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In the global efforts to combat antimicrobial resistance and reduce antimicrobial use in pig production, there is a continuous search for methods to prevent and/or treat infections. Within this scope, we explored the relationship between the developing piglet nasal microbiome and (zoonotic) bacterial pathogens from birth until 10 weeks of life. The nasal microbiome of 54 pigs was longitudinally studied over 16 timepoints on 9 farms in 3 European countries (Germany, Ireland, and the Netherlands) using amplicon sequencing targeting the V3-V4 16S rRNA region as well as the tuf gene for its staphylococcal discrimination power. The piglets' age, the farm, and the litter affected the nasal microbiome, with piglets' age explaining 19% of the variation in microbial composition between samples. Stabilization of the microbiome occurred around 2 weeks post-weaning. Notably, while opportunistic pathogens were ubiquitously present, they did not cause disease. The piglet nasal microbiome often carried species associated with gut, skin, or vagina, which suggests that contact with the vaginal and fecal microbiomes shapes the piglet nasal microbiome. We identified bacterial co-abundance groups of species that were present in the nasal microbiomes in all three countries over time. Anti-correlation between these species and known bacterial pathogens identified species that might be exploited for pathogen reduction. Further experimental evidence is required to confirm these findings. Overall, this study advances our understanding of the piglet nasal microbiome, the factors influencing it, and its longitudinal development, providing insights into its role in health and disease. IMPORTANCE: Our study on the nasal microbiota development in piglets across farms in three European countries found that the microbiomes developed similarly in all locations. Additionally, we observed that the colonization of porcine pathogens was either positively or negatively associated with the presence of other bacterial species. These findings enhance our knowledge of co-colonizing species in the nasal cavity and the identified microbial interactions that can be explored for the development of interventions to control pathogens in porcine husbandry.
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INTRODUCTION: Emerging evidence indicates that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected individuals are at an increased risk for co-infections. This retrospective study aims to expand the knowledge of associated factors of respiratory co-infection in SARS-CoV-2 positivity. METHODOLOGY: A retrospective study was conducted to recruit fifty-five patients with laboratory-confirmed SARS-CoV-2 positivity. We additionally tested 29 other respiratory pathogens using RT-PCR assay for the same specimens tested for laboratory-confirmed SARS-CoV-2. Both univariate and multivariate analysis were performed to identify independent factors for co-infection. Cox regression was conducted to detect the association between co-infection and viral load after controlling other related factors. RESULTS: Among all the fifty-five COVID-19 patients, the rate of co-infection with at least one other respiratory pathogen was 76.4% (42/55). The rate of bacterial co-infections was 83.3% (35/42), among which Streptococcus pneumonia was the most common co-infection. Over 70% of neutrophils proportion (OR: 4.563; 95% CI: 1.116-18.648) was an independently associated factor for bacterial co-infection, whereas fever (OR: 4.506; 95% CI: 1.044-19.441) and chest tightness (OR: 0.106; 95% CI: 0.015-0.743) for viral co-infection. The strongest promotion of SARS-CoV-2 viral decreasing load was detected from co-infection of only viruses (HR: 4.039; 95% CI: 1.238-13.177), and the weakest was found from co-infection of only bacteria (HR: 2.909; 95% CI: 1.308-6.472). CONCLUSIONS: Various co-infections variously promote SARS-CoV-2 viral decreasing load. Timely identification of co-infections aggressively contributes to COVID-19 patient management.
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COVID-19 , Coinfección , SARS-CoV-2 , Carga Viral , Humanos , COVID-19/complicaciones , Coinfección/virología , Coinfección/epidemiología , Estudios Retrospectivos , Masculino , Femenino , Persona de Mediana Edad , SARS-CoV-2/aislamiento & purificación , Adulto , Anciano , Factores de Riesgo , Infecciones del Sistema Respiratorio/virología , Infecciones del Sistema Respiratorio/epidemiología , Infecciones Bacterianas/epidemiología , Infecciones Bacterianas/complicacionesRESUMEN
Background: Metagenomic next-generation sequencing (mNGS), which provides untargeted and unbiased pathogens detection, has been extensively applied to improve diagnosis of pulmonary infection. This study aimed to compare the clinical performance between mNGS and targeted NGS (tNGS) for microbial detection and identification in bronchoalveolar lavage fluid (BALF) from kidney transplantation recipients (KTRs). Methods: BALF samples with microbiological results from mNGS and conventional microbiological test (CMT) were included. For tNGS, samples were extracted, amplified by polymerase chain reaction with pathogen-specific primers, and sequenced on an Illumina Nextseq. Results: A total of 99 BALF from 99 KTRs, among which 93 were diagnosed as pulmonary infection, were analyzed. Compared with CMT, both mNGS and tNGS showed higher positive rate and sensitivity (p<0.001) for overall, bacterial and fungal detection. Although the positive rate for mNGS and tNGS was comparable, mNGS significantly outperformed tNGS in sensitivity (100% vs. 93.55%, p<0.05), particularly for bacteria and virus (p<0.001). Moreover, the true positive rate for detected microbes of mNGS was superior over that of tNGS (73.97% vs. 63.15%, p<0.05), and the difference was also significant when specific for bacteria (94.59% vs. 64.81%, p<0.001) and fungi (93.85% vs. 72.58%, p<0.01). Additionally, we found that, unlike most microbes such as SARS-CoV-2, Aspergillus, and EBV, which were predominantly detected from recipients who underwent surgery over 3 years, Torque teno virus (TTV) were principally detected from recipients within 1-year post-transplant, and as post-transplantation time increased, the percentage of TTV positivity declined. Conclusion: Although tNGS was inferior to mNGS owing to lower sensitivity and true positive rate in identifying respiratory pathogens among KTRs, both considerably outperformed CMT.
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Líquido del Lavado Bronquioalveolar , Secuenciación de Nucleótidos de Alto Rendimiento , Trasplante de Riñón , Metagenómica , Humanos , Trasplante de Riñón/efectos adversos , Líquido del Lavado Bronquioalveolar/microbiología , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Metagenómica/métodos , Persona de Mediana Edad , Masculino , Femenino , Adulto , Bacterias/aislamiento & purificación , Bacterias/genética , Receptores de Trasplantes , Anciano , Hongos/aislamiento & purificación , Hongos/genéticaRESUMEN
Background: The implementation of a zero-COVID policy for 3 years in China during the COVID-19 pandemic significantly impacted a broad spectrum of acute respiratory tract infections (ARTIs). The epidemiological characteristics of ARTI pathogens in children following the cessation of the zero-COVID policy remain unclear. Methods: Etiologically diagnostic data from 82,708 children with ARTIs at the Children's Hospital of Soochow University during 2016-2023 were analyzed for 8 pathogens (human respiratory syncytial virus [HRSV], influenza A [FluA], FluB, human parainfluenza virus [HPIV], adenovirus [ADV], human rhinovirus [HRV], bocavirus [BoV], and mycoplasma pneumoniae [MP]). The changes in respiratory infections in Suzhou, China during the first year (2020, Phase I) and the second and third years of the pandemic (2021-2022, Phase II) and the first year after the end of zero-COVID policy (2023, Phase III) versus that in the pre-pandemic years (2016-2019) were compared. Results: When compared with the average pre-pandemic levels, the pathogen-positive rate decreased by 19.27% in Phase I (OR: 0.70; 95% CI: 0.67-0.74), increased by 32.87% in Phase II (OR: 1.78; 95% CI: 1.72-1.84), and increased by 79.16% in Phase III (OR: 4.58; 95% CI: 4.37-4.79). In Phase I, the positive rates of HRSV, FluA, ADV, and MP decreased by 26.72, 58.97, 72.85, and 67.87%, respectively, and the positive rates of FluB, HPIV, HRV, and BoV increased by 86.84, 25, 32.37, and 16.94%, respectively. In Phase III, the positive rates of HRSV, FluA, FluB, HPIV, ADV, and HRV increased by 39.74, 1046.15, 118.42, 116.57, 131.13, and 146.40%, respectively, while the positive rate of BoV decreased by 56.12%. MP was inhibited during the epidemic, and MP showed a delayed outbreak after the ending of the zero-COVID policy. Compared with the average pre-pandemic levels, the MP-positive rate in Phase III increased by 116.7% (OR: 2.86; 95% CI: 2.74-2.99), with the highest increase in 0-1-year-old children. Conclusion: The strict and large-scale implementation of the zero-COVID policy in the early stages of the COVID-19 pandemic was the main driving factor for the sharp reduction in the rate of children's respiratory pathogenic infections. The termination of this policy can cause a resurgence or escalation of pathogenic infections.
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COVID-19 , Infecciones del Sistema Respiratorio , SARS-CoV-2 , Humanos , COVID-19/epidemiología , China/epidemiología , Infecciones del Sistema Respiratorio/epidemiología , Niño , Preescolar , Lactante , Pandemias , Femenino , Política de Salud , Masculino , Adolescente , Gripe Humana/epidemiologíaRESUMEN
BACKGROUND: Co-detection of respiratory pathogens with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is poorly understood. This descriptive epidemiological study aimed to determine the effect of the interaction of different respiratory pathogens on clinical variables. METHODS: We retrospectively reviewed the results of comprehensive multiplex polymerase chain reaction (PCR) testing from November 2020 to March 2023 to estimate respiratory pathogen co-detection rates in Shinjuku, Tokyo. We evaluated the interactions of respiratory pathogens, particularly SARS-CoV-2, between observed and expected co-detection. We estimated the trend of co-detection with SARS-CoV-2 in terms of age and sex and applied a multiple logistic regression model adjusted for age, testing period, and sex to identify influencing factors between co-detection and single detection for each pathogen. RESULTS: Among 57,746 patients who underwent multiplex PCR testing, 10,516 (18.2%) had positive for at least one of the 22 pathogens. Additionally, 881 (1.5%) patients were confirmed to have a co-detection. SARS-CoV-2 exhibited negative interactions with adenovirus, coronavirus, human metapneumovirus, parainfluenza virus, respiratory syncytial virus, and rhino/enterovirus. SARS-CoV-2 co-detection with other pathogens occurred most frequently in patients of the youngest age group (0-4 years). A multiple logistic regression model indicated that younger age was the most influential factor for SARS-CoV-2 co-detection with other respiratory pathogens. CONCLUSION: The study highlights the prevalence of SARS-CoV-2 co-detection with other respiratory pathogens in younger age groups, necessitating further exploration of the clinical implications and severity of SARS-CoV-2 co-detection.
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COVID-19 , Coinfección , Reacción en Cadena de la Polimerasa Multiplex , SARS-CoV-2 , Humanos , COVID-19/epidemiología , COVID-19/diagnóstico , Masculino , Persona de Mediana Edad , Femenino , Anciano , Adulto , Estudios Retrospectivos , Coinfección/epidemiología , Adolescente , Niño , Preescolar , SARS-CoV-2/genética , SARS-CoV-2/aislamiento & purificación , Lactante , Adulto Joven , Anciano de 80 o más Años , Infecciones del Sistema Respiratorio/epidemiología , Infecciones del Sistema Respiratorio/virología , Factores de Edad , Metapneumovirus/aislamiento & purificación , Metapneumovirus/genética , Tokio/epidemiología , Recién NacidoRESUMEN
Water supply and sanitation are essential household services frequently shared in resource-poor settings. Shared sanitation can increase the risk of enteric pathogen transmission due to suboptimal cleanliness of facilities used by large numbers of individuals. It also can potentially increase the risk of respiratory disease transmission. As sanitation is an essential need, shared sanitation facilities may act as important respiratory pathogen transmission venues even with strict control measures such as stay-at-home recommendations in place. This analysis explores how behavioral and infrastructural conditions surrounding shared sanitation may individually and interactively influence respiratory pathogen transmission. We developed an individual-based community transmission model using COVID-19 as a motivating example parameterized from empirical literature to explore how transmission in shared latrines interacts with transmission at the community level. We explored mitigation strategies, including infrastructural and behavioral interventions. Our review of empirical literature confirms that shared sanitation venues in resource-poor settings are relatively small with poor ventilation and high use patterns. In these contexts, shared sanitation facilities may act as strong drivers of respiratory disease transmission, especially in areas reliant on shared facilities. Decreasing dependence on shared latrines was most effective at attenuating sanitation-associated transmission. Improvements to latrine ventilation and handwashing behavior were also able to decrease transmission. The type and order of interventions are important in successfully attenuating disease risk, with infrastructural and engineering controls being most effective when administered first, followed by behavioral controls after successful attenuation of sufficient alternate transmission routes. Beyond COVID-19, our modeling framework can be extended to address water, sanitation, and hygiene measures targeted at a range of environmentally mediated infectious diseases.
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Mucus and its movements are essential to epithelial tissue immune defenses against pathogens, including fungal pathogens, which can infect respiratory, gastrointestinal or the genito-urinary tracts. Several epithelial cell types contribute to their immune defense. This review focuses on the respiratory tract because of its paramount importance, but the observations will apply to epithelial cell defenses of other mucosal tissue, including the gastrointestinal and genito-urinary tracts. Mucus and its movements can enhance or degrade the immune defenses of the respiratory tract, particularly the lungs. The enhancements include inhaled pathogen entrapments, including fungal pathogens, pollutants and particulates, for their removal. The detriments include smaller lung airway obstructions by mucus, impairing the physical removal of pathogens and impairing vital transfers of oxygen and carbon dioxide between the alveolar circulatory system and the pulmonary air. Inflammation, edema and/or alveolar cellular damage can also reduce vital transfers of oxygen and carbon dioxide between the lung alveolar circulatory system and the pulmonary air. Furthermore, respiratory tract defenses are affected by several fatty acid mediators which activate cellular receptors to manipulate neutrophils, macrophages, dendritic cells, various innate lymphoid cells including the natural killer cells, T cells, γδ T cells, mucosal-associated invariant T cells, NKT cells and mast cells. These mediators include the inflammatory and frequently immunosuppressive prostaglandins and leukotrienes, and the special pro-resolving mediators, which normally resolve inflammation and immunosuppression. The total effects on the various epithelial cell and immune cell types, after exposures to pathogens, pollutants or particulates, will determine respiratory tract health or disease.
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Células Epiteliales , Humanos , Células Epiteliales/inmunología , Células Epiteliales/microbiología , Hongos , AnimalesRESUMEN
BACKGROUND: Acute respiratory infections are a leading cause of morbidity and mortality in children. However, studies on the prevalence of respiratory viruses among children with acute respiratory infections in Kunming, China, are lacking. Therefore, we aimed to investigate the epidemiological characteristics of respiratory pathogens among children with acute respiratory infections in Kunming during the coronavirus disease 2019 pandemic. METHODS: Nasopharyngeal swab samples were collected from 4956 children with acute respiratory infections at Yunnan Provincial First People's Hospital between January 2020 and December 2022, patients with COVID-19 were excluded from the study. Multiplex reverse transcription polymerase chain reaction was used to detect respiratory pathogens. RESULTS: The frequency of respiratory pathogens among children was significantly lower in 2020 than in 2021 and 2022. The following pathogens had the highest prevalence rates (in descending order) from 2020 to 2022: HRV > RSV > PIV > ADV > MP; HRV > RSV > HADV > PIV > MP and HRV > Mp > HADV > H3N2 > HMPV. The overall frequency of respiratory pathogens exhibited an inverted U-shape with increasing age among the children. Human bocavirus, human parainfluenza virus, and human respiratory syncytial virus were the dominant respiratory viruses in children aged ≤ 3 years, whereas Mycoplasma pneumoniae was the dominant respiratory pathogen in children aged > 3 years. HRV has the highest prevalence and is the main pathogen of mixed infection. The prevalence of the influenza A virus has decreased significantly, whereas HRSV and Mp are found to be seasonal. CONCLUSIONS: Our findings offer an objective evaluation of transmission dynamics and epidemiological shifts in respiratory pathogens during the coronavirus disease 2019 pandemic in Kunming, serving as a basis for informed decision-making, prevention, and treatment strategies.
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COVID-19 , Infecciones del Sistema Respiratorio , SARS-CoV-2 , Humanos , COVID-19/epidemiología , COVID-19/transmisión , China/epidemiología , Preescolar , Infecciones del Sistema Respiratorio/epidemiología , Infecciones del Sistema Respiratorio/virología , Lactante , Niño , Femenino , Masculino , SARS-CoV-2/genética , SARS-CoV-2/aislamiento & purificación , Prevalencia , Adolescente , Nasofaringe/virología , Recién NacidoRESUMEN
Influenza-like illness (ILI) patients co-detected with respiratory pathogens exhibit poorer health outcomes than those with single infections. To address the paucity of knowledge concerning the incidence of concurrent respiratory pathogens, their relationships, and the clinical differences between patients detected with single and multiple pathogens, we performed an in-depth characterization of the oropharyngeal samples of primary care patients collected in Genoa (Northwest Italy), during winter seasons 2018/19-2019/20.The apriori algorithm was employed to evaluate the incidence of viral, bacterial, and viral-bacterial pairs during the study period. The grade of correlation between pathogens was investigated using the Phi coefficient. Factors associated with viral, bacterial or viral-bacterial co-detection were assessed using logistic regression.The most frequently identified pathogens included influenza A, rhinovirus, Haemophilus influenzae and Streptococcus pneumoniae. The highest correlations were found between bacterial-bacterial and viral-bacterial pairs, such as Haemophilus influenzae-Streptococcus pneumoniae, adenovirus-Haemophilus influenzae, adenovirus-Streptococcus pneumoniae, RSV-A-Bordetella pertussis, and influenza B Victoria-Bordetella parapertussis. Viruses were detected together at significantly lower rates. Notably, rhinovirus, influenza, and RSV exhibited significant negative correlations with each other. Co-detection was more prevalent in children aged < 4, and cough was shown to be a reliable indicator of viral co-detection.Given the evolving epidemiological landscape following the COVID-19 pandemic, future research utilizing the methodology described here, while considering the circulation of SARS-CoV-2, could further enrich the understanding of concurrent respiratory pathogens.
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Coinfección , Infecciones del Sistema Respiratorio , Humanos , Coinfección/epidemiología , Coinfección/virología , Coinfección/microbiología , Masculino , Femenino , Persona de Mediana Edad , Adulto , Italia/epidemiología , Infecciones del Sistema Respiratorio/epidemiología , Infecciones del Sistema Respiratorio/virología , Infecciones del Sistema Respiratorio/microbiología , Infecciones del Sistema Respiratorio/diagnóstico , Adolescente , Anciano , Preescolar , Niño , Adulto Joven , Lactante , Gripe Humana/epidemiología , Gripe Humana/virología , Estaciones del Año , Bacterias/aislamiento & purificación , Bacterias/clasificación , Bacterias/genética , Orofaringe/microbiología , Orofaringe/virología , Virus/aislamiento & purificación , Virus/clasificación , Virus/genética , Anciano de 80 o más Años , Infecciones Bacterianas/epidemiología , Infecciones Bacterianas/microbiología , Infecciones Bacterianas/diagnóstico , Recién NacidoRESUMEN
SUMMARYThis guidance presents recommendations for clinical microbiology laboratories for processing respiratory samples from people with cystic fibrosis (pwCF). Appropriate processing of respiratory samples is crucial to detect bacterial and fungal pathogens, guide treatment, monitor the epidemiology of cystic fibrosis (CF) pathogens, and assess therapeutic interventions. Thanks to CF transmembrane conductance regulator modulator therapy, the health of pwCF has improved, but as a result, fewer pwCF spontaneously expectorate sputum. Thus, the collection of sputum samples has decreased, while the collection of other types of respiratory samples such as oropharyngeal and bronchoalveolar lavage samples has increased. To optimize the detection of microorganisms, including Pseudomonas aeruginosa, Staphylococcus aureus, Haemophilus influenzae, and Burkholderia cepacia complex; other less common non-lactose fermenting Gram-negative bacilli, e.g., Stenotrophomonas maltophilia, Inquilinus, Achromobacter, Ralstonia, and Pandoraea species; and yeasts and filamentous fungi, non-selective and selective culture media are recommended for all types of respiratory samples, including samples obtained from pwCF after lung transplantation. There are no consensus recommendations for laboratory practices to detect, characterize, and report small colony variants (SCVs) of S. aureus, although studies are ongoing to address the potential clinical impact of SCVs. Accurate identification of less common Gram-negative bacilli, e.g., S. maltophilia, Inquilinus, Achromobacter, Ralstonia, and Pandoraea species, as well as yeasts and filamentous fungi, is recommended to understand their epidemiology and clinical importance in pwCF. However, conventional biochemical tests and automated platforms may not accurately identify CF pathogens. MALDI-TOF MS provides excellent genus-level identification, but databases may lack representation of CF pathogens to the species-level. Thus, DNA sequence analysis should be routinely available to laboratories for selected clinical circumstances. Antimicrobial susceptibility testing (AST) is not recommended for every routine surveillance culture obtained from pwCF, although selective AST may be helpful, e.g., for unusual pathogens or exacerbations unresponsive to initial therapy. While this guidance reflects current care paradigms for pwCF, recommendations will continue to evolve as CF research expands the evidence base for laboratory practices.
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Fibrosis Quística , Infecciones del Sistema Respiratorio , Manejo de Especímenes , Humanos , Fibrosis Quística/microbiología , Fibrosis Quística/complicaciones , Infecciones del Sistema Respiratorio/microbiología , Infecciones del Sistema Respiratorio/diagnóstico , Manejo de Especímenes/métodos , Manejo de Especímenes/normas , Técnicas Microbiológicas/métodos , Técnicas Microbiológicas/normas , Bacterias/aislamiento & purificación , Bacterias/clasificación , Sistema Respiratorio/microbiología , Hongos/aislamiento & purificación , Hongos/clasificaciónRESUMEN
OBJECTIVES: In the fall-winter of 2023, China experienced its first epidemic season of respiratory diseases since the COVID-19 pandemic. Gathering timely data about pathogenetic characteristics of respiratory infections is crucial to complement current respiratory surveillance mechanisms in China. Data from direct-to-consumer (DTC) multi-respiratory pathogen (MRP) testing could serve as a novel source of multi-pathogen data for community-based surveillance. METHODS: A pioneering initiative was launched to detect multiple respiratory pathogens in Beijing and Guangzhou, China. DTC MRP tests were used to provide proactive surveillance ahead of medical services. RESULTS: A total of 28,018 participants were enrolled between 22 August and 10 December 2023. Positive findings for at least one respiratory pathogen were observed in 26,202 (93.5%) participants. Influenza virus A, respiratory syncytial virus (RSV), and human adenovirus are the three leading viral pathogens detected with proportions of 18.0%, 10.6%, and 8.8%. Viral-bacterial pathogens were co-detected in 9736 (34.7%) of participants, which reduced to 22.2% for bacterial-bacterial co-detection, and 22.0% for bacterial mono-detection. The epidemiological ecology of respiratory pathogens within both viral clusters and specific pathogens varied among cities. The peak of RSV epidemics in Guangzhou occurred in the fall of 2023, earlier than in Beijing. CONCLUSION: The innovative program offered enhanced surveillance capabilities beyond traditional methods, enabling prompt feedback about test results and mitigating the risk of cross-infection caused by waits in healthcare facilities.
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Respiratory viral infections, including respiratory syncytial virus (RSV), parainfluenza viruses and type A and B influenza viruses, can have severe outcomes. Bacterial infections frequently follow viral infections, and influenza or other viral epidemics periodically have higher mortalities from secondary bacterial pneumonias. Most secondary bacterial infections can cause lung immunosuppression by fatty acid mediators which activate cellular receptors to manipulate neutrophils, macrophages, natural killer cells, dendritic cells and other lung immune cells. Bacterial infections induce synthesis of inflammatory mediators including prostaglandins and leukotrienes, then eventually also special pro-resolving mediators, including lipoxins, resolvins, protectins and maresins, which normally resolve inflammation and immunosuppression. Concurrent viral and secondary bacterial infections are more dangerous, because viral infections can cause inflammation and immunosuppression before the secondary bacterial infections worsen inflammation and immunosuppression. Plausibly, the higher mortalities of secondary bacterial pneumonias are caused by the overwhelming inflammation and immunosuppression, which the special pro-resolving mediators might not resolve.
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Neumonía Bacteriana , Humanos , Neumonía Bacteriana/mortalidad , Neumonía Bacteriana/microbiología , Neumonía Bacteriana/inmunología , Mediadores de Inflamación/metabolismo , Coinfección/microbiología , Coinfección/mortalidad , Coinfección/inmunología , Coinfección/virología , Pulmón/microbiología , Pulmón/virología , Pulmón/patología , Ácidos Docosahexaenoicos , Tolerancia Inmunológica , Prostaglandinas/metabolismo , Lipoxinas/metabolismo , Inflamación , Leucotrienos/metabolismoRESUMEN
Symptom propagation occurs when the symptom set an individual experiences is correlated with the symptom set of the individual who infected them. Symptom propagation may dramatically affect epidemiological outcomes, potentially causing clusters of severe disease. Conversely, it could result in chains of mild infection, generating widespread immunity with minimal cost to public health. Despite accumulating evidence that symptom propagation occurs for many respiratory pathogens, the underlying mechanisms are not well understood. Here, we conducted a scoping literature review for 14 respiratory pathogens to ascertain the extent of evidence for symptom propagation by two mechanisms: dose-severity relationships and route-severity relationships. We identify considerable heterogeneity between pathogens in the relative importance of the two mechanisms, highlighting the importance of pathogen-specific investigations. For almost all pathogens, including influenza and SARS-CoV-2, we found support for at least one of the two mechanisms. For some pathogens, including influenza, we found convincing evidence that both mechanisms contribute to symptom propagation. Furthermore, infectious disease models traditionally do not include symptom propagation. We summarize the present state of modelling advancements to address the methodological gap. We then investigate a simplified disease outbreak scenario, finding that under strong symptom propagation, isolating mildly infected individuals can have negative epidemiological implications.
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COVID-19 , Gripe Humana , Salud Pública , SARS-CoV-2 , Humanos , COVID-19/epidemiología , Gripe Humana/epidemiología , Infecciones del Sistema Respiratorio/epidemiología , Infecciones del Sistema Respiratorio/virología , Modelos BiológicosRESUMEN
In previous studies, it was demonstrated that Corynebacterium pseudodiphtheriticum 090104, isolated from the human nasopharynx, modulates respiratory immunity, improving protection against infections. Here, the antagonistic effect of the 090104 strain on respiratory pathogens, including Streptococcus pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii, was explored. In a series of in vitro studies, the capacity of C. pseudodiphtheriticum 090104, its bacterium-like particles, and its culture supernatants to coaggregate, inhibit the growth, and change the virulent phenotype of pathogenic bacteria was evaluated. The results showed that the 090104 strain was able to exert a bacteriostatic effect on K. pneumoniae and S. pneumoniae growth. In addition, C. pseudodiphtheriticum 090104 coaggregated, inhibited biofilm formation, and induced phenotypic changes in all the respiratory pathogens evaluated. In conclusion, this work demonstrated that, in addition to its beneficial effects exerted by host-microbe interactions, C. pseudodiphtheriticum 090104 can enhance protection against respiratory pathogens through its microbe-microbe interactions. The mechanisms involved in such interactions should be evaluated in future research.
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Aim: To co-create parental presence practice recommendations across Canadian NICUs during pandemics caused by respiratory pathogens such as COVID-19. Methods: Recommendations were developed through evidence, context, Delphi and Values and Preferences methods. For Delphi 1 and 2, participants rated 50 items and 20 items respectively on a scale from 1 (very low importance) to 5 (very high). To determine consensus, evidence and context of benefits and harms were presented and discussed within the Values and Preference framework for the top-ranked items. An agreement of 80% or more was deemed consensus. Results: After two Delphi rounds (n = 59 participants), 13 recommendations with the highest rated importance were identified. Consensus recommendations included 6 strong recommendations (parents as essential caregivers, providing skin-to-skin contact, direct or mothers' own expressed milk feeding, attending medical rounds, mental health and psychosocial services access, and inclusion of parent partners in pandemic response planning) and 7 conditional recommendations (providing hands-on care tasks, providing touch, two parents present at the same time, food and drink access, use of communication devices, and in-person access to medical rounds and mental health and psychosocial services). Conclusion: These recommendations can guide institutions in developing strategies for parental presence during pandemics caused by respiratory pathogens like COVID-19.
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Background Coronaviruses (CoVs) pose significant health risks to humans, with recent outbreaks like severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscoring their zoonotic potential. Dromedary camels (Camelus dromedarius) have been implicated as intermediate hosts for MERS-CoV, prompting heightened surveillance efforts. This study aims to identify non-MERS-CoV CoVs in imported camels at the Jeddah seaport, Saudi Arabia, using molecular techniques. Methods Camel nasal swabs (n = 337) were collected from imported dromedary camels arriving at the Jeddah Islamic seaport from Sudan and Djibouti. Samples were tested for CoVs using real-time real-time reverse transcription polymerase chain reaction (RT-PCR) targeting the RNA-dependent RNA polymerase gene. Positive samples were confirmed by conventional RT-PCR and Sanger sequencing. Selected samples underwent RNA sequencing to identify viral genomes. The study underscores the importance of molecular surveillance in camels to mitigate zoonotic risks. Results Out of 337 camel samples tested, 28 (8.30%) were positive for CoVs, predominantly from camels imported from Djibouti, compared to Sudan (13.39% vs. 5.78%). Sequence analysis confirmed the presence of non-MERS CoVs, including camel alpha-coronavirus and human CoV-229E-related strains. These findings highlight potential viral diversity and transmission risks in imported camel populations. Conclusion This study identifies diverse CoVs circulating in imported dromedary camels at the Jeddah Islamic seaport, Saudi Arabia, underscoring their potential role in zoonotic transmission. Enhanced surveillance and collaborative efforts are essential to mitigate public health risks associated with novel coronavirus strains from camel populations.
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Background: Adults with community-acquired pneumonia (CAP) in China suffer high morbidity. CAP is caused by a multitude of pathogens; however, pathogen-directed clinical symptoms are often lacking. Therefore, patients lacking an accurate microbiological diagnosis are administered with empirical antimicrobials. Methods: We collected bronchoalveolar lavage fluid, as well as clinical and laboratory data from 650 adult patients with CAP admitted to three hospitals in Hubei, Sichuan, and Zhejiang provinces in China. Specimens were cultured and tested using real-time reverse transcription qPCR (RT-qPCR) assays for the presence of 42 respiratory bacteria and viruses. CAP was investigated with respect to regions, genders, and age and patterns of infections or co-infections. Employing clinical guidelines adapted for diagnosis, we assessed retrospectively the appropriate pathogen-directed therapy and compared it with the initial empirical therapies. Results: Our study identified that 21.38% (139/650) of the patients were classified as having Severe CAP (S-CAP), with a higher prevalence among males, older adults, and during the warm season. Bacterial pathogens were detected in 35.53% (231/650) of cases. K. pneumoniae, H. influenzae, and S. aureus were the most prevalent bacteria across different demographics and regions. Viral pathogens were found in 48.76% (317/650) of patients Epstein-Barr, Human rhinovirus, and Cytomegalovirus were the most common viruses. Co-infections were present in 24.31% (158/650) of cases, with viral-bacterial co-infections being the most frequent. The RT-qPCR demonstrated significantly higher detection rates for key pathogens compared to standard culture methods. It showed potential in optimizing antimicrobial prescriptions by allowing for de-escalation in 18.30% (95/518) of patients, among which reducing the number of excessive antibiotics mainly comprised decreasing the use of 2nd or 3rd generation cephalosporins (5.79%, 30/518) and ß-lactamase inhibitor combinations. Conclusion: The study highlights the significant burden of S-CAP, particularly among specific demographics and seasons. The prevalence of bacterial and viral pathogens, along with the high rate of co-infections, emphasizes the need for comprehensive diagnostic approaches. The RT-qPCR assays emerge as a superior diagnostic tool, offering enhanced pathogen detection capabilities and facilitating more precise antimicrobial therapy. This could lead to improved patient outcomes and contribute to the rational use of antimicrobials, addressing the growing concern of antibiotic resistance.
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Respiratory pathogens, such as SARS-CoV-2 and influenza A/B, can cause severe illnesses in susceptible individuals. This research evaluated a novel digital microfluidic point-of-care testing platform designed to detect 23 pathogens, comparing its performance to conventional laboratory-based nucleic acid tests. The platform integrates nucleic acid extraction and amplification processes for rapid detection with only 2 min of hands-on time. Performance assays demonstrated that the platform has high sensitivity (87 %-100 %) and specificity (99 %-100 %) for the detection of the evaluated 3 viruses. Additionally, the platform can be adapted for the detection of other respiratory pathogens, aiding in the early diagnosis of respiratory diseases, identifying the source of an outbreak or epidemic, and curbing the spread of the disease.
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COVID-19 , Virus de la Influenza A , Virus de la Influenza B , Gripe Humana , Pruebas en el Punto de Atención , SARS-CoV-2 , Sensibilidad y Especificidad , Humanos , Gripe Humana/diagnóstico , Gripe Humana/virología , COVID-19/diagnóstico , SARS-CoV-2/aislamiento & purificación , SARS-CoV-2/genética , Virus de la Influenza B/aislamiento & purificación , Virus de la Influenza B/genética , Virus de la Influenza A/aislamiento & purificación , Virus de la Influenza A/genética , Microfluídica/métodos , Microfluídica/instrumentación , Sistemas de Atención de PuntoRESUMEN
Despite the prevalence of co-infections and the association of over 50 viral and 46 bacterial pathogens with pig diseases, little is known about their simultaneous occurrence, particularly in commercial pig farming environments where health programs are in place. To address this knowledge gap, this study aimed to evaluate the pathogen threshold of respiratory and enteric pathogens in pig herds using the Pork MultiPath™ (PMP1 and PMP2, respiratory and enteric respectively) technology, which detects multiple pathogens simultaneously in a single reaction with high sensitivity and specificity. In this study the most prevalent respiratory pathogens, Mycoplasma hyrohinis, Pasteurella multocida, and Haemophilus parasuis detected by PMP1 were effectively controlled during the nursery stage through strategic treatment with tiamulin. Even though the major respiratory incidences were reduced, the recorded coughing and sneezing rates were associated with the levels of H. parasuis and M. hyrohinis, which were set at 1356 and 1275 copies/reaction, respectively. In addition, one of the identified co-infection patterns indicated a strong relationship between the occurrence of H. parasuis and M. hyorhinis at the sample and pen levels, highlighting the high likelihood of detecting these two pathogens together. Testing with enteric panel PMP2 revealed that the most frequently detected virulence factors during the early nursery stage were Escherichia coli genes for toxins - ST1, ST2, and fimbriae - F4 and F18. Moreover, a co-infection with Rotavirus B and C was often observed during the nursery stage, and a strong positive correlation between these two markers has been identified. Additionally, the levels of several markers, namely E. coli F4, F5, F18, LT, ST1, and ST2, have been associated with a higher likelihood of sickness in pig populations. In addition, the onset of Brachyspira pilosicoli during the nursery and grower stages was found to be associated with an increased risk of diarrhoea, with a set threshold at around 500 copies/reaction. Although simultaneous detection of multiple pathogens is not yet widely used in the pig industry, it offers a significant advantage in capturing the diversity and interactions of co-infections. Testing pooled samples with Pork MultiPath™ is cost-effective and practical to regularly monitor the health status of pig populations.
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Enfermedades de los Porcinos , Animales , Enfermedades de los Porcinos/microbiología , Enfermedades de los Porcinos/epidemiología , Enfermedades de los Porcinos/virología , Porcinos , Coinfección/veterinaria , Coinfección/microbiología , Coinfección/epidemiología , Monitoreo Epidemiológico/veterinariaRESUMEN
Environmental exposures are known to be associated with pathogen transmission and immune impairment, but the association of exposures with aetiology and severity of community-acquired pneumonia (CAP) are unclear. A retrospective observational study was conducted at nine hospitals in eight provinces in China from 2014 to 2019. CAP patients were recruited according to inclusion criteria, and respiratory samples were screened for 33 respiratory pathogens using molecular test methods. Sociodemographic, environmental and clinical factors were used to analyze the association with pathogen detection and disease severity by logistic regression models combined with distributed lag nonlinear models. A total of 3323 CAP patients were included, with 709 (21.3%) having severe illness. 2064 (62.1%) patients were positive for at least one pathogen. More severe patients were found in positive group. After adjusting for confounders, particulate matter (PM) 2.5 and 8-h ozone (O3-8h) were significant association at specific lag periods with detection of influenza viruses and Klebsiella pneumoniae respectively. PM10 and carbon monoxide (CO) showed cumulative effect with severe CAP. Pollutants exposures, especially PM, O3-8h, and CO should be considered in pathogen detection and severity of CAP to improve the clinical aetiological and disease severity diagnosis.