RESUMO
BACKGROUND: Haemophilus influenzae causes life-threatening invasive diseases such as septicaemia and meningitis. Reports on circulating H. influenzae causing invasive disease in lower-middle income settings, including Indonesia, are lacking. This study describes the serotype distributions and whole-genome sequence (WGS) data of H. influenzae isolated from hospitalized patients at Soetomo Hospital, Surabaya, Indonesia. METHODS: H. influenzae isolates were isolated from blood and pleural fluid specimens and identified using culture-based and molecular methods, followed by serotyping and WGS using RTâPCR and Illumina MiSeq, respectively. Sequencing reads were assembled, and further analyses were undertaken to determine the genomic content and reconstruct the phylogeny. A second dataset consisting of publicly available H. influenzae genomes was curated to conduct phylogenetic analyses of isolates in this study in the context of globally circulating isolates. RESULTS: Ten H. influenzae isolates from hospitalized patients were collected, and septicaemia was the most common diagnosis (n=8). RTâPCR and WGS were performed to determine whether all the isolates were nontypeable H. influenzae (NTHi). There were four newly identified STs distributed across the two main clusters. A total of 91 out of 126 virulence factor (VF)-related genes in Haemophilus sp. were detected in at least one isolate. Further evaluation incorporating a global collection of H. influenzae genomes confirmed the diverse population structure of NTHi in this study. CONCLUSION: This study showed that all H. influenzae recovered from invasive disease patients were nonvaccine-preventable NTHi isolates. The inclusion of WGS revealed four novel STs and the possession of key VF-associated genes.
Assuntos
Genoma Bacteriano , Infecções por Haemophilus , Haemophilus influenzae , Filogenia , Centros de Atenção Terciária , Sequenciamento Completo do Genoma , Humanos , Indonésia/epidemiologia , Haemophilus influenzae/genética , Haemophilus influenzae/isolamento & purificação , Haemophilus influenzae/classificação , Infecções por Haemophilus/microbiologia , Infecções por Haemophilus/epidemiologia , Centros de Atenção Terciária/estatística & dados numéricos , Feminino , Masculino , Pessoa de Meia-Idade , Adulto , Fatores de Virulência/genética , Idoso , Adulto Jovem , Sorotipagem , Sorogrupo , Criança , Adolescente , Pré-EscolarRESUMO
Dengue viruses are the causative agents of dengue fever, dengue hemorrhagic fever, and dengue shock syndrome, which are mainly transmitted by Aedes aegypti and Aedes albopictus mosquitoes, and cost billions of dollars annually in patient treatment and mosquito control. Progress in understanding DENV pathogenesis and developing effective treatments has been hampered by the lack of a suitable small pathological animal model. Until now, the candidate vaccine, antibody, and drug for DENV have not been effectively evaluated. Here, we analyzed the pathogenicity of DENV-1 in type â and type â ¡ interferon receptor-deficient mice (AGB6) by intraperitoneal inoculation. Infected mice showed such neurological symptoms as opisthotonus, hunching, ataxia, and paralysis of one or both hind limbs. Viremia can be detected 3 days after infection. It was found that 6.98 × 103 PFU or higher dose induce 100% mortality. To determine the cause of lethality in mice, heart, liver, spleen, lung, kidney, intestinal, and brain tissues were collected from AGB6 mice (at an attack dose of 6.98 × 103 PFU) for RNA quantification, and it was found that the viral load in brain tissues peaked at moribund states (14 dpi) and that the viral loads in the other tissues and organs decreased over time. Significant histopathologic changes were observed in brain tissue (hippocampal region and cerebral cortex). Hematological analysis showed hemorrhage and hemoconcentration in infected mice. DENV-1 can be isolated from the brain tissue of infected mice. Subsequently, brain tissue transcriptome sequencing was performed to assess host response characteristics in infected AGB6 mice. Transcriptional patterns in brain tissue suggest that aberrant expression of pro-inflammatory cytokines induces antiviral responses and tissue damage. Screening of hub genes and their characterization by qPCR and ELISA, it was hypothesized that IL-6 and IFN-γ might be the key factors in dengue virus-induced inflammatory response. Therefore, this study provides an opportunity to decipher certain aspects of dengue pathogenesis further and provides a new platform for drug, antibody, and vaccine testing.
Assuntos
Vírus da Dengue , Dengue , Modelos Animais de Doenças , Transcriptoma , Carga Viral , Animais , Vírus da Dengue/patogenicidade , Vírus da Dengue/genética , Dengue/virologia , Dengue/imunologia , Camundongos , Sorogrupo , Perfilação da Expressão Gênica , Encéfalo/virologia , Encéfalo/patologia , Virulência , Viremia , Camundongos KnockoutRESUMO
BACKGROUND: Streptococcus pneumoniae, a major contributor to global morbidity and mortality, disproportionately affects children, the elderly, and immunocompromised individuals. Despite vaccination efforts, the challenge of serotype replacement highlights the ongoing struggle against invasive pneumococcal diseases (IPD) in Morocco, emphasizing the need for updated public health strategies and vaccine efficacy assessments. METHODS: This study was conducted at the Ibn Rochd University Hospital Center and the Mohammed VI University Hospital Center from 2019 to 2022, focusing on hospitalized children. It involved the analysis of 74 strains of IPD, assessing the distribution of pneumococcal serotypes and their antibiotic sensitivity in the post-vaccination era. RESULTS: The prevalence of meningitis or meningo-encephalitis was found to be 66% among the study subjects, with the most frequent serotypes being 3, 19A, 6B, 14, and 11. These serotypes varied significantly by age and location. Coverage rates for the pneumococcal conjugate vaccines, PCV-10 and PCV-13, were 20.27% and 56.75%, respectively. Notably, 43% of the strains were non-vaccine serotypes, with serotypes 3 and 19 accounting for 36% of the infections in children, indicating a lack of vaccine efficacy against these types. Additionally, 31.3% of the strains were Penicillin non-susceptible Streptococcus pneumoniae (PNSP), with 81.25% associated with non-vaccine serotypes. CONCLUSIONS: This study highlights the persistence of IPD in Moroccan children, revealing significant challenges despite vaccination efforts. With the reintroduction of PCV-13, concerns about the efficacy against non-vaccine serotypes, particularly 3 and 19A, remain. Continuous surveillance and adaptable vaccination strategies are essential to combat these serotype replacements and ensure the effectiveness of future preventive measures.
Assuntos
Infecções Pneumocócicas , Vacinas Pneumocócicas , Sorogrupo , Streptococcus pneumoniae , Humanos , Marrocos/epidemiologia , Vacinas Pneumocócicas/administração & dosagem , Vacinas Pneumocócicas/imunologia , Infecções Pneumocócicas/prevenção & controle , Infecções Pneumocócicas/epidemiologia , Infecções Pneumocócicas/microbiologia , Pré-Escolar , Streptococcus pneumoniae/imunologia , Streptococcus pneumoniae/classificação , Streptococcus pneumoniae/isolamento & purificação , Lactente , Criança , Masculino , Feminino , Vacinação/estatística & dados numéricos , Adolescente , Antibacterianos/uso terapêutico , PrevalênciaRESUMO
BACKGROUND: Pneumococcus is a common cause of pneumonia, meningitis, and other serious infections in children. The previous study has proved that the 13-valent pneumococcal conjugate vaccine (PCV13) has sufficient immunogenicity in children. The data on long-term persistence of immunity will help the follow-up development work of pneumococcal vaccines. METHODS: Children who received the full vaccination course of the tested PCV13 in the previous clinical trial were enrolled again, and these who received other pneumococcal vaccines, or were infected with one or more serotypes of S. pneumoniae corresponding to PCV13 before enrollment were excluded. Participants were divided into four groups by age which is same as that of previous trial. The study lasted for 5 years, during which we measured pneumococcal antibodies of 13 serotypes included in PCV13 at particular points in time. Geometric mean concentrations (GMCs) and seropositive rates (the rate of IgG concentration ≥0.35 µg/mL) of antibodies against 13 serotypes were calculated. RESULTS: For the participants aged 2 months, five years after primary vaccination, except for serotypes 3 and 4, seropositive rates were 100%. GMCs of IgG antibodies against 13 serotypes ranged from 0.733 to 15.160 µg/mL. All of the participants aged 7-11 months had the serotype-specific IgG concentration ≥0.35 µg/mL four years after primary vaccination with the exception of serotypes 3, 4, 6 A and 9 V. IgG GMCs were 0.753-11.031 µg/mL. All participants aged 12-23 months and 2-5 years old had the serotype-specific IgG concentration ≥0.35 µg/mL three or two years after primary vaccination respectively, except for serotype 3. IgG GMCs ranged from 0.815 to 13.111 µg/mL, and 0.684 to 12.282 µg/mL respectively. CONCLUSION: PCV13 was applied to the population aged 2 months and 7 months - 5 years old with a good immune persistence, providing more extensive evidence of long-term efficacy for that vaccine. TRIAL REGISTRATION: The trial was registered with ClinicalTrials.gov, number NCT06210737.
Assuntos
Anticorpos Antibacterianos , Imunoglobulina G , Infecções Pneumocócicas , Vacinas Pneumocócicas , Sorogrupo , Streptococcus pneumoniae , Humanos , Vacinas Pneumocócicas/imunologia , Vacinas Pneumocócicas/administração & dosagem , Lactente , Anticorpos Antibacterianos/sangue , Anticorpos Antibacterianos/imunologia , Pré-Escolar , Streptococcus pneumoniae/imunologia , Streptococcus pneumoniae/classificação , Feminino , Masculino , Infecções Pneumocócicas/prevenção & controle , Infecções Pneumocócicas/imunologia , Imunoglobulina G/sangue , Imunoglobulina G/imunologia , Vacinas Conjugadas/imunologia , Vacinas Conjugadas/administração & dosagem , Vacinação/métodosRESUMO
Objective: To understand the incidence trend of meningococcal meningitis from 1990 to 2023 and major pathogenic serogroups of Neisseria (N.) meningitidis from 2006 to 2023 in China and the time trend of the incidence of meningococcal meningitis caused by main pathogenic serogroups, and provide reference for the prevention and control of meningococcal meningitis. Methods: The study used the data from "National Epidemic Data Compile" from 1990 to 2003 and the data from China Notifiable Infectious Disease Reporting System from 2004 to 2023 to analyze the incidence trend of meningococcal meningitis in China from 1990 to 2023 by Joinpoint regression method. Based on the data of the national meningococcal meningitis surveillance information reporting and management system from 2006 to 2023, the incidence of meningococcal meningitis caused by different serogroups of N. meningitidis was described and analyzed, and the trend χ2 test was performed to analyze the change of the incidence of meningococcal meningitis caused by N. meningitidis A, B, and C. Results: The overall incidence of meningococcal meningitis in China showed a downward trend from 1990 to 2023 [average annual percent change (AAPC)=-14.80%, P<0.001], with the most obvious decline from 2005 to 2012 [annual percent change (APC)=-31.01%, P<0.001]. The incidence of meningococcal meningitis decreased in both men and women (AAPC=-14.69% and -15.05%, both P<0.001). A total of 1 178 serogroup specific cases of meningococcal meningitis were reported in China from 2006 to 2023, the proportion of serogroup C was highest (32.5%), followed by unclassified (22.3%), B (20.1%), A (18.4%), W (4.5%), Y (2.0%) and X (0.2%). The results of trend χ2 test indicated that the incidence of meningococcal meningitis caused by N. meningitidis A and C showed downward trends (both P<0.001) and the incidence of meningococcal meningitis caused by N. meningitidis B showed an upward trend in general population and young children (0-4 years old group) from 2006 to 2023 (both P<0.05). Conclusion: The incidence of meningococcal meningitis showed a downward trend in China from 1990 to 2023, but it is still necessary to pay more attention to the incidence of meningococcal meningitis caused by N. meningitidis B in age group aged 0-4 years and by multi serogroups at same time in general population.
Assuntos
Meningite Meningocócica , Neisseria meningitidis , Sorogrupo , China/epidemiologia , Humanos , Incidência , Meningite Meningocócica/epidemiologia , Meningite Meningocócica/microbiologia , Neisseria meningitidis/classificação , Feminino , MasculinoRESUMO
Objective: To establish a matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) assay for the identification of common Salmonella serotypes and provide etiology evidence for the early precise treatment of salmonellosis. Methods: A total of 500 strains were collected from different regions and sources and five predominant Salmonella serotypes (Salmonella Typhi, Salmonella Paratyphi A, Salmonella Typhimurium, Salmonella Enteritidis, and Salmonella Indiana) of each strain was identified by agglutination test and whole-genome sequencing. The protein complex of the strains was extracted by using optimized pretreatment method to establish the fingerprint database of peptides for each Salmonella serotype. The new serotyping assays were established by using different modules based on the mass spectra database. Additional 155 strains with specified serotypes and variant sources were used to test and evaluate the accuracy of the new typing assays. Results: Five MALDI-TOF MS databases were established, and two new serotyping assays were established via peptide fingerprint mapping/matching and machine learning of the neuronal convolutional network respectively based on the databases. The results showed that the fingerprint matching approach could quickly identify five common Salmonella serotypes in clinical practice compared with the machine learning method, the accuracy of fingerprint matching assay to identify five Salmonella serotypes reached 100.00% and the serotyping can be conducted within a short time (15-20 minutes) and had a good reproducibility, while the machine learning method could not completely identify these serotypes. Moreover the sensitivity and specificity of fingerprint matching assay were all 100.00% respectively, while they were only 82.23% and 95.81% for machine learning method. Conclusion: The established Salmonella serotyping assay based on MALDI-TOF MS in this study can easily, rapidly and accurately identify different serotypes of Salmonella.
Assuntos
Salmonella , Sorotipagem , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Sorotipagem/métodos , Salmonella/classificação , Sorogrupo , Infecções por Salmonella/microbiologia , HumanosRESUMO
Streptococcus suis is a major swine pathogen and zoonotic agent, causing important economic losses to the porcine industry. Here, we used genomics approaches to characterize 251 S. suis isolates recovered from diseased pigs across Belgium, France, Germany, Hungary, the Netherlands, Spain, and the United Kingdom. We identified 13 serotypes, being serotypes 9 and 2 the most prevalent, and 34 sequence types (STs), including 16 novel STs, although ST16 and ST1 dominated the strain population. Phylogenetic analysis revealed complex genetic relationships, notable geographic clustering, and potential differential capacity for capsular switching among serotype 9 isolates. We found antimicrobial resistance (AMR) genes in 85.3% of the isolates, with high frequencies of genes conferring resistance to tetracyclines and macrolides. Specifically, 49.4% of the isolates harbored the tetO gene, and 64.9% possessed the ermB gene. Additionally, we observed a diverse array of virulence-associated genes (VAGs), including the classical VAGs mrp, epf, and sly, with variable presence across different genotypes. The high genetic diversity among European S. suis isolates highlights the importance of targeted antimicrobial use and flexible vaccine strategies. Rapid strain characterization is crucial for optimizing swine health management, enabling tailored interventions like the development of autovaccines to mitigate S. suis infections.
Assuntos
Infecções Estreptocócicas , Streptococcus suis , Doenças dos Suínos , Animais , Streptococcus suis/genética , Streptococcus suis/efeitos dos fármacos , Suínos , Doenças dos Suínos/microbiologia , Doenças dos Suínos/epidemiologia , Infecções Estreptocócicas/veterinária , Infecções Estreptocócicas/microbiologia , Infecções Estreptocócicas/epidemiologia , Europa (Continente)/epidemiologia , Filogenia , Sorogrupo , Variação Genética , Farmacorresistência Bacteriana/genética , Sus scrofa , Virulência , Antibacterianos/farmacologiaRESUMO
This study explored the molecular epidemiology and resistance mechanisms of 271 non-duplicate Salmonella enterica (S. enterica) strains, isolated mainly from adults (209/271) in a tertiary hospital in Hangzhou between 2020 and 2021. Through whole-genome sequencing and bioinformatics, the bacterial strains were classified into 46 serotypes and 54 sequence types (ST), with S. Enteritidis, S. 1,4,[5],12:i:-, and S. Typhimurium being the most prevalent serotypes and ST11, ST34, and ST19 the most common STs. The strains isolated from adults were primarily S. Enteritidis (59/209), while from children were mainly S. 1,4,[5],12:i:- (20/62). Worryingly, 12.55% strains were multi-drug resistant (MDR), with resistance rates to cefepime (FEP), ceftazidime (CAZ), ceftriaxone (CRO) and cefotaxime (CTX) of 7.38%, 9.23%, 15.87% and 16.24%, respectively, and resistance rates to levofloxacin (LEV) and ciprofloxacin (CIP) of 8.49% and 19.19%, respectively. It is worth noting that the resistance rates of CRO and CTX in children reached 30.65%. A total of 34 strains carried extended-spectrum ß-lactamase (ESBL) genes, dominated by blaCTX-M-65 (13/34) and blaCTX-M-55 (12/34); it is notable that one strain of S. Saintpaul carried both blaCTX-M-27 and blaCTX-M-55. The resistance mechanism to cephalosporins was mainly due to ESBL genes (20/43), and other genes included AmpC and ß-lactamase genes. The strains resistant to quinolones mainly carried qnrS1 (27/53), and others included qnrB6, aac(6')-Ib-cr, and mutations in gyrA and parC. One strain did not carry common quinolone resistance genes but had a parC (p.T57S) mutation to cause CIP resistance. This research provides vital insights into the molecular epidemiology and resistance mechanisms of clinical S. enterica, implicating possible infection control strategies.
Assuntos
Antibacterianos , Farmacorresistência Bacteriana Múltipla , Testes de Sensibilidade Microbiana , Infecções por Salmonella , Sequenciamento Completo do Genoma , Humanos , China/epidemiologia , Infecções por Salmonella/microbiologia , Infecções por Salmonella/epidemiologia , Antibacterianos/farmacologia , Farmacorresistência Bacteriana Múltipla/genética , Prevalência , Adulto , Criança , Salmonella enterica/efeitos dos fármacos , Salmonella enterica/genética , Salmonella enterica/isolamento & purificação , Salmonella enterica/classificação , Sorogrupo , Genoma Bacteriano , Salmonella/efeitos dos fármacos , Salmonella/genética , Salmonella/isolamento & purificação , Salmonella/classificação , Epidemiologia Molecular , beta-Lactamases/genéticaRESUMO
Dengue virus (DENV) is one of the most significant mosquito-borne diseases in Nepal. In 2023, DENV outbreaks began in Eastern Nepal, near the border with India, and rapidly spread nationwide. The study aims to describe the outbreak's epidemiological pattern, laboratory characteristics, DENV serotypes, and genotypes. A hospital-based cross-sectional study was conducted in four hospitals in Jhapa, Eastern Nepal, in 2023. Acute serum samples were obtained from dengue suspected patients within 7 days of illness and subjected to virus isolation, conventional and real-time polymerase chain reaction (RT-PCR), and phylogenetic analysis. Out of 60 samples, 42 (70 %), 11 (18.3 %) and 7 (11.7 %) were primary, secondary and non-dengue infection, respectively. Among 53 dengue confirmed patients, 46 (86.7 %) were positive for NS1 and 12 (22.6 %) were positive for both NS1 and IgM. Out of 42 dengue isolates, a new clade of the cosmopolitan genotype of DENV-2 was the most prevalent (28, 66.7 %), followed by genotype III of DENV-3 (11, 26.2 %) and genotype V of DENV-1 (3, 7.1 %). Genotype III of DENV-3 was first introduced in 2022-2023 in Nepal. Phylogenetic analysis of the E gene revealed the DENV-2 isolates from Nepal had 98 % homologous nucleotide similarity with the strains from India and Bangladesh. To our knowledge, this is the first report of circulating serotypes and genotypes of DENV in Jhapa. Integrating molecular findings into the dengue control plan can enhance surveillance efforts, monitor disease trends, and implement proactive measures to reduce the burden of dengue and prevent fatalities in future outbreaks.
Assuntos
Vírus da Dengue , Dengue , Surtos de Doenças , Genótipo , Filogenia , Sorogrupo , Humanos , Vírus da Dengue/genética , Vírus da Dengue/classificação , Vírus da Dengue/isolamento & purificação , Dengue/epidemiologia , Dengue/virologia , Nepal/epidemiologia , Estudos Transversais , Adulto , Masculino , Feminino , Adolescente , Adulto Jovem , Pessoa de Meia-Idade , Criança , Pré-Escolar , Idoso , RNA Viral/genéticaRESUMO
Foot-and-mouth disease (FMD) is one of the most infectious viral transboundary diseases of livestock, which causes devastating global economic losses. Different enzyme-linked immunosorbent assays (ELISAs) are used for sero-surveillance of the foot-and-mouth disease virus (FMDV). However, more sensitive, accurate, and convenient ELISAs are still required to detect antibodies against FMDV serotypes. The primary goal of this study was to establish serotype-specific monoclonal antibody (mAb)-based blocking ELISAs (mAb-bELISAs) that would provide better performance characteristics or be equivalent in performance characteristics compared with a conventional polyclonal antibody (pAb)-based competitive ELISA (pAb-cELISA). Four mAb-bELISAs were developed using FMDV serotype-specific mAbs for the detection of anti-FMDV/O/A/Asia1/SAT2 antibodies. Using a 50% cut-off, all four mAb-bELISAs exhibited species-independent 99.74%, 98.01%, 96.59%, and 98.55% diagnostic specificity (DSp) and 98.93%, 98.25%, 100%, and 87.50% diagnostic sensitivity (DSe) for FMDV serotypes O, A, Asia1, and SAT2, respectively. In addition, a 100% DSe of serotypes O- and SAT2-specific mAb-bELISAs was observed for porcine sera when the cut-off was 30%. All mAb-bELISAs developed in this study displayed high repeatability/reproducibility without cross-reactivity. Finally, the diagnostic performance of mAb-bELISAs was found to be better than or equivalent to compared with pAb-cELISAs, suggesting that mAb-bELISAs can be used to replace existing pAb-ELISAs for the detection of antibodies against these four FMDV serotypes.
Assuntos
Anticorpos Monoclonais , Anticorpos Antivirais , Ensaio de Imunoadsorção Enzimática , Vírus da Febre Aftosa , Febre Aftosa , Sensibilidade e Especificidade , Sorogrupo , Ensaio de Imunoadsorção Enzimática/métodos , Vírus da Febre Aftosa/imunologia , Vírus da Febre Aftosa/classificação , Anticorpos Antivirais/sangue , Anticorpos Antivirais/imunologia , Animais , Anticorpos Monoclonais/imunologia , Febre Aftosa/diagnóstico , Febre Aftosa/imunologia , Febre Aftosa/virologia , Suínos , Bovinos , Doenças dos Suínos/diagnóstico , Doenças dos Suínos/virologia , Doenças dos Suínos/imunologia , Camundongos , Reprodutibilidade dos TestesRESUMO
Background: The emergence of ESBLs producing cephalosporin-resistant Escherichia coli isolates poses a threat to public health. This study aims to decipher the genetic landscape and gain insights into ESBL-producing E. coli strains belonging to the high-risk clone ST410 from pediatric patients. Methods: 29 E. coli ST410 isolates were collected from young children and subjected to antimicrobial susceptibility testing, Whole-genome sequencing (WGS), serotype analysis, MLST, ESBL genes, virulence genes, and plasmid profiling. Results: Antimicrobial susceptibility testing demonstrated a high level of resistance to cephalosporins followed by aminoglycoside, sulfonamide, carbapenem and penicillin group of antibiotics. However, n=20/29 shows MDR phenotype. Phylogenetic group B2 (n=15) dominated, followed by group D (n=7), group A (n=4), and group B1 (n=3). Serotyping analysis identified O1:H7 (n=8), O2:H1 (n=6), O8:H4 (n=5), O16:H5 (n=4), and O25:H4 (n=3). Other serotypes identified included O6:H1, O15:H5, and O18:H7 (n=1 each). The most commonly detected ESBL genes were bla CTX-M, (n=26), followed by bla TEM (n=23), and bla SHV (n=18). Additionally, bla OXA-1 (n=10), bla OXA-48 (n=5), bla KPC-2 (n=3), bla KPC-3 (n=2), bla NDM-1 (n=4), bla NDM-5 (n=1), bla GES-1 (n=2), bla GES-5 (n=1), and bla CYM-1 (n=3). Notable virulence genes identified within the ST410 isolates included fimH (n=29), papC (n=24), hlyA (n=22), and cnf1 (n=18), among others. Diverse plasmids were observed including IncFIS, IncX4, IncFIA, IncCol, IncI2 and IncFIC with transmission frequency ranges from 1.3X10-2 to 2.7X10-3. Conclusion: The ST410 clone exhibited a complex resistance profile, diverse serotypes, the presence of specific resistance genes (ESBL genes), virulence gene repertoire, and diverse plasmids. The bla CTX-M was the most prevalent ESBL gene detected.
Assuntos
Antibacterianos , Infecções por Escherichia coli , Escherichia coli , Testes de Sensibilidade Microbiana , Tipagem de Sequências Multilocus , Filogenia , Plasmídeos , Fatores de Virulência , Sequenciamento Completo do Genoma , beta-Lactamases , Humanos , beta-Lactamases/genética , Escherichia coli/genética , Escherichia coli/efeitos dos fármacos , Escherichia coli/isolamento & purificação , Infecções por Escherichia coli/microbiologia , Infecções por Escherichia coli/epidemiologia , China/epidemiologia , Pré-Escolar , Antibacterianos/farmacologia , Lactente , Fatores de Virulência/genética , Plasmídeos/genética , Sorogrupo , Masculino , Criança , Feminino , Farmacorresistência Bacteriana Múltipla/genética , Sorotipagem , GenótipoRESUMO
Diarrheagenic Escherichia coli serotypes are associated with various clinical syndromes, yet the precise correlation between serotype and pathotype remains unclear. A major barrier to such studies is the reliance on antisera-based serotyping, which is culture-dependent, low-throughput, and cost-ineffective. We have established a highly multiplex PCR-based serotyping assay, termed the MeltArray E. coli serotyping (EST) assay, capable of identifying 163 O-antigen-encoding genes and 53 H-antigen-encoding genes of E. coli. The assay successfully identified serotypes directly from both simulated and real fecal samples, as demonstrated through spike-in validation experiments and a retrospective study. In a multi-province study involving 637 E. coli strains, it revealed that the five major diarrheagenic pathotypes have distinct serotype compositions. Notably, it differentiated 257 Shigella isolates into four major Shigella species, distinguishing them from enteroinvasive E. coli based on their distinct serotype profiles. The assay's universality was further corroborated by in silico analysis of whole-genome sequences from the EnteroBase. We conclude that the MeltArray EST assay represents a paradigm-shifting tool for molecular serotyping of E. coli, with potential routine applications for comprehensive serotype analysis, disease diagnosis, and outbreak detection.
Assuntos
Infecções por Escherichia coli , Escherichia coli , Fezes , Reação em Cadeia da Polimerase Multiplex , Sorogrupo , Sorotipagem , Sorotipagem/métodos , Infecções por Escherichia coli/microbiologia , Humanos , Escherichia coli/genética , Escherichia coli/classificação , Reação em Cadeia da Polimerase Multiplex/métodos , Fezes/microbiologia , Estudos Retrospectivos , Antígenos O/genética , Diarreia/microbiologia , Shigella/genética , Shigella/classificação , Shigella/isolamento & purificação , Antígenos de Bactérias/genética , Proteínas de Escherichia coli/genéticaRESUMO
Objective: To express and purify the phage depolymerase from hypervirulent Klebsiella pneumoniae (hvKp) serotype K1 and validate its function. Methods: Phage that infected serotype K1-type hvKp was isolated from hospital sewage. The biology and morphology of the phage were determined by plaque assay and transmission electron microscopy. The whole genome of the phage was sequenced by the Illumina HiSeq 2500 platform. The presence of depolymerase was determined by observing the plaque halo. Bioinformatic analysis and prokaryotic protein expression system were further used to predict and identify phage depolymerase. The depolymerase gene fragment was obtained by PCR and cloned into the pET28a expression vector, and the expression and purification of the depolymerase were completed in strain BL21. The depolymerase activities on the capsular polysaccharide of serotype K1-type hvKp clinical isolates were detected by plaque assay and low-speed centrifugation assay. Results: A lytic phage (phiA2) that infected serotype K1-type hvKp clinical isolate was isolated from hospital sewage. It was typical of the Caudovirales order and Autographiviridae family, and its whole genome was 43 526 bp in length and contained 51 coding domain sequences. The phage phiA2-derived depolymerase phiA2-dep was predicted, expressed and purified. The plaque assay and low-speed centrifugation assay indicated that the depolymerase phiA2-dep had good lytic activity on the capsular polysaccharide of serotype K1-type hvKp clinical isolates. Conclusion: Depolymerase phiA2-dep can specifically degrade the capsular polysaccharide of serotype K1-type hvKp, which has potential application value in treating bacterial infection.
Assuntos
Bacteriófagos , Klebsiella pneumoniae , Sorogrupo , Klebsiella pneumoniae/genética , Bacteriófagos/genética , Bacteriófagos/isolamento & purificação , Esgotos/microbiologia , Genoma ViralRESUMO
Streptococcus agalactiae (S. agalactiae) is an opportunistic pathogen, and to date, studies have mainly focused on S. agalactiae strains isolated from humans, dairy cows, and fish. We reported one S. agalactiae strain, named CFFB, which was isolated from a healthy Sichuan golden snub-nosed monkey. Classical bacteriological approaches, as well as, next-generation sequencing, comparative genomics, and mice challenge test were used to characterize this strain. CFFB was identified as serotype III, ST19 combination which is a common type found in human strains. Phylogenetic analysis showed that the genome of CFFB was closely related to human clinical isolates, rather far away from animal strains. In total, CFFB contained fewer virulence-associated genes and antibiotic resistance genes than human isolates that were close to CFFB in evolutionary relationships. In the mice challenge test, CFFB had a relative weak virulence that just caused death in 33 % of ICR mice at a dose of 108 CFU by intraperitoneal injection, and CFFB was reisolated from the cardiac blood of the dead mice. Meanwhile, two intact prophages (prophage 1 and 2) were identified in the CFFB genome and shared high similarities with phage Javan52 and Javan29 which from human S. agalactiae isolate Gottschalk 1002A and RBH03, respectively. Moreover, the type II-A CRISPR-Cas system was detected in the CFFB genome, and the spacers from CFFB were the same to the streptococci isolates from human. These results suggest that CFFB isolated from healthy Sichuan golden snub-nosed monkeys may have its origin in human S. agalactiae. Our results suggested some genomic similarities between the S. agalactiae colonized in Sichuan golden snub-nosed monkey and those in infected humans.
Assuntos
Genoma Bacteriano , Filogenia , Infecções Estreptocócicas , Streptococcus agalactiae , Animais , Streptococcus agalactiae/genética , Streptococcus agalactiae/isolamento & purificação , Streptococcus agalactiae/patogenicidade , Infecções Estreptocócicas/microbiologia , Infecções Estreptocócicas/veterinária , China , Virulência/genética , Camundongos , Colobinae/microbiologia , Humanos , Prófagos/genética , Camundongos Endogâmicos ICR , Fatores de Virulência/genética , Sorogrupo , Sequenciamento de Nucleotídeos em Larga Escala , Doenças dos Macacos/microbiologiaRESUMO
Moraxella catarrhalis has been recognized as an important cause of upper respiratory tract and middle ear infections in children, as well as chronic obstructive pulmonary disease and chronic bronchitis in adults. We aim to study the clonal structure, antimicrobial resistance, and serotypes of M. catarrhalis strains recovered from patients of different ages. Nasopharyngeal swabs, middle ear fluid, and sputum samples were collected. In vitro susceptibility testing was performed according to EUCAST criteria. The monoclonal Ab hybridoma technique was used for serotyping. All strains were subjected to MLST. The studied population demonstrated susceptibility to all tested antimicrobials M. catarrhalis strains, with the majority being serotype A (90.4%), followed by B (6.8%), and C (2.7%). We observed a predominant clonal complex CC224 (21.9%) along with other clusters including CC141 (8.2%), CC184 (8.2%), CC449 (6.8%), CC390 (5.5%), and CC67 (2.7%). Two primary founders, namely, ST224 and ST141, were identified. The analyzed genetic lineages displayed diversity but revealed the predominance of two main clusters, CC224 and CC141, encompassing multidrug-resistant sequence types distributed in other regions. These data underscore the need for ongoing epidemiological monitoring of successfully circulating clones and the implementation of adequate antibiotic policies to limit or delay the spread of multidrug-resistant strains in our region.
Assuntos
Moraxella catarrhalis , Infecções por Moraxellaceae , Tipagem de Sequências Multilocus , Filogenia , Moraxella catarrhalis/genética , Moraxella catarrhalis/isolamento & purificação , Moraxella catarrhalis/efeitos dos fármacos , Humanos , Infecções por Moraxellaceae/microbiologia , Criança , Adulto , Bulgária/epidemiologia , Feminino , Masculino , Antibacterianos/farmacologia , Testes de Sensibilidade Microbiana , Pré-Escolar , Adolescente , Pessoa de Meia-Idade , Idoso , Sorogrupo , Adulto Jovem , LactenteRESUMO
Invasive pneumococcal disease (IPD) due to non-vaccine serotypes after the introduction of pneumococcal conjugate vaccines (PCV) remains a global concern. This study used pathogen genomics to evaluate changes in invasive pneumococcal lineages before, during and after vaccine introduction in South Africa. We included genomes (N = 3104) of IPD isolates from individuals aged <18 years (2005-20), spanning four periods: pre-PCV, PCV7, early-PCV13, and late-PCV13. Significant incidence reductions occurred among vaccine-type lineages in the late-PCV13 period compared to the pre-PCV period. However, some vaccine-type lineages continued to cause invasive disease and showed increasing effective population size trends in the post-PCV era. A significant increase in lineage diversity was observed from the PCV7 period to the early-PCV13 period (Simpson's diversity index: 0.954, 95% confidence interval 0.948-0.961 vs 0.965, 0.962-0.969) supporting intervention-driven population structure perturbation. Increases in the prevalence of penicillin, erythromycin, and multidrug resistance were observed among non-vaccine serotypes in the late-PCV13 period compared to the pre-PCV period. In this work we highlight the importance of continued genomic surveillance to monitor disease-causing lineages post vaccination to support policy-making and future vaccine designs and considerations.
Assuntos
Infecções Pneumocócicas , Vacinas Pneumocócicas , Streptococcus pneumoniae , Vacinas Conjugadas , Humanos , Infecções Pneumocócicas/prevenção & controle , Infecções Pneumocócicas/epidemiologia , Infecções Pneumocócicas/microbiologia , Infecções Pneumocócicas/imunologia , África do Sul/epidemiologia , Vacinas Pneumocócicas/imunologia , Vacinas Pneumocócicas/administração & dosagem , Streptococcus pneumoniae/imunologia , Streptococcus pneumoniae/genética , Streptococcus pneumoniae/classificação , Streptococcus pneumoniae/isolamento & purificação , Criança , Pré-Escolar , Vacinas Conjugadas/imunologia , Lactente , Sorogrupo , Adolescente , Penicilinas , Eritromicina/uso terapêutico , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Masculino , Feminino , Genoma BacterianoRESUMO
Objective: To describe the profile of Streptococcus pneumoniae, identify research gaps, and provide in-depth insights into various aspects related to the pathogen. Methods: Google Scholar, PubMed, and ScienceDirect were searched for all studies on the pneumococcus in Ghana that reported on specimen collected, population and sample size, carriage prevalence, incidence of pneumococcal diseases, age of the study population, types of test performed, serotypes identified, antimicrobial susceptibilities, or molecular analysis on the pneumococci for data extraction. Results: Overall, a total of 7954 results were obtained from the three-database search, and of this, 24 articles were selected after screening. A total of 924 isolates were accounted for by serotyping/serogrouping. The prevalence of pneumococcal carriage in Ghana ranges from 11.0% to 51.4% in the population depending on the age (≤ 24-80 years), sickle cell disease (SCD), human immunodeficiency virus (HIV) status, or health of the study population, and penicillin (Pen)-nonsusceptible isolates ranged from 17% to 63%. The prevalence of pneumococci found as the etiologic agent of diseases among Ghanaians ranges from 3.4% for otitis media to 77.7% for meningitis. Overall, the 13-valent pneumococcal conjugate vaccine (PCV) (PCV-13) carriage serotypes accounted for 28.4% of the reported pneumococcal isolates. PCV-13 invasive serotypes accounted for 22.4% of the reported isolates. The non-PCV-13 carriage serotypes accounted for most (43.9%) of the reported isolates. In the pre-PCV-13 era, the nontypeable (NT) (5.5%) and other nonvaccine types (NVTs) (6.4%) were reported as being predominant. The non-PCV-13 serotypes accounted for 4.4% of the reported isolates in invasive pneumococcal disease (IPD) cases. Multidrug resistance (MDR) ranged from 7.8% to 100%. Conclusion: Predicting the invasiveness of pneumococci using molecular typing is the way to go in the future as this will provide answers to the extent to which capsular switching is contributing to the pneumococcal disease burden in Ghana almost a decade after introducing PCV-13. Continuous monitoring of antibiotic resistance patterns at both phenotypic and genotypic levels, along with serotyping and molecular typing, should be a standard practice in the surveillance of pneumococcal disease burden in Ghana.
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Infecções Pneumocócicas , Vacinas Pneumocócicas , Streptococcus pneumoniae , Humanos , Gana/epidemiologia , Streptococcus pneumoniae/patogenicidade , Streptococcus pneumoniae/isolamento & purificação , Infecções Pneumocócicas/epidemiologia , Infecções Pneumocócicas/microbiologia , Prevalência , Sorogrupo , Adulto , Idoso , Pessoa de Meia-Idade , Idoso de 80 Anos ou mais , Sorotipagem , Feminino , Antibacterianos/farmacologia , Antibacterianos/uso terapêuticoRESUMO
Streptococcus pneumoniae, a medically important opportunistic bacterial pathogen of the upper respiratory tract, is a major public health concern, causing a wide range of pneumococcal illnesses, both invasive and noninvasive. It is associated with significant global morbidity and mortality, including pneumonia, meningitis, sepsis, and acute otitis media. The major purpose of this study was to determine the molecular epidemiology of Streptococcus pneumoniae strains that cause invasive and noninvasive infections in Ethiopia. A prospective study was undertaken in two regional hospitals between January 2018 and December 2019. Whole-genome sequencing was used to analyze all isolates. Serotypes and multilocus sequence types (MLST) were derived from genomic data. The E-test was used for antimicrobial susceptibility testing. Patient samples obtained 54 Streptococcus pneumoniae isolates, 33 from invasive and 21 from noninvasive specimens. Our findings identified 32 serotypes expressed by 25 Global Pneumococcal Sequence Clusters (GPSCs) and 42 sequence types (STs), including 21 new STs. The most common sequence types among the invasive isolates were ST3500, ST5368, ST11162, ST15425, ST15555, ST15559, and ST15561 (2/33, 6% each). These sequence types were linked to serotypes 8, 7 C, 15B/C, 16 F, 10 A, 15B, and 6 A, respectively. Among the noninvasive isolates, only ST15432, associated with serotype 23 A, had numerous isolates (4/21, 19%). Serotype 14 was revealed as the most resistant strain to penicillin G, whereas isolates from serotypes 3, 8, 7 C, and 10 A were resistant to erythromycin. Notably, all serotype 6 A isolates were resistant to both erythromycin and penicillin G. Our findings revealed an abnormally significant number of novel STs, as well as extremely diversified serotypes and sequence types, implying that Ethiopia may serve as a breeding ground for novel STs. Recombination can produce novel STs that cause capsular switching. This has the potential to influence how immunization campaigns affect the burden of invasive pneumococcal illness. The findings highlight the importance of continuous genetic surveillance of the pneumococcal population as a vital step toward enhancing future vaccine design.
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Antibacterianos , Testes de Sensibilidade Microbiana , Epidemiologia Molecular , Tipagem de Sequências Multilocus , Infecções Pneumocócicas , Sorogrupo , Streptococcus pneumoniae , Sequenciamento Completo do Genoma , Streptococcus pneumoniae/genética , Streptococcus pneumoniae/isolamento & purificação , Streptococcus pneumoniae/efeitos dos fármacos , Streptococcus pneumoniae/classificação , Humanos , Etiópia/epidemiologia , Infecções Pneumocócicas/microbiologia , Infecções Pneumocócicas/epidemiologia , Masculino , Criança , Feminino , Pré-Escolar , Adolescente , Adulto , Pessoa de Meia-Idade , Estudos Prospectivos , Lactente , Adulto Jovem , Antibacterianos/farmacologia , IdosoRESUMO
Background Dengue, a viral infection highly prevalent in tropical regions, exhibits local variations in risks that are influenced by a combination of climatic, socioeconomic, and environmental factors. It is caused by four distinct, yet closely related serotypes of the dengue virus. Objective To identify the different serotypes of dengue virus responsible for the 2022 outbreak in Nepal, where dengue has been prevalent since 2006 but with limited availability of molecular information on the serotypes. Method Serum samples from suspected dengue patients visiting Dhulikhel Hospital were analyzed using Dengue Rapid Test, for the presence of IgG/IgM antibodies or NS1 Ag. The positive samples were stored at -80°C, and 89 samples were selected for further analysis. RNA was extracted from those positive samples and RT-PCR was performed to identify the serotypes present. Result A higher percentage of sero-positivity was observed in females(52%) compared to males. Positive cases were distributed in 14 different districts, with the highest percentage(58.4%) in Kavre. RT-PCR, of 53 out of 89 serologically positive samples, by RT-PCR revealed that DENV1 was the predominant, followed by DEN3(24.5%) and DENV2(16.9%). DENV4 was not detected in any of the samples. The average Ct-value of all serotypes was 17.6, with DENV3 having the lowest Ct-value of 16.6, indicating slightly higher viremia. Conclusion Our study, although limited in its coverage of Nepal, has provided molecular information on the serotypes responsible for the 2022 dengue outbreak. The high prevalence of DENV1 was observed, while prevalence of DENV3 was accompanied by high viral load.
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Vírus da Dengue , Dengue , Surtos de Doenças , Sorogrupo , Humanos , Nepal/epidemiologia , Vírus da Dengue/genética , Vírus da Dengue/imunologia , Dengue/epidemiologia , Dengue/virologia , Masculino , Feminino , Adulto , Adolescente , Pessoa de Meia-Idade , Adulto Jovem , RNA Viral/genéticaRESUMO
Porcine circovirus type 2 (PCV2) often causes disease through coinfection with other bacterial pathogens, including Glaesserella parasuis (G. parasuis), which causes high morbidity and mortality, but the role played by PCV2 and bacterial and host factors contributing to this process have not been defined. Bacterial attachment is assumed to occur via specific receptor-ligand interactions between adhesins on the bacterial cell and host proteins adsorbed to the implant surface. Mass spectrometry (MS) analysis of PCV2-infected swine tracheal epithelial cells (STEC) revealed that the expression of Extracellular matrix protein (ECM) Fibronectin (Fn) increased significantly on the infected cells surface. Importantly, efficient G. parasuis serotype 4 (GPS4) adherence to STECs was imparted by interactions with Fn. Furthermore, abrogation of adherence was gained by genetic knockout of Fn, Fn and Integrin ß1 antibody blocking. Fn is frequently exploited as a receptor for bacterial pathogens. To explore the GPS4 adhesin that interacts with Fn, recombinant Fn N-terminal type I and type II domains were incubated with GPS4, and the interacting proteins were pulled down for MS analysis. Here, we show that rare lipoprotein A (RlpA) directly interacts with host Fibronectin mediating GPS4 adhesion. Finally, we found that PCV2-induced Fibronectin expression and adherence of GPS4 were prevented significantly by TGF-ß signaling pathway inhibitor SB431542. Our data suggest the RlpA-Fn interaction to be a potentially promising novel therapeutic target to combat PCV2 and GPS4 coinfection.