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1.
Int J Food Microbiol ; 366: 109572, 2022 Apr 02.
Article in English | MEDLINE | ID: covidwho-1719840

ABSTRACT

Listeria monocytogenes remains a significant public health threat, leading to invasive listeriosis with severe manifestations (i.e. septicemia, meningitis, and abortion) and up to 30% of fatal cases. Here, we aimed to investigate genotypic diversity, virulence profiles, antimicrobial resistance patterns from a large and integrated population of L. monocytogenes isolates in China (n = 369), including food (n = 326), livestock (n = 25), and hospitalized humans (n = 18) over the years (2002-2019). PCR-based serogrouping showed the dominance of serogroup 1/2a-3a (37.4%) in food, 4a-4c (76%) in livestock, and 1/2a-3a (44.4%) in humans. Phylogenetic lineage analysis revealed the dominance of lineage II (63.4%) in food, lineage III (76%) in livestock, and lineage II (55.5%) in humans. Altogether, 369 isolates were grouped into 55 sequence types (STs) via multi-locus sequence typing (MLST), which belonged to 26 clonal complexes (CCs) and 17 singletons. Among various STs, ST9 (26%) was the most abundant in food, ST202 (76%) in livestock, and ST8 (16.6%) in humans. Overall, ST4/CC4, ST218/CC218, and ST619 isolates harbored both LIPI-3 and LIPI-4 genes subsets indicating their hypervirulence potential. Additionally, a low resistance was observed towards tetracycline (5.1%), erythromycin (3.2%), cotrimoxazole (2.9%), chloramphenicol (2.7%), gentamicin (2.4%), and ampicillin (2.1%). Collectively, detection of hypervirulent determinants and antimicrobial-resistant phenotype among Chinese isolates poses an alarming threat to food safety and public health, which requires a continued and enhanced surveillance system for further prevention of human listeriosis.


Subject(s)
Drug Resistance, Bacterial , Listeria monocytogenes , Animals , Anti-Bacterial Agents/pharmacology , China/epidemiology , Food Microbiology , Genetic Variation , Humans , Listeria monocytogenes/drug effects , Listeria monocytogenes/genetics , Listeriosis/epidemiology , Listeriosis/veterinary , Livestock/microbiology , Multilocus Sequence Typing , Phylogeny , Virulence Factors/genetics
2.
J Virol ; 96(3): e0184221, 2022 02 09.
Article in English | MEDLINE | ID: covidwho-1691423

ABSTRACT

Middle East respiratory syndrome coronavirus (MERS-CoV) is a beta coronavirus that emerged in 2012, causing severe pneumonia and renal failure. MERS-CoV encodes five accessory proteins. Some of them have been shown to interfere with host antiviral immune response. However, the roles of protein 8b in innate immunity and viral virulence was rarely studied. Here, we introduced individual MERS-CoV accessory protein genes into the genome of an attenuated murine coronavirus (Mouse hepatitis virus, MHV), respectively, and found accessory protein 8b could enhance viral replication in vivo and in vitro and increase the lethality of infected mice. RNA-seq analysis revealed that protein 8b could significantly inhibit type I interferon production (IFN-I) and innate immune response in mice infected with MHV expressing protein 8b. We also found that MERS-CoV protein 8b could initiate from multiple internal methionine sites and at least three protein variants were identified. Residues 1-23 of protein 8b was demonstrated to be responsible for increased virulence in vivo. In addition, the inhibitory effect on IFN-I of protein 8b might not contribute to its virulence enhancement as aa1-23 deletion did not affect IFN-I production in vitro and in vivo. Next, we also found that protein 8b was localized to the endoplasmic reticulum (ER)/Golgi membrane in infected cells, which was disrupted by C-terminal region aa 88-112 deletion. This study will provide new insight into the pathogenesis of MERS-CoV infection. IMPORTANCE Multiple coronaviruses (CoV) cause severe respiratory infections and become global public health threats such as SARS-CoV, MERS-CoV, and SARS-CoV-2. Each coronavirus contains different numbers of accessory proteins which show high variability among different CoVs. Accessory proteins are demonstrated to play essential roles in pathogenesis of CoVs. MERS-CoV contains 5 accessory proteins (protein 3, 4a, 4b, 5, 8b), and deletion of all four accessory proteins (protein 3, 4a, 4b, 5), significantly affects MERS-CoV replication and pathogenesis. However, whether ORF8b also regulates MERS-CoV infection is unknown. Here, we constructed mouse hepatitis virus (MHV) recombinant virus expressing MERS-CoV protein 8b and demonstrated protein 8b could significantly enhance the virulence of MHV, which is mediated by N-terminal domain of protein 8b. This study will shed light on the understanding of pathogenesis of MERS-CoV infection.


Subject(s)
Middle East Respiratory Syndrome Coronavirus/physiology , Murine hepatitis virus/physiology , Protein Interaction Domains and Motifs , Viral Regulatory and Accessory Proteins/genetics , Animals , Coronavirus Infections/immunology , Coronavirus Infections/virology , Host-Pathogen Interactions/immunology , Immunity, Innate , Mice , Mortality , Viral Regulatory and Accessory Proteins/chemistry , Viral Tropism , Virulence/genetics , Virulence Factors/genetics
3.
Int J Mol Sci ; 23(2)2022 Jan 16.
Article in English | MEDLINE | ID: covidwho-1639094

ABSTRACT

The main purpose of this review is to present justification for the urgent need to implement specific prophylaxis of invasive Staphylococcus aureus infections. We emphasize the difficulties in achieving this goal due to numerous S. aureus virulence factors important for the process of infection and the remarkable ability of these bacteria to avoid host defense mechanisms. We precede these considerations with a brief overview of the global necessitiy to intensify the use of vaccines against other pathogens as well, particularly in light of an impasse in antibiotic therapy. Finally, we point out global trends in research into modern technologies used in the field of molecular microbiology to develop new vaccines. We focus on the vaccines designed to fight the infections caused by S. aureus, which are often resistant to the majority of available therapeutic options.


Subject(s)
Staphylococcal Infections/prevention & control , Staphylococcal Vaccines/therapeutic use , Staphylococcus aureus/immunology , Drug Resistance, Bacterial/drug effects , Humans , Staphylococcal Infections/immunology , Staphylococcal Vaccines/immunology , Staphylococcal Vaccines/pharmacology , Staphylococcus aureus/genetics , Staphylococcus aureus/pathogenicity , Virulence Factors/genetics , Virulence Factors/immunology
4.
J Virol ; 96(3): e0184221, 2022 02 09.
Article in English | MEDLINE | ID: covidwho-1532965

ABSTRACT

Middle East respiratory syndrome coronavirus (MERS-CoV) is a beta coronavirus that emerged in 2012, causing severe pneumonia and renal failure. MERS-CoV encodes five accessory proteins. Some of them have been shown to interfere with host antiviral immune response. However, the roles of protein 8b in innate immunity and viral virulence was rarely studied. Here, we introduced individual MERS-CoV accessory protein genes into the genome of an attenuated murine coronavirus (Mouse hepatitis virus, MHV), respectively, and found accessory protein 8b could enhance viral replication in vivo and in vitro and increase the lethality of infected mice. RNA-seq analysis revealed that protein 8b could significantly inhibit type I interferon production (IFN-I) and innate immune response in mice infected with MHV expressing protein 8b. We also found that MERS-CoV protein 8b could initiate from multiple internal methionine sites and at least three protein variants were identified. Residues 1-23 of protein 8b was demonstrated to be responsible for increased virulence in vivo. In addition, the inhibitory effect on IFN-I of protein 8b might not contribute to its virulence enhancement as aa1-23 deletion did not affect IFN-I production in vitro and in vivo. Next, we also found that protein 8b was localized to the endoplasmic reticulum (ER)/Golgi membrane in infected cells, which was disrupted by C-terminal region aa 88-112 deletion. This study will provide new insight into the pathogenesis of MERS-CoV infection. IMPORTANCE Multiple coronaviruses (CoV) cause severe respiratory infections and become global public health threats such as SARS-CoV, MERS-CoV, and SARS-CoV-2. Each coronavirus contains different numbers of accessory proteins which show high variability among different CoVs. Accessory proteins are demonstrated to play essential roles in pathogenesis of CoVs. MERS-CoV contains 5 accessory proteins (protein 3, 4a, 4b, 5, 8b), and deletion of all four accessory proteins (protein 3, 4a, 4b, 5), significantly affects MERS-CoV replication and pathogenesis. However, whether ORF8b also regulates MERS-CoV infection is unknown. Here, we constructed mouse hepatitis virus (MHV) recombinant virus expressing MERS-CoV protein 8b and demonstrated protein 8b could significantly enhance the virulence of MHV, which is mediated by N-terminal domain of protein 8b. This study will shed light on the understanding of pathogenesis of MERS-CoV infection.


Subject(s)
Middle East Respiratory Syndrome Coronavirus/physiology , Murine hepatitis virus/physiology , Protein Interaction Domains and Motifs , Viral Regulatory and Accessory Proteins/genetics , Animals , Coronavirus Infections/immunology , Coronavirus Infections/virology , Host-Pathogen Interactions/immunology , Immunity, Innate , Mice , Mortality , Viral Regulatory and Accessory Proteins/chemistry , Viral Tropism , Virulence/genetics , Virulence Factors/genetics
5.
Microbiologyopen ; 10(3): e1211, 2021 06.
Article in English | MEDLINE | ID: covidwho-1281235

ABSTRACT

Tuberculosis (TB) is the leading cause of death in humans by a single infectious agent worldwide with approximately two billion humans latently infected with the bacterium Mycobacterium tuberculosis. Currently, the accepted method for controlling the disease is Tuberculosis Directly Observed Treatment Shortcourse (TB-DOTS). This program is not preventative and individuals may transmit disease before diagnosis, thus better understanding of disease transmission is essential. Using whole-genome sequencing and single nucleotide polymorphism analysis, we analyzed genomes of 145 M. tuberculosis clinical isolates from active TB cases from the Rubaga Division of Kampala, Uganda. We established that these isolates grouped into M. tuberculosis complex (MTBC) lineages 1, 2, 3, and 4, with the most isolates grouping into lineage 4. Possible transmission pairs containing ≤12 SNPs were identified in lineages 1, 3, and 4 with the prevailing transmission in lineages 3 and 4. Furthermore, investigating DNA codon changes as a result of specific SNPs in prominent virulence genes including plcA and plcB could indicate potentially important modifications in protein function. Incorporating this analysis with corresponding epidemiological data may provide a blueprint for the integration of public health interventions to decrease TB transmission in a region.


Subject(s)
Mycobacterium tuberculosis/genetics , Mycobacterium tuberculosis/isolation & purification , Polymorphism, Single Nucleotide , Tuberculosis/microbiology , Bacterial Proteins/genetics , Cities/statistics & numerical data , Cross-Sectional Studies , Genome, Bacterial , Genotype , Humans , Mycobacterium tuberculosis/classification , Mycobacterium tuberculosis/physiology , Phylogeny , Tuberculosis/epidemiology , Tuberculosis/transmission , Uganda/epidemiology , Virulence Factors/genetics , Whole Genome Sequencing
6.
Vet Microbiol ; 254: 109014, 2021 Mar.
Article in English | MEDLINE | ID: covidwho-1107294

ABSTRACT

TW-like infectious bronchitis virus (IBV) with high pathogenicity is becoming the predominant IBV type circulating in China. To develop vaccines against TW-like IBV strains and investigate the critical genes associated with their virulence, GD strain was attenuated by 140 serial passages in specific-pathogen-free embryonated eggs and the safety and efficacy of the attenuated GD strain (aGD) were examined. The genome sequences of GD and aGD were also compared and the effects of mutations in the S gene were observed. The results revealed that aGD strain showed no obvious pathogenicity with superior protective efficacy against TW-like and QX-like virulent IBV strains. The genomes of strains aGD and GD shared high similarity (99.87 %) and most of the mutations occurred in S gene. Recombinant IBV strain rGDaGD-S, in which the S gene was replaced with the corresponding regions from aGD, showed decreased pathogenicity compared with its parental strain. In conclusion, attenuated TW-like IBV strain aGD is a potential vaccine candidate and the S gene is responsible for its attenuation. Our research has laid the foundation for future exploration of the attenuating molecular mechanism of IBV.


Subject(s)
Chickens/virology , Infectious bronchitis virus/genetics , Infectious bronchitis virus/pathogenicity , Spike Glycoprotein, Coronavirus/genetics , Viral Vaccines/genetics , Virulence Factors/genetics , Animals , Chick Embryo , Coronavirus Infections/prevention & control , Infectious bronchitis virus/immunology , Poultry Diseases/prevention & control , Poultry Diseases/virology , Reverse Genetics/methods , Serial Passage , Specific Pathogen-Free Organisms , Spike Glycoprotein, Coronavirus/immunology , Vaccines, Attenuated/immunology , Viral Vaccines/immunology
7.
Virus Res ; 300: 198441, 2021 07 15.
Article in English | MEDLINE | ID: covidwho-1221063

ABSTRACT

One of the most important proteins for COVID-19 pathogenesis in SARS-CoV-2 is the ORF3a which is the largest accessory protein among others coded by the SARS-CoV-2 genome. The major roles of the protein include virulence, infectivity, ion channel activity, morphogenesis, and virus release. The coronavirus, SARS-CoV-2 is mutating rapidly, therefore, critical study of mutations in ORF3a is certainly important from the pathogenic perspective. Here, a sum of 175 non-synonymous mutations in the ORF3a of SARS-CoV-2 were identified from 7194 complete genomes of SARS-CoV-2 available from NCBI database. Effects of these mutations on structural stability, and functions of ORF3a were also studied. Broadly, three different classes of mutations, such as neutral, disease, and mixed (neutral and disease) types of mutations were observed. Consecutive phenomena of mutations in ORF3a protein were studied based on the timeline of detection of the mutations. Considering the amino acid compositions of the ORF3a protein, twenty clusters were detected using the K-means clustering method. The present findings on 175 novel mutations of ORF3a proteins will extend our knowledge on ORF3a, a vital accessory protein in SARS-CoV-2, to enlighten the pathogenicity of this life-threatening virus.


Subject(s)
COVID-19/virology , SARS-CoV-2 , Viroporin Proteins , Virulence Factors , Databases, Genetic , Genes, Viral , Genetic Variation , Humans , Mutation, Missense , SARS-CoV-2/genetics , SARS-CoV-2/pathogenicity , Structure-Activity Relationship , Viroporin Proteins/chemistry , Viroporin Proteins/genetics , Virulence Factors/chemistry , Virulence Factors/genetics
8.
Genome Med ; 12(1): 113, 2020 12 09.
Article in English | MEDLINE | ID: covidwho-964565

ABSTRACT

BACKGROUND: Antibiotic-resistant Klebsiella pneumoniae are a major cause of hospital- and community-acquired infections, including sepsis, liver abscess, and pneumonia, driven mainly by the emergence of successful high-risk clonal lineages. The K. pneumoniae sequence type (ST) 307 lineage has appeared in several different parts of the world after first being described in Europe in 2008. From June to October 2019, we recorded an outbreak of an extensively drug-resistant ST307 lineage in four medical facilities in north-eastern Germany. METHODS: Here, we investigated these isolates and those from subsequent cases in the same facilities. We performed whole-genome sequencing to study phylogenetics, microevolution, and plasmid transmission, as well as phenotypic experiments including growth curves, hypermucoviscosity, siderophore secretion, biofilm formation, desiccation resilience, serum survival, and heavy metal resistance for an in-depth characterization of this outbreak clone. RESULTS: Phylogenetics suggest a homogenous phylogram with several sub-clades containing either isolates from only one patient or isolates originating from different patients, suggesting inter-patient transmission. We identified three large resistance plasmids, carrying either NDM-1, CTX-M-15, or OXA-48, which K. pneumoniae ST307 likely donated to other K. pneumoniae isolates of different STs and even other bacterial species (e.g., Enterobacter cloacae) within the clinical settings. Several chromosomally and plasmid-encoded, hypervirulence-associated virulence factors (e.g., yersiniabactin, metabolite transporter, aerobactin, and heavy metal resistance genes) were identified in addition. While growth, biofilm formation, desiccation resilience, serum survival, and heavy metal resistance were comparable to several control strains, results from siderophore secretion and hypermucoviscosity experiments revealed superiority of the ST307 clone, similar to an archetypical, hypervirulent K. pneumoniae strain (hvKP1). CONCLUSIONS: The combination of extensive drug resistance and virulence, partly conferred through a "mosaic" plasmid carrying both antibiotic resistance and hypervirulence-associated features, demonstrates serious public health implications.


Subject(s)
Anti-Bacterial Agents/pharmacology , Drug Resistance, Bacterial/genetics , Iron/metabolism , Klebsiella Infections/microbiology , Klebsiella pneumoniae/drug effects , Klebsiella pneumoniae/genetics , Bacterial Proteins/genetics , Biofilms/growth & development , Disease Outbreaks , Genes, Bacterial/genetics , Germany/epidemiology , Humans , Klebsiella Infections/epidemiology , Klebsiella pneumoniae/classification , Klebsiella pneumoniae/growth & development , Phylogeny , Plasmids , Polymorphism, Single Nucleotide , Virulence/drug effects , Virulence/genetics , Virulence Factors/genetics , Whole Genome Sequencing
9.
Front Immunol ; 11: 582102, 2020.
Article in English | MEDLINE | ID: covidwho-918145

ABSTRACT

The suppressor of cytokine signaling (SOCS) family of intracellular checkpoint inhibitors has received little recognition compared to other checkpoint inhibitors. Two members of this family, SOCS1 and SOCS3, are indispensable, since SOCS1 knockout in mice results in neonatal death due to interferon gamma (IFNγ) induced inflammatory disease, and SOCS3 knockout leads to embryonic lethality. We have shown that SOCS1 and SOCS3 (SOCS1/3) function as virus induced intrinsic virulence factors for influenza A virus, EMC virus, herpes simplex virus 1 (HSV-1), and vaccinia virus infections. Other viruses such as pathogenic pig enteric coronavirus and coronavirus induced severe acute respiratory syndrome (SARS) spike protein also induce SOCS virus intrinsic virulence factors. SOCS1/3 exert their viral virulence effect via inhibition of type I and type II interferon (IFN) function. Specifically, the SOCS bind to the activation loop of receptor-associated tyrosine kinases JAK2 and TYK2 through the SOCS kinase inhibitory region (KIR), which inhibits STAT transcription factor activation by the kinases. Activated STATs are required for IFN function. We have developed a small peptide antagonist of SOCS1/3 that blocks SOCS1/3 inhibitory activity and prevents virus pathogenesis. The antagonist, pJAK2(1001-1013), is comprised of the JAK2 activation loop, phosphorylated at tyrosine 1007 with a palmitate for cell penetration. The remarkable thing about SOCS1/3 is that it serves as a broad, simple tool of perhaps most pathogenic viruses to avoid innate host IFN defense. We suggest in this Perspective that SOCS1/3 antagonist is a simple counter measure to SOCS1/3 and should be an effective mechanism as a prophylactic and/or therapeutic against the COVID-19 pandemic that is caused by coronavirus SARS-CoV2.


Subject(s)
COVID-19/drug therapy , COVID-19/immunology , SARS-CoV-2/physiology , Suppressor of Cytokine Signaling 1 Protein/immunology , Suppressor of Cytokine Signaling 3 Protein/immunology , Virulence Factors/immunology , Animals , COVID-19/genetics , COVID-19/virology , Humans , Interferons/genetics , Interferons/immunology , Mice , SARS-CoV-2/genetics , Suppressor of Cytokine Signaling 1 Protein/genetics , Suppressor of Cytokine Signaling 3 Protein/genetics , Virulence Factors/genetics
10.
mBio ; 11(3)2020 05 29.
Article in English | MEDLINE | ID: covidwho-432175

ABSTRACT

A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was recently identified as the causative agent for the coronavirus disease 2019 (COVID-19) outbreak that has generated a global health crisis. We use a combination of genomic analysis and sensitive profile-based sequence and structure analysis to understand the potential pathogenesis determinants of this virus. As a result, we identify several fast-evolving genomic regions that might be at the interface of virus-host interactions, corresponding to the receptor binding domain of the Spike protein, the three tandem Macro fold domains in ORF1a, and the uncharacterized protein ORF8. Further, we show that ORF8 and several other proteins from alpha- and beta-CoVs belong to novel families of immunoglobulin (Ig) proteins. Among them, ORF8 is distinguished by being rapidly evolving, possessing a unique insert, and having a hypervariable position among SARS-CoV-2 genomes in its predicted ligand-binding groove. We also uncover numerous Ig domain proteins from several unrelated metazoan viruses, which are distinct in sequence and structure but share comparable architectures to those of the CoV Ig domain proteins. Hence, we propose that SARS-CoV-2 ORF8 and other previously unidentified CoV Ig domain proteins fall under the umbrella of a widespread strategy of deployment of Ig domain proteins in animal viruses as pathogenicity factors that modulate host immunity. The rapid evolution of the ORF8 Ig domain proteins points to a potential evolutionary arms race between viruses and hosts, likely arising from immune pressure, and suggests a role in transmission between distinct host species.IMPORTANCE The ongoing COVID-19 pandemic strongly emphasizes the need for a more complete understanding of the biology and pathogenesis of its causative agent SARS-CoV-2. Despite intense scrutiny, several proteins encoded by the genomes of SARS-CoV-2 and other SARS-like coronaviruses remain enigmatic. Moreover, the high infectivity and severity of SARS-CoV-2 in certain individuals make wet-lab studies currently challenging. In this study, we used a series of computational strategies to identify several fast-evolving regions of SARS-CoV-2 proteins which are potentially under host immune pressure. Most notably, the hitherto-uncharacterized protein encoded by ORF8 is one of them. Using sensitive sequence and structural analysis methods, we show that ORF8 and several other proteins from alpha- and beta-coronavirus comprise novel families of immunoglobulin domain proteins, which might function as potential immune modulators to delay or attenuate the host immune response against the viruses.


Subject(s)
Coronavirus/genetics , Coronavirus/pathogenicity , Evolution, Molecular , Viral Proteins/genetics , Virulence Factors/genetics , Amino Acid Sequence , Animals , Betacoronavirus/chemistry , Betacoronavirus/classification , Betacoronavirus/genetics , Betacoronavirus/pathogenicity , Coronavirus/chemistry , Coronavirus/classification , Genome, Viral/genetics , Host Specificity , Humans , Immunoglobulin Domains/genetics , Models, Molecular , Open Reading Frames , Phylogeny , SARS-CoV-2 , Viral Proteins/chemistry , Virulence Factors/chemistry
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