borne colistin resistance gene mcr-1 in a multidrug resistant Salmonella enterica serovar Typhimurium isolate from an infant with acute diarrhea in China.

Int J Infect Dis 2021 Feb 16;103:13-18. Epub 2020 Nov 16.

Chinese PLA Center for Disease Control and Prevention, Beijing, China. Electronic address:

Background: Antimicrobial resistance of Salmonella enterica is a major global concern. Recent findings suggest that colistin as a last resort treatment for multidrug-resistant gram-negative bacteria is seriously threatened by the report of plasmid-mediated colistin resistance gene mcr-1 in China.

Methods: A total of 827 S. Typhimurium isolates were recovered from 4 cities of China, including Henan, Shanghai, Zhejiang, and Hubei provinces. Subsequently, mcr-1 presence was identified by PCR screening. Antimicrobial susceptibility testing was performed by broth microdilution using a 96-well microtiter plate. Plasmid conjugation transfer experiments were conducted using Escherichia coli J53 as the recipient.

Results: Only one mcr-1 positive strain from the stool sample of an infant with acute diarrhea was isolated. Apart from colistin, the mcr-1-positive isolate showed co-resistance to the third-generation cephalosporins, ampicillin, nalidixic acid, tetracycline, chloramphenicol, sulfisoxazole, gentamicin, and cefotaxime revealing a multidrug-resistant phenotype. This strain harbored mcr-1 on a 227 kb IncHI2 plasmid, termed pJZ26, which could be transferred to E. coli J53. In addition to mcr-1, pJZ26 coharbored other resistance genes, including aph(4)-Ia, aac(3)-IVa, fosA, floR, sul2, and bla. Compared with p2474-MCR1 and pHYEC7-IncHI2, pJZ26 contains an additional 4.6 kb fragment harboring the resistance gene tet(A) and its regulator tetR located on TnAs1 transposable element, which could mediate resistance to tetracycline.

Conclusions: These findings highlight that the fact the mcr-1-harboring plasmid pJZ26 has a high potential to disseminate the mcr-1 gene and further challenge the clinical treatment.
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http://dx.doi.org/10.1016/j.ijid.2020.11.150DOI Listing
February 2021

Characterization of a Novel NDM-5-Harboring Plasmid from a Carbapenem-Resistant Isolate from China.

Infect Drug Resist 2020 2;13:3929-3935. Epub 2020 Nov 2.

Center for Disease Control and Prevention of PLA, Beijing, People's Republic of China.

Background: A carbapenem-resistant (sequence type 5415) strain was isolated from a male patient through routine surveillance in 2018 in Guangzhou, China.

Materials And Methods: Bacteria were isolated from a sputum culture and identified by using the Vitek 2 compact system. The gene was amplified and confirmed by sequencing. Antimicrobial susceptibility testing was determined by a Vitek 2 compact system. The gene was located by Southern blotting. Whole-genome sequencing was carried out using both Illumina MiSeq and Oxford Nanopore MinION.

Results: S1-PFGE and Southern blotting showed that the gene was located on a novel 66-kb IncFII [F2:A-:B-] plasmid. Conjugation assays revealed that the -bearing plasmid was self-transferrable. Genomic sequencing and comparative analysis suggested that plasmid p2947-NDM5 likely originated from a combination of an IncFII-type backbone and the flanking genetic elements.

Conclusion: This is the first report of an ST5414 strain expressing an NDM-5 β-lactamase. This study highlights the genetic complexity of carrying plasmids and the urgent need for continuous active monitoring.
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http://dx.doi.org/10.2147/IDR.S277997DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7646509PMC
November 2020

Characterization of an New Delhi-Metallo-1-Producing ST418 Strain from a Patient in Guangzhou, China.

Microb Drug Resist 2020 Oct 21. Epub 2020 Oct 21.

Department of Biosecurity, Chinese PLA Center for Disease Control and Prevention, Beijing, China.

New Delhi-Metallo-1-producing (NDM-1-producing) is one of the highly resistant pathogens affecting the intensive care unit. A previous study reported that ST418 was the main epidemic type of NDM-1-producing in Shenzhen, China. However, few NDM-1-producing carbapenem-resistant ST418 strains have been described. In this study, we collected and characterized an NDM-1-producing carbapenem-resistant strain, E70, from a patient in Guangzhou. E70 was resistant to multiple antibiotics, including imipenem and meropenem. S1-Pulsed field gel electrophoresis and southern blotting showed that E70 harbored four plasmids and that the gene was located on an ∼50 kb plasmid. Conjugation experiments revealed that the two smaller plasmids were transferable and that transconjugants obtaining one or both plasmids acquired different antimicrobial resistances. Whole-genome sequencing and analysis revealed that E70 belonged to ST418. The and genes coexisted on the 53.7 kb IncX3 plasmid pE70-NDM1, whereas the and genes were located on another untyped 26.0 kb plasmid, pE70-TEM1. The plasmids in ST418 may serve as an important vehicle in the dissemination of NDM, and the coexistence of transferable plasmids increases the possibility of rapid horizontal spread of multidrug resistance genes. Long-term monitoring and detailed study are necessary for the prevention of -carrying infection.
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http://dx.doi.org/10.1089/mdr.2020.0035DOI Listing
October 2020

A Novel sRNA in That Regulates Tolerance and Virulence Under Hyperosmotic Pressure.

Front Cell Infect Microbiol 2020 16;10:483. Epub 2020 Sep 16.

Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China.

Regulation of the environmental stress response and virulence of may involve multiple signaling pathways; however, these mechanisms are not well-defined. In bacteria, small regulatory RNAs (sRNAs) regulate bacterial growth, metabolism, virulence, and environmental stress response. Therefore, identifying novel functional sRNAs in could help elucidate pathogenic adaptations to host micro-environmental stresses and associated virulence. The aim of this study was to confirm the presence of an sRNA, , in and to determine its functions and possible mechanism of action. was found to regulate tolerance and virulence under hyperosmotic pressure. Its expression was verified by qRT-PCR and Northern blotting, and its genomic position was confirmed by 5'-rapid amplification of cDNA ends. expression was significantly decreased (~ 80%) under hyperosmotic conditions (680 mM NaCl), and the survival rate of the deletion strain increased by 20% under these conditions. This suggested that has been selected to promote host survival under hyperosmotic conditions. Additionally, virulence assessment, including guinea pig Sereny test and competitive invasion assays in mouse lungs, revealed that deletion significantly decreased virulence. Two-dimensional gel analyses suggest that may modulate the expression of , and genes, which may affect the virulence and survival of under osmotic pressures. Furthermore, expression has been shown to improve the survival of under osmotic pressures. These results suggest that has a broad range of action in response to hyperosmotic environmental stresses and in controlling its virulence to adapt to environmental stresses encountered during host infection.
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http://dx.doi.org/10.3389/fcimb.2020.00483DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7526569PMC
September 2020

Characterization of a New Transposon, Tn, on a -Carrying Plasmid From Multidrug-Resistant ssp. in China.

Front Microbiol 2020 15;11:525479. Epub 2020 Sep 15.

Center for Disease Control and Prevention of People's Liberation Army, Beijing, China.

Background: is an opportunistic pathogen which is responsible for serious nosocomial infections. A gene which plays an important role in resistance to carbapenems is the New Delhi metallo-β-lactamase 1 (NDM-1). Currently, the spread of NDM-1-producing strains is a serious public threat.

Methods: A multidrug-resistant ssp. strain CBG15936 was recovered in 2017 in Guangzhou, China. PCR, S1-pulsed-field gel electrophoresis, and Southern blotting were performed to locate the gene. Susceptibility testing and conjugation experiments were also performed. Illumina HiSeq and Nanopore sequencers were used to perform whole-genome sequencing.

Results: Strain CBG15936 belongs to ST932 and is resistant to carbapenems. The gene was found on a ∼62-kb plasmid, which has a conjugation frequency of 1.68 × 10 events per donor cell. Genome sequencing and analysis revealed that the NDM-1-carrying IncN1 plasmid contained a new transposon Tn, which consists of an intact -carrying Tn element, an inverted 8.3-kb Tn remnant, IS, Δ, and IS.

Conclusion: A new transposon, Tn, has been detected on a -carrying plasmid recovered from multidrug-resistant ssp. CBG15936 from China. This finding provides a new perspective regarding the potential for to undergo horizontal transfer among drug-resistant bacteria.
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http://dx.doi.org/10.3389/fmicb.2020.525479DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7522282PMC
September 2020

Genetic characterisation of a complex class 1 integron in an NDM-1-producing Citrobacter freundii ST396 clinical strain isolated from a urine sample.

J Glob Antimicrob Resist 2020 12 18;23:64-66. Epub 2020 Aug 18.

Center for Disease Control and Prevention of PLA, 20 DongDa Street, Fengtai District, Beijing 100071, China. Electronic address:

Objectives: The aim of this study was to characterise a multidrug-resistant (MDR) Citrobacter freundii strain carrying a bla-harbouring conjugative IncA/C2-type plasmid in China.

Methods: The whole genome of C. freundii strain L75 was sequenced both on HiSeq® (Novogene Corp., China) and GridION X5 (GrandOmics Biosciences Co., Ltd.) platforms. De novo genome assembly, genome annotation, multilocus sequence typing (MLST) and plasmid replicon typing were performed.

Results: Citrobacter freundii L75 was assigned to ST396 and contains a 5.1-Mb chromosome and two plasmids (∼146 kb and ∼73 kb) designated pCf75 and pCf76, respectively. The antibiotic resistance determinants bla, sul1, sul2, arr-3, mph(A), aadA16, aph(3")-Ib, aac(3)-IId, aph(6)-Id, aac(6')-Ib-cr and dfrA27 were located on plasmid pCf75, whilst bla was chromosomally encoded. A 22.1-kb MDR-encoding region (MDRR) in a complex class 1 integron contained all of the resistance genes of plasmid pCf75.

Conclusions: We detected and characterised a plasmid carrying a novel MDRR in which a complex class 1 integron plays an essential role. In addition, this study provides fresh genomic insights into the diversity of C. freundii ST396 prevalent in Guangzhou Province, China, and underscores the increasing clinical relevance of the IncA/C2 plasmid family.
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http://dx.doi.org/10.1016/j.jgar.2020.08.002DOI Listing
December 2020

Genomic features of an Escherichia coli ST156 strain harboring chromosome-located mcr-1 and plasmid-mediated bla.

Infect Genet Evol 2020 11 11;85:104499. Epub 2020 Aug 11.

Center for Disease Control and Prevention of PLA, Beijing, China. Electronic address:

The emergence of Escherichia coli strains coharboring the bla and mcr genes has become a new challenge in clinical therapy because of their resistance to most antibiotics. This study reports the emergence of an E. coli strain GZEC065 isolated from blood sample of a patient in China with both chromosome-located mcr-1 and plasmid-mediated bla genes. Antimicrobial susceptibility testing showed that GZEC065 was resistant to most tested antimicrobials, including imipenem and polymyxin B. S1-nuclease-pulsed-field gel electrophoresis, Southern blotting analysis and conjugation assay was performed to determine the location and conjugative ability of mcr-1 and bla genes. Whole genome sequencing and analysis showed that GZEC065 belonged to sequence type ST156 and contained three different plasmids (46 kb, 88 kb and 142 kb) with multiple resistance genes, such as mcr-1, bla and bla. The bla gene was carried by the 46 kb conjugative IncX3 plasmid, which has been reported frequently in China. The mcr-1 gene was located on the chromosome mediated by the Tn6330 mobile element and showed genetic complexity among different strains. The emergence of E. coli strains coharboring both chromosome-located mcr-1 and plasmid-mediated bla genes highlights the urgent need for alternative antibiotic treatment and continuous active surveillance.
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http://dx.doi.org/10.1016/j.meegid.2020.104499DOI Listing
November 2020

A new plasmid carrying mphA causes prevalence of azithromycin resistance in enterotoxigenic Escherichia coli serogroup O6.

BMC Microbiol 2020 08 11;20(1):247. Epub 2020 Aug 11.

Academy of Military Medical Sciences, NO.20 Dongda Street, Fengtai District, Beijing, 100071, China.

Background: At present, azithromycin has become an effective treatment for severe diarrhea caused by Enterotoxigenic Escherichia coli (ETEC) infection. However, enterobacteria have begun to develop resistance to azithromycin and have attracted attention in recent years. This study conducted to described the emergence of a high proportion of azithromycin-resistant ETEC serogroup O6 strains in Shanghai and to analyzed the mechanisms of azithromycin resistance.

Results: Strains from adult diarrhea patients with ETEC serogroup O6 infections were collected by Shanghai Diarrhea Surveillance Network and the Foodborne Surveillance Network from 2016 to 2018. We tested 30 isolates of ETEC O6 serogroup, 26 of which were resistant to azithromycin. Phylogenetic analysis revealed that these ETEC serogroup O6 strains have formed an independent dominant clone. S1-PFGE and southern blotting revealed the presence of the mphA gene on the 103 kb plasmid. Illumina and Nanopore sequencing and plasmid coverage analysis further confirmed that azithromycin-resistant strains carried a novel IncFII plasmid harboring mphA and blaTEM-1 resistance genes.

Conclusions: This is the first study to report a high proportion of azithromycin resistance in a particular ETEC serogroup due to a specific plasmid carrying mphA. Our findings indicate the rapid spread of azithromycin resistance, highlighting the urgency of stringent surveillance and control measure.
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http://dx.doi.org/10.1186/s12866-020-01927-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7418381PMC
August 2020

Phylogenetic Characterization Reveals Prevalent Shigella flexneri ST100 Clone in Beijing, China, 2005 to 2018.

mSphere 2020 07 15;5(4). Epub 2020 Jul 15.

Chinese PLA Center for Disease Control and Prevention, Beijing, China

is a major cause of bacillary dysentery in Beijing, China. The genetic features and population structure of locally circulating clones remained unclear. In this study, we sequenced the genomes of 93 isolates from patients in Beijing from 2005 to 2018. Phylogenetic analysis revealed a predominant lineage comprised of ST100 isolates that had acquired an extensive repertoire of antimicrobial resistance determinants. A rapid local expansion of the largest clade of this lineage began in 2008 and gradually resulted in the dominance of serotype 2a. Other clades showed substantial evidence of interregional spread from other areas of China. Another lineage consisting of ST18 isolates was also identified and appeared to have persisted locally for nearly 6 decades. These findings suggest that epidemics in Beijing were caused by both local expansion and interregional transmission. Beijing is the largest transportation hub in China, with a highly mobile population. is a major cause of bacillary dysentery in Beijing. However, little is known about the genetic features and population structure of locally circulating clones. Whole-genome sequencing of 93 isolates revealed that epidemics in Beijing were predominantly caused by an ST100 clone. Interregional spread, rapid local expansion, and acquirement of antimicrobial resistance determinants have cocontributed to the epidemics of this clone. Another ST18 clone was also identified and showed long-term colonization in Beijing. Our study provides comprehensive insights into the population structure and evolutionary history of in Beijing.
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http://dx.doi.org/10.1128/mSphere.00161-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7364208PMC
July 2020

The phenotypic and molecular characteristics of antimicrobial resistance of Salmonella enterica subsp. enterica serovar Typhimurium in Henan Province, China.

BMC Infect Dis 2020 Jul 15;20(1):511. Epub 2020 Jul 15.

State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Beijing, 100071, Fengtai District, China.

Background: Salmonella enterica subsp. enterica serovar Typhimurium infections continue to be a significant public health threat worldwide. The aim of this study was to investigate antibiotic resistance among 147 S. Typhimurium isolates collected from patients in Henan, China from 2006 to 2015.

Methods: 147 S. Typhimurium isolates were collected from March 2006 to November 2015 in Henan Province, China. Antimicrobial susceptibility testing was performed, and the resistant genes of ciprofloxacin, cephalosporins (ceftriaxone and cefoxitin) and azithromycin were detected and sequenced. Clonal relationships were assessed by multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE).

Results: Of the 147 isolates, 91.1% were multidrug resistant (MDR), with 4.1% being resistant to all antibiotic classes tested. Of concern, 13 MDR isolates were co-resistant to the first-line treatments cephalosporins and ciprofloxacin, while three were also resistant to azithromycin. Seven PFGE patterns were identified among the 13 isolates. All of the isolates could be assigned to one of four main groups, with a similarity value of 89%. MLST assigned the 147 isolates into five STs, including two dominant STs (ST19 and ST34). Of the 43 ciprofloxacin-resistant isolates, 39 carried double gyrA mutations (Ser83Phe, Asp87Asn/Tyr/Gly) and a single parC (Ser80Arg) mutation, including 1 isolate with four mutations (gyrA: Ser83Phe, Asp87Gly; parC: Ser80Arg; parE: Ser458Pro). In addition, 12 isolates not only carried mutations in gyrA and parC but also had at least one plasmid-mediated quinolone resistance (PMQR) gene. Among the 32 cephalosporin-resistant isolates, the most common extended-spectrum β-lactamase (ESBL) gene was bla, followed by bla, bla, and bla. Moreover, the mphA gene was identified in 5 of the 15 azithromycin-resistant isolates. Four MDR isolates contained ESBL and PMQR genes, and one of them also carried mphA in addition.

Conclusion: The high level of antibiotic resistance observed in S. Typhimurium poses a great danger to public health, so continuous surveillance of changes in antibiotic resistance is necessary.
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http://dx.doi.org/10.1186/s12879-020-05203-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7362628PMC
July 2020

Phage-delivered sensitisation with subsequent antibiotic treatment reveals sustained effect against antimicrobial resistant bacteria.

Theranostics 2020 15;10(14):6310-6321. Epub 2020 May 15.

Academy of Military Medical Sciences, 27 Taiping Road, Haidian District, Beijing 100850, China.

Temperate phages integrated with clustered regularly interspaced short palindromic repeat (CRISPR)/Cas systems have been gaining attention as potential strategies for combating bacteria resistant to antimicrobials. To further advance this technology, phage recombination procedure should be improved, and the bactericidal effect should be examined in detail and compared with conventional lytic phage strategy. The possibility of the emergence of mutational resistance, a phenomenon commonly observed with lytic phage therapy, should be illustrated. : Here, we developed a novel one-step cloning method to fulfil the recombination of CRISPR/Cas9 system within the genome of a new isolated lysogenic phage. Then, we proposed and developed a phage-delivered resistance eradication with subsequent antibiotic treatment (PRESA) strategy. The removal efficiency and antimicrobial effect of the plasmids were analysed. Long-term antimicrobial effect was evaluated by continued OD monitoring for 240 hours to illustrate the potential mutational resistance, compared with the lytic phage strategy. The treatment effect of PRESA was evaluated by determining bacterial loads in the skin and intestine of infected mice, in contrast with lytic phage therapy. Genome sequencing was performed to identify mutations in bacterial cells treated with phage strategies. : Phage-delivered CRISPR targeting efficiently eradicated and blocked the transfer of the antibiotic resistance plasmid. PRESA decreased the bacterial load by over 6- and 5-logs and , respectively. Importantly, while lytic phages induced mutational phage resistance at 24 h and 48 hours , PRESA demonstrated a constant effect and revealed no resistant mutants. Genes involved in DNA mismatch repair were upregulated in cells undergoing Cas9-based plasmid cleavage, which may reduce the development of mutations. : The PRESA strategy for eradicating resistant bacteria showed high bactericidal efficacy and a sustained inhibition effect against resistant bacteria. By restoring the efficacy of low-cost antibiotics, PRESA could be developed as an efficient and economical therapy for infections of antibiotic resistant bacteria.
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http://dx.doi.org/10.7150/thno.42573DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7255016PMC
May 2020

Metagenomic Diagnosis for a Culture-Negative Sample From a Patient With Severe Pneumonia by Nanopore and Next-Generation Sequencing.

Front Cell Infect Microbiol 2020 5;10:182. Epub 2020 May 5.

Center for Disease Control and Prevention of PLA, Beijing, China.

Rapid and accurate etiologic diagnosis accelerates targeted antimicrobial therapy. Metagenomic analysis has played a critical role in pathogen identification. In this study, we leveraged the advantages of both the MinION and BGISEQ-500 platforms to make a bacteriologic diagnosis from a culture-negative lung tissue sample from an immunocompromised patient with severe pneumonia. Real-time nanopore sequencing rapidly identified by an 823 bp specific sequence within 1 min. Genomic analysis further identified , , , , and other resistance genes. The same sample was further sequenced on the BGISEQ-500 platform, which presented consistent results regarding the most top dominant pathogens and provided additional information of resistance genes. Revised antibiotic treatment was followed by the patient's clinical recovery. Though sample preparation and the interpretation of final results still need to be improved further, metagenomic sequencing contributes to the accurate diagnosis of culture-negative infections and facilitates the rational antibiotic therapy.
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http://dx.doi.org/10.3389/fcimb.2020.00182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7214676PMC
May 2020

Investigation of a Salmonellosis Outbreak Caused by Multidrug Resistant Typhimurium in China.

Front Microbiol 2020 29;11:801. Epub 2020 Apr 29.

Academy of Military Medical Sciences, Beijing, China.

The rapid emergence of multidrug resistant is a global public-health concern as outbreaks in recent years have mostly been caused by multidrug resistant strains. Here, we evaluated an outbreak in China caused by multidrug resistant serovar Typhimurium (. Typhimurium) by employing an epidemiological and laboratory investigation using conventional methods and whole genome sequencing (WGS). Eleven of the 12 people who participated in a banquet showed gastrointestinal symptoms, and 8. Typhimurium strains were recovered. Isolated outbreak strains showed multidrug resistance (MDR), and decreased susceptibility to ciprofloxacin, a first-line drug recommended by WHO for clinical treatment of intestinal infections. Antimicrobial resistance (AMR) gene analysis indicated that the MDR phenotype of these outbreak strains may be due to the presence of a number of AMR genes, including the OXA-1 and TEM-1 β-lactamase genes, which are often plasmid-borne and easily transferred. Further virulence gene analysis indicated that these outbreak strains also carried a large number of virulence genes, including 2 types of pathogenicity islands (SPI-1 and SPI-2) and many adhesion-related virulence genes. Cluster analysis based on pulse-field gel electrophoresis data and phylogenetic analysis based on WGS revealed that the outbreak clone was closely related to and thus probably derived from local strains. This outbreak caused by multidrug resistant Typhimurium highlights the need for government improved strategies for the prevention and control of infections.
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http://dx.doi.org/10.3389/fmicb.2020.00801DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7200987PMC
April 2020

An NDM-1-Producing Isolate from Hospital Sewage in China.

Infect Drug Resist 2020 16;13:1105-1110. Epub 2020 Apr 16.

Center for Disease Control and Prevention of PLA, Beijing, People's Republic of China.

Background: The New Delhi metallo-β-lactamase-1 (NDM-1)-positive plasmid and its variants pose daunting threats to public health. Hospital sewage was considered as an important reservoir of antibiotic genes. Numerous and diverse taxa of multidrug-resistant (MDR) bacteria carrying NDM-1-positive plasmids have been identified during routine surveillance of hospital sewage. We herein report a carbapenem-resistant strain AeBJ009 with an NDM-1-positive plasmid isolated from hospital sewage.

Materials And Methods: Bacteria were isolated from cultures of hospital sewage and identified by using the Vitek 2 compact system and 16S rRNA sequencing. The gene was amplified and confirmed by sequencing. Antimicrobial susceptibility testing was performed using AST-GN14 on the Vitek2 compact system. In addition, the gene was located by Southern blotting. Conjugation experiment and whole-genome sequencing were performed for further analysis.

Results: Strain AeBJ009 was isolated from hospital sewage and identified as . Antimicrobial susceptibility testing revealed an MDR phenotype. Pulsed-field gel electrophoresis and Southern blotting showed that strain AeBJ009 carries three plasmids and that is located on the 47kb plasmid pNDM-AeBJ009. However, the conjugation experiment to transfer pNDM-AeBJ009 to strain J53 was unsuccessful. Whole-genome sequencing found that pNDM-AeBJ009 contains a Tn element carrying . The gene downstream of displayed a single-nucleotide polymorphism compared to its homologue on plasmid pM131_NDM1. BLAST analysis using the Comprehensive Antibiotic Resistance Database identified no gene polymorphisms with 100% identity to our variant.

Conclusion: The strain AeBJ009 exhibiting an extended spectrum of antibiotic resistance was isolated from hospital sewage and may potentially exacerbate the risk of MDR bacterial infections. The prevention of nosocomial infections due to drug-resistant bacteria will require enhanced monitoring and control of MDR pathogens in environmental reservoirs.
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http://dx.doi.org/10.2147/IDR.S246697DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7170623PMC
April 2020

Evaluation of control measures for COVID-19 in Wuhan, China.

J Infect 2020 08 10;81(2):318-356. Epub 2020 Apr 10.

Center for Disease Control and Prevention of Chinese People's Liberation Army, 20 Dong-Da-Jie Street, Fengtai District, Beijing, 100071, China. Electronic address:

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http://dx.doi.org/10.1016/j.jinf.2020.03.043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7194628PMC
August 2020

CRISPR-Cas13a Cleavage of Dengue Virus NS3 Gene Efficiently Inhibits Viral Replication.

Mol Ther Nucleic Acids 2020 Mar 5;19:1460-1469. Epub 2020 Feb 5.

State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China. Electronic address:

The CRISPR-Cas9 system has been applied to DNA editing with precision in eukaryotic and prokaryotic systems, but it is unable to edit RNA directly. A recently developed CRISPR-Cas13a system has been shown to be capable of effectively knocking down RNA expression in mammalian and plant cells. In this study, we employ the CRISPR-Cas13a system to achieve reprogrammable inactivation of dengue virus in mammalian cells. Quantitative reverse transcription PCR (qRT-PCR), fluorescence-activated cell sorting (FACS), and plaque assays showed that CRISPR RNA (crRNA) targeting the NS3 region led to the greatest viral inhibition among 10 crRNAs targeting different regions along the dengue viral genomic RNA. Deletions and insertions had also been found adjacent to the NS3 region after NS3-crRNA/Cas13a complex transfection. Our results demonstrate that the CRISPR-Cas13a system is a novel and effective technology to inhibit dengue viral replication, suggesting that such a programmable method may be further developed into a novel therapeutic strategy for dengue and other RNA viruses.
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http://dx.doi.org/10.1016/j.omtn.2020.01.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7056623PMC
March 2020

Coexistence of Two Genes Carried on IncX3 and IncFII Plasmids in an Isolate Revealed by Illumina and Nanopore Sequencing.

Front Microbiol 2020 13;11:195. Epub 2020 Feb 13.

Center for Disease Control and Prevention, PLA, Beijing, China.

The emergence of carbapenem-resistant poses a significant threat to public health worldwide. Here, we reported a multidrug-resistant strain with two different -carrying plasmids from China. Illumina short-read and MinION long-read whole genome sequencing were performed. Genomic analysis found that one gene together with was located on a 55-kb IncX3 plasmid, while the other gene was on a novel 68-kb IncFII plasmid. Susceptibility testing and quantitative reverse transcription PCR results further indicated that the transconjugants with the IncX3 plasmid exhibited higher-level carbapenem resistance and expression of than those with both plasmids or the IncFII plasmid. Two other β-lactamase genes ( and ) were also detected on another 160-kb IncF plasmid. This is the first report of coexistence of two -carrying plasmids in a single bacterial isolate, highlighting the genetic complexity of NDM-5 carbapenemase circulation, and the urgent need for continued active surveillance.
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http://dx.doi.org/10.3389/fmicb.2020.00195DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7031209PMC
February 2020

Characterization of blaNDM-1- and blaSHV-12-Positive IncX3 Plasmid in an New Sequence Type 1000 from China.

Infect Drug Resist 2020 13;13:145-153. Epub 2020 Jan 13.

Center for Disease Control and Prevention of PLA, Beijing, People's Republic of China.

Purpose: Carbapenem-resistant complex has been reported worldwide and becomes a new challenge for clinical management. The present study was to characterize the IncX3 plasmid encoding and gene in sequence.

Materials And Methods: EcHK001 was recovered from the sputum sample of a patient. Species identification and antimicrobial susceptibility testing were performed using the VITEK 2 system, while further classification was carried out by hsp60 typing. The presence of NDM-1 was detected by PCR and sequencing. Conjugation experiments and southern blotting were carried out to determine the transferability of the NDM-1-carrying plasmid. Whole-genome sequencing and analysis were conducted to better understand the molecular characteristics of the multi-drug resistant isolate.

Results: Strain EcHK001 was classified as of new sequence type 1000. Multiple drug-resistant genes were detected. The and genes were located on a self-transferable IncX3 plasmid. Synonymous mutations were identified in the genes encoding TEM-1 and ACT-17. Phylogenetic analysis indicated that EcHK001 clustered into a different clade from domestic strains.

Conclusion: The rapid spread of the recurrent IncX3 plasmid highlights the need for continuous surveillance of the NDM-1 dissemination. The presence of mutations in existing carbapenem-resistant genes may generate potential new variants and raise serious challenges for clinical treatment.
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http://dx.doi.org/10.2147/IDR.S231366DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6968821PMC
January 2020

Physiological responses to cold and starvation stresses in the liver of yellow drum (Nibea albiflora) revealed by LC-MS metabolomics.

Sci Total Environ 2020 May 25;715:136940. Epub 2020 Jan 25.

Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China. Electronic address:

As global climate changes, mass mortality in farmed fish associated with the severely cold weather has aroused growing concerns. Yellow drum (Nibea albiflora) is an important maricultured fish in China, whereby its aquaculture suffered from overwinter mortality associated with cold and cold-induced-fasting stresses. Here, by using LC-MS metabolomics combined with transcriptomics, we investigated the physiological responses of yellow drum liver to cold and starvation stresses. The experiment involved four groups: 16 °C fed group (CG1), 16 °C unfed group (CG2), 8 °C fed group (EG1), and 8 °C unfed group (EG2). Under cold stress, a total of 308 and 257 differential metabolites were identified in EG1 vs. CG1 and EG2 vs. CG2, respectively, showing 5 overlapping significant pathways: glutathione metabolism, biosynthesis of unsaturated fatty acids, galactose metabolism, arginine and proline metabolism, and ABC transporters. Intersection analysis identified that glutamate, oxidized glutathione (GSSG), and eicosenoic acid were the common metabolites induced by cold stress. Under starvation stress, a total of 300 and 215 differential metabolites were identified in CG2 vs. CG1 and EG2 vs. EG1, respectively, showing 2 overlapping significant pathways: glutathione metabolism and galactose metabolism. Intersection analysis revealed that glutamate and GSSG were the common metabolites caused by fasting. Under cold and starvation combined stresses, 286 differential metabolites were identified in EG2 vs. CG1, showing 7 influenced pathways: glycerophospholipid metabolism, biosynthesis of unsaturated fatty acids, glutathione metabolism, sphingolipid metabolism, glycosylphosphatidylinositol (GPI)-anchor biosynthesis, autophagy, and purine metabolism. Interestingly, the glutamate and GSSG were induced by both single and combined stresses of cold and starvation treatments. These findings suggest that glutathione metabolism and its related metabolites (glutamate and GSSG) could be potential biomarkers of cold and starvation stresses in yellow drum. Overall, the results of this study provided insights into the physiological regulation in response to cold and starvation stresses in this fish.
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http://dx.doi.org/10.1016/j.scitotenv.2020.136940DOI Listing
May 2020

Prediction model for dengue fever based on interactive effects between multiple meteorological factors in Guangdong, China (2008-2016).

PLoS One 2019 9;14(12):e0225811. Epub 2019 Dec 9.

College of Military Medicine, Academy of Military Sciences, Beijing, China.

Introduction: In order to improve the prediction accuracy of dengue fever incidence, we constructed a prediction model with interactive effects between meteorological factors, based on weekly dengue fever cases in Guangdong, China from 2008 to 2016.

Methods: Dengue fever data were derived from statistical data from the China National Notifiable Infectious Disease Reporting Information System. Daily meteorological data were obtained from the China Integrated Meteorological Information Sharing System. The minimum temperature for transmission was identified using data fitting and the Ross-Macdonald model. Correlations and interactive effects were examined using Spearman's rank correlation and multivariate analysis of variance. A probit regression model to describe the incidence of dengue fever from 2008 to 2016 and forecast the 2017 incidence was constructed, based on key meteorological factors, interactive effects, mosquito-vector factors, and other important factors.

Results: We found the minimum temperature suitable for dengue transmission was ≥18°C, and as 97.91% of cases occurred when the minimum temperature was above 18 °C, the data were used for model training and construction. Epidemics of dengue are related to mean temperature, maximum/minimum and mean atmospheric pressure, and mean relative humidity. Moreover, interactions occur between mean temperature, minimum atmospheric pressure, and mean relative humidity. Our weekly probit regression prediction model is 0.72. Prediction of dengue cases for the first 41 weeks of 2017 exhibited goodness of fit of 0.60.

Conclusion: Our model was accurate and timely, with consideration of interactive effects between meteorological factors.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0225811PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6901221PMC
March 2020

New Delhi Metallo-β-Lactamase 1-Producing ST719 Isolated from a Neonate in China.

Microb Drug Resist 2020 May 15;26(5):492-496. Epub 2019 Nov 15.

Center for Disease Control and Prevention of PLA, Beijing, China.

The spread of carbapenem-resistant has become a significant problem for public health in recent years. In this study, we reported a New Delhi metallo-β-lactamase 1 (NDM-1)-producing strain KP14003 from a neonate in Beijing, China. Whole-genome sequencing was performed. The strain belonged to sequence type ST719. Coexistence of and was found on a self-transferable plasmid, which had a typical IncX3 backbone. The horizontal transfer of was associated with Tn followed by possible transposition events. Other class A extended-spectrum β-lactamase genes ( and ) were also identified on chromosome or plasmid. The dissemination of NDM-1-producing causes great challenges to the treatment of clinical infections. Effective actions need to be taken to control the further spread of this pathogen.
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http://dx.doi.org/10.1089/mdr.2019.0058DOI Listing
May 2020

Deciphering the Origin and Evolution of the XXY System in Two Closely-Related Species (Oplegnathidae and Centrarchiformes).

Int J Mol Sci 2019 Jul 22;20(14). Epub 2019 Jul 22.

Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos SP 13565-905, Brazil.

and . (Teleostei: Centrarchiformes: Oplegnathidae), are commercially important rocky reef fishes, endemic to East Asia. Both species present an XXY sex chromosome system. Here, we investigated the evolutionary forces behind the origin and differentiation of these sex chromosomes, with the aim to elucidate whether they had a single or convergent origin. To achieve this, conventional and molecular cytogenetic protocols, involving the mapping of repetitive DNA markers, comparative genomic hybridization (CGH), and whole chromosome painting (WCP) were applied. Both species presented similar 2n, karyotype structure and hybridization patterns of repetitive DNA classes. 5S rDNA loci, besides being placed on the autosomal pair 22, resided in the terminal region of the long arms of both X chromosomes in females, and on the X and Y chromosomes in males. Furthermore, WCP experiments with a probe derived from the Y chromosome of . (OFAS-Y) entirely painted the X and X chromosomes in females and the X, X, and Y chromosomes in males of both species. CGH failed to reveal any sign of sequence differentiation on the Y chromosome in both species, thereby suggesting the shared early stage of neo-Y chromosome differentiation. Altogether, the present findings confirmed the origin of the XXY sex chromosomes via Y-autosome centric fusion and strongly suggested their common origin.
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http://dx.doi.org/10.3390/ijms20143571DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6678977PMC
July 2019

Structural and positional impact on DNAzyme-based electrochemical sensors for metal ions.

Nanomedicine 2019 10 19;21:102035. Epub 2019 Jun 19.

Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; Chinese PLA Center for Disease Control and Prevention, Beijing, China. Electronic address:

The rapid, accurate and convenient detection of heavy metal is very important to public health. Here, we developed a DNAzyme-based electrochemical sensor for Pb. A DNAzyme-including and Pb active probe was anchored to the biosensing interface, based on the well-defined self-assembled, three-dimensional DNA nanostructure. The results indicate that the detection performance depends on the change of distances between the methylene blue and the electrode surface. The limit of detection (LOD) could reach the concentration of 0.01 μM Pb, and the signal change shows semi-logarithmic relationship with the concentration of Pb from 0.01 μM to 100 μM. The biosensor also presents good stability and specificity to detect Pb in tap or river water. This method not only provides promising approach for improving the performance of tetrahedra in detecting Pb, but helps deepen the understanding of tetrahedral structure design and how the position of electroactive groups affects the performance of electrochemical sensing.
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http://dx.doi.org/10.1016/j.nano.2019.102035DOI Listing
October 2019

Overwinter mortality in yellow drum (Nibea albiflora): Insights from growth and immune responses to cold and starvation stress.

Fish Shellfish Immunol 2019 Sep 13;92:341-347. Epub 2019 Jun 13.

Marine Fishery Institute of Zhejiang Province, Key Lab of Mariculture and Enhancement of Zhejiang province, Zhoushanm, 316100, Zhejiang Province, PR China.

The yellow drum (Nibea albiflora) is an economically important maricultured fish in China, but the aquaculture of this species has recently been limited by an increase in overwinter mortalities associated with cold and starvation stress due to global climate changes. To better understand the interaction between starvation and cold-stress-driven overwinter mortality, we investigated the effects of these stresses on the growth performance, liver lesions, and immune response of yellow drum fish. The fish were subjected to different cold treatments and under starvation stress. The experiment lasted 30 days and involved four experimental groups: a fed group and a fasted group maintained at 16 °C (control), and a fed group and a fasted group subjected to cold stress at 8 °C. We found that the growth of yellow drum was severely affected by cold temperatures and starvation. Throughout the experimental period, the body weights were significantly lower in the groups subjected to starvation and cold stress than in the control group. The liver cells showed irregular shapes and disorderly arrangements in the stress groups; indicating liver lesions. The gene expressions of antioxidant enzymes (copper, zinc superoxide dismutase, manganese superoxide dismutase, iron superoxide dismutase, and catalase) in the liver were lower in the groups subjected to starvation and cold stress than in the control groups. These results were basically consistent with the enzyme activities of superoxide dismutase and catalase tested in the livers. In addition, activities of immunomodulatory enzymes (alkaline phosphatase and acid phosphatase) were also inhibited in groups subjected to stress throughout the experiment period. These findings suggested that starvation and cold stress inhibited growth, depressed liver function, and suppressed the immune system of yellow drum, which likely would lead to physiological failure and increased susceptibility to infection. The present study offers insights into the physiological and immune response of yellow drum under cold and starvation stress. These insights not only provide baseline information from which effective strategies can be established and appropriate management decisions formulated, but can also be used to improve the overwinter survival of this important fish species in China.
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http://dx.doi.org/10.1016/j.fsi.2019.06.030DOI Listing
September 2019

CSESA: an R package to predict Salmonella enterica serotype based on newly incorporated spacer pairs of CRISPR.

BMC Bioinformatics 2019 Apr 27;20(1):215. Epub 2019 Apr 27.

Center for Disease Control and Prevention of PLA, Beijing, China.

Background: Salmonella enterica is a major cause of bacterial food-borne disease worldwide. Immunological serotyping is the most commonly used typing method to characterize S. enterica isolates, but is time-consuming and requires expensive reagents. Here, we developed an R package CSESA (CRISPR-based Salmonella enterica Serotype Analyzer) to predict the serotype based on the CRISPR loci of S. enterica.

Results: CSESA has implemented the CRISPR typing method CLSPT and extended its coverage on diverse S. enterica serotypes. This package takes CRISPR sequences or the genome sequences as input and provides users with the predicted serotypes. CSESA has shown excellent performance with currently available sequences of S. enterica.

Conclusions: CSESA is a convenient and useful tool for the prediction of S. enterica serotypes. The application of CSESA package can improve the efficiency of serotyping for S. enterica and reduce the burden of manpower resources. CSESA is freely available from CRAN at https://cran.r-project.org/web/packages/CSESA/ .
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http://dx.doi.org/10.1186/s12859-019-2806-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6486994PMC
April 2019

The dengue outbreak of 2014 transformed the epidemic characteristics of dengue in Guangdong Province, China.

J Infect 2019 06 5;78(6):491-503. Epub 2019 Mar 5.

Center for Disease Control and Prevention of Chinese People's Liberation Army, 20 Dongdajie Street, Fengtai District, Beijing 100071, China. Electronic address:

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http://dx.doi.org/10.1016/j.jinf.2019.03.001DOI Listing
June 2019

Biosafety and biosecurity.

J Biosaf Biosecur 2019 Mar 20;1(1):15-18. Epub 2019 Feb 20.

State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.

With the profound changes in the international security situation, the progression of globalization, and the continuous advancement of biotechnology, the risks and challenges posed by major infectious diseases and bioterrorism to the international community are also increasing. Biosafety, therefore, presents new opportunities for international cooperation and global governance. The world has become more integrated and now shares a common destiny in terms of biosafety. In the face of the current risks and challenges, the international community must work together to avert threats, advance mutual interests, and safeguard global biosecurity. In the context of the current situation regarding biosafety and biosecurity, we conducted the present analysis, and present here some appropriate countermeasures.
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http://dx.doi.org/10.1016/j.jobb.2019.01.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7148603PMC
March 2019

Severe Pneumonia Caused by Coinfection With Influenza Virus Followed by Methicillin-Resistant Induces Higher Mortality in Mice.

Front Immunol 2018 30;9:3189. Epub 2019 Jan 30.

Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China.

Coinfection with influenza virus and bacteria is a major cause of high mortality during flu pandemics. Understanding the mechanisms behind such coinfections is of utmost importance both for the clinical treatment of influenza and the prevention and control of epidemics. To investigate the cause of high mortality during flu pandemics, we performed coinfection experiments with H1N1 influenza virus and in which mice were infected with bacteria at time points ranging from 0 to 7 days after infection with influenza virus. The mortality rates of mice infected with bacteria were highest 0-3 days after infection with influenza virus; lung tissues extracted from these co-infected mice showed higher infiltrating cells and thicker lung parenchyma than lung samples from coinfected mice in which influenza virus was introduced at other times and sequences. The levels of interferon (IFN)-γ, tumor necrosis factor (TNF)-α, interleukin (IL)-8, and IL-6 in the 0-3 day coinfected group were significantly higher than those in the other groups ( < 0.01), as were the mRNA levels of IFN-γ, IL-6, and TNF-α. Coinfection with influenza virus and led to high mortality rates that are directly dependent on the sequence and timing of infection by both pathogens. Moreover, coinfection following this particular schedule induced severe pneumonia, leading to increased mortality. Our data suggest that prevention of bacterial co-infection in the early stage of influenza virus infection is critical to reducing the risk of clinical mortality.
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http://dx.doi.org/10.3389/fimmu.2018.03189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364753PMC
October 2019