High Rates Of Co-infection Research Articles

Ampullaviruses: From Extreme Environments to Biotechnological Innovation.

Ampullaviruses are unique among viruses. They live in extreme environments and have special bottle-shaped architecture. These features make them useful tools for biotechnology. These viruses have compact genomes. They encode a range of enzymes and proteins. Their natural environment highlights their suitability for industrial applications. Ongoing research explores ways in which these viruses can improve enzyme stability. They are also employed in the creation of new biosensors and the development of new bioremediation techniques. High coinfection rates and the ecology of ampullaviruses at larger scales can also reveal new viral vectors. They can also help improve phage therapy. Here, we have explored the structure and function of ampullaviruses. We have focused on their use in biotechnology. We have also identified their characteristics that could prove to be useful. We have also pointed out key knowledge gaps and bridging them could further extend the biotechnological uses.

Viral gene drive spread during herpes simplex virus 1 infection in mice

Gene drives are genetic modifications designed to propagate efficiently through a population. Most applications rely on homologous recombination during sexual reproduction in diploid organisms such as insects, but we recently developed a gene drive in herpesviruses that relies on co-infection of cells by wild-type and engineered viruses. Here, we report on a viral gene drive against human herpes simplex virus 1 (HSV-1) and show that it propagates efficiently in cell culture and during HSV-1 infection in mice. We describe high levels of co-infection and gene drive-mediated recombination in neuronal tissues during herpes encephalitis as the infection progresses from the site of inoculation to the peripheral and central nervous systems. In addition, we show evidence that a superinfecting gene drive virus could recombine with wild-type viruses during latent infection. These findings indicate that HSV-1 achieves high rates of co-infection and recombination during viral infection, a phenomenon that is currently underappreciated. Overall, this study shows that a viral gene drive could spread in vivo during HSV-1 infection, paving the way toward therapeutic applications.

Epidemiology and Diagnostic Accuracy of Respiratory Pathogens in Pediatric Populations: Insights From Global Studies.

Lower respiratory tract infections (LRTIs) are the most common cause for going to the doctor's at pediatric age. Respiratory infections are still of interest because they are widespread, significantly impact public health by potentially leading to pandemics, drive antimicrobial resistance through antibiotic misuse, more often spread globally due to traveling, and benefit from ongoing advancements in diagnostics and research for better management.This paper's main aim was to offer a systematic review of the literature published over the last 10 years on the etiology of LRTIs. The search strategy was based on reviewing original articles, systematic reviews, position papers, and guidelines published in MEDLINE, EMBASE, Cochrane Library, and PubMed. The review was previously registered with PROSPERO. The final review included 27 articles that met the eligibility criteria (studies identifying the etiology of inferior respiratory infections in children, according to the WHO definition, published in the last 10 years). Statistical analysis was performed using Microsoft Excel Version 2406 (Microsoft Corporation, Redmond, Washington, USA) and SPSS Statistics V.23 (IBM Corp., Armonk, New York, USA). The total number of patients was 2,193,978. Eight articles focused on children younger than five years, and two included children under the age of two.The results revealed that Mycoplasma pneumoniae and respiratory syncytial virus (RSV) are significant respiratory pathogens with seasonal peaks and age-specific prevalence and that nasopharyngeal aspirates (NPAs) are more reliable than throat swabs for confirming infections due to their higher positive predictive value (PPV).The impact of COVID-19 interventions led to reduced infections from RSV, adenovirus, and influenza viruses, but an increase in rhinovirus post-reopening, with high co-infection rates. Co-infections are common, particularly with pathogens like human bocavirus (HBoV) and RSV, underscoring the need for comprehensive diagnostic approaches. The impact of non-pharmaceutical interventions during the COVID-19 pandemic significantly reduced the prevalence of many respiratory pathogens, except for rhinovirus, which increased post-reopening. Understanding these dynamics is crucial for managing respiratory infections, especially in pediatric populations.

Weak association of Usutu virus and haemosporidian infection in birds collected in Germany

The Usutu Virus (USUV) is a mosquito-borne flavivirus originated in Africa. The virus circulates in Germany since 2010. It is primarily transmitted and maintained in the natural cycle by Culex mosquitoes and primarily affects birds, particularly Eurasian blackbird (Turdus merula), leading to significant mortality. Several studies have reported a high co-infection rate of European birds with both USUV and haemosporidians. Haemosporidians are blood parasites which maintain an enzootic life cycle with birds via different arthropod vectors. This study conducted screenings of birds from Germany received through a citizen's science project for both, USUV and haemosporidians between 2016 and 2021. The prevalence of USUV reached its peak in 2018, when it was first detected throughout most parts of Germany rather than being limited to localised hotspots. Subsequently, USUV prevalence consistently declined. On the other hand, the prevalence of haemosporidians initially declined between 2016 and 2019, but experienced a subsequent increase in the following years, exhibiting a more or less inverse pattern compared to the prevalence of USUV. In 2020, a statistically significant positive association between both pathogens was found, which was also detected across all years combined, indicating if at all a weak relationship between these pathogens.

High rates of anal Merkel Cell Polyomavirus and HPV co-infection among people living with HIV.

Knowledge of Human Polyomavirus (HPyV) infection in the anal area and its association with sexually transmitted infections such as Human Papillomavirus (HPV) and Human Immunodeficiency Virus (HIV) remains limited. Therefore, anal specimens from 150 individuals of both sexes were analyzed for screening purposes. HPV DNA was found in 50.7% of cases, with a predominance of high-risk (HR) genotypes. HPyV DNA was found in 39.3% of samples, with Merkel Cell Polyomavirus (MCPyV) being the most common, with a higher viral load than JCPyV and BKPyV. In addition, MCPyV viral load increased in people living with HIV (PLWH) with HPV infection (p < 0.0001).

Post-pandemic trends: Epidemiological and etiological insights into acute respiratory infections in southern China

Data on people suspected with acute respiratory infections (ARIs) from August 2022 to December 2023 in southern China were analyzed. Following the COVID-19 pandemic, the positive detection rates of respiratory pathogens increased to 56.9%. Influenza A virus (IAV) emerged as the predominant prevalence pathogen (52.1%), followed by Mycoplasma pneumoniae (Mp: 21.2%), and SARS-CoV-2 (11.6%). Mp, IAV, and Human rhinovirus (HRV) infection were the primary etiologies of ARIs patients under age 18, accounting for 49.4%, 48.6%, and 21.7%, respectively. Mp, HRV, Respiratory syncytial virus (RSV), and Adenovirus (ADV) contributed to ARIs cases in virtually every month in this group, with Mp being particularly notable for its consistent presence and high co-infection rate (31.0%). IAV was predominant in the 19 to 59 age group (88.6%), SARS-CoV-2 was responsible for most of ARIs in the elderly group (82.5%). This study provides valuable insights into the dynamic nature of respiratory pathogens post COVID-19 era.

High frequencies of alpha common cold coronavirus/SARS-CoV-2 cross-reactive functional CD4+ and CD8+ memory T cells are associated with protection from symptomatic and fatal SARS-CoV-2 infections in unvaccinated COVID-19 patients.

Cross-reactive SARS-CoV-2-specific memory CD4+ and CD8+ T cells are present in up to 50% of unexposed, pre-pandemic, healthy individuals (UPPHIs). However, the characteristics of cross-reactive memory CD4+ and CD8+ T cells associated with subsequent protection of asymptomatic coronavirus disease 2019 (COVID-19) patients (i.e., unvaccinated individuals who never develop any COVID-19 symptoms despite being infected with SARS-CoV-2) remains to be fully elucidated. This study compares the antigen specificity, frequency, phenotype, and function of cross-reactive memory CD4+ and CD8+ T cells between common cold coronaviruses (CCCs) and SARS-CoV-2. T-cell responses against genome-wide conserved epitopes were studied early in the disease course in a cohort of 147 unvaccinated COVID-19 patients who were divided into six groups based on the severity of their symptoms. Compared to severely ill COVID-19 patients and patients with fatal COVID-19 outcomes, the asymptomatic COVID-19 patients displayed significantly: (i) higher rates of co-infection with the 229E alpha species of CCCs (α-CCC-229E); (ii) higher frequencies of cross-reactive functional CD134+CD137+CD4+ and CD134+CD137+CD8+ T cells that cross-recognized conserved epitopes from α-CCCs and SARS-CoV-2 structural, non-structural, and accessory proteins; and (iii) lower frequencies of CCCs/SARS-CoV-2 cross-reactive exhausted PD-1+TIM3+TIGIT+CTLA4+CD4+ and PD-1+TIM3+TIGIT+CTLA4+CD8+ T cells, detected both ex vivo and in vitro. These findings (i) support a crucial role of functional, poly-antigenic α-CCCs/SARS-CoV-2 cross-reactive memory CD4+ and CD8+ T cells, induced following previous CCCs seasonal exposures, in protection against subsequent severe COVID-19 disease and (ii) provide critical insights into developing broadly protective, multi-antigen, CD4+, and CD8+ T-cell-based, universal pan-Coronavirus vaccines capable of conferring cross-species protection.

Parasite and bacterial co-infections with Leishmania spp. in dogs

Canine visceral leishmaniasis (CVL) is a major disease affecting dogs and is often associated with other illnesses. In this study, we investigated the distribution of helminths, ectoparasites and bacteria in dogs of an endemic urban area of CVL. A total of 71 dogs, uninfected or naturally infected with Leishmania spp. were studied. Splenic samples were cultured for Leishmania identification, and anti-Leishmania antibodies were measured in the serum. Helminths were diagnosed in the feces using flotation or spontaneous sedimentation techniques. Serum antibodies against six ectoparasite-transmitted pathogens were detected. Microbial growth from eyes, skin, urine, and blood samples were evaluated. To our knowledge, this is the first time that co-infections with Leishmania spp., parasites and bacteria together has been reported. Co-infections with Leishmania were observed in 89% of the animals with helminths and 95% with ectoparasites. Most of the dogs were positive for Ehrlichia spp. and Anaplasma spp. Coagulase-negative Staphylococcus was the most frequently isolated organism. It is found that Leishmania positivity dogs from endemic area in Brazil have a higher rate of co-infections with helminths, ectoparasites and bacteria. Therefore, effective treatment and public measures are needed to contain the spread of canine leishmaniasis and other infections.

Difference in the impact of coinfections and secondary infections on antibiotic use in patients hospitalized with COVID-19 between the Omicron-dominant period and the pre-Omicron period

IntroductionThis study evaluated the effect of coinfections and/or secondary infections on antibiotic use in patients hospitalized with coronavirus disease 2019 (COVID-19). MethodDays of therapy per 100 bed days (DOT) in a COVID-19 ward were compared between 2022 (Omicron period) and 2021 (pre-Omicron period). Antibiotics were categorized as antibiotics predominantly used for community-acquired infections (CAIs) and antibiotics predominantly used for health care-associated infections (HAIs). Bacterial and/or fungal infections which were proved or assumed on admission were defined as coinfections. Secondary infections were defined as infections that occurred following COVID-19. ResultsPatients with COVID-19 during the Omicron period were older and had more comorbidities. Coinfections were more common in the Omicron period than in the pre-Omicron period (44.4% [100/225] versus 0.8% [2/257], respectively, p < 0.001), and the mean DOT of antibiotics for CAIs was significantly increased in the Omicron period (from 3.60 to 17.84, p < 0.001). Secondary infection rate tended to be higher in the Omicron period (p = 0.097). Mean DOT of antibiotics for HAIs were appeared to be lower in the COVID-19 ward than in the general ward (pre-Omicron, 3.33 versus 6.37, respectively; Omicron, 3.84 versus 5.22, respectively). No multidrug-resistant gram-negative organisms were isolated in the COVID-19 ward. ConclusionAntibiotic use for CAIs was limited in the pre-Omicron period but increased in the Omicron period because of a high coinfection rate on admission. With the antimicrobial stewardship, excessive use of antibiotics for HAIs was avoided in the COVID-19 ward during both periods.

Avian H6 Influenza Viruses in Vietnamese Live Bird Markets during 2018-2021.

Avian influenza viruses of the H6 subtype are prevalent in wild ducks and likely play an important role in the ecology of influenza viruses through reassortment with other avian influenza viruses. Yet, only 152 Vietnamese H6 virus sequences were available in GISAID (Global Initiative on Sharing All Influenza Data) prior to this study with the most recent sequences being from 2018. Through surveillance in Vietnamese live bird markets from 2018 to 2021, we identified 287 samples containing one or several H6 viruses and other influenza A virus subtypes, demonstrating a high rate of co-infections among birds in Vietnamese live bird markets. For the 132 H6 samples with unique influenza virus sequences, we conducted phylogenetic and genetic analyses. Most of the H6 viruses were similar to each other and closely related to other H6 viruses; however, signs of reassortment with other avian influenza viruses were evident. At the genetic level, the Vietnamese H6 viruses characterized in our study encode a single basic amino acid at the HA cleavage site, consistent with low pathogenicity in poultry. The Vietnamese H6 viruses analyzed here possess an amino acid motif in HA that confers binding to both avian- and human-type receptors on host cells, consistent with their ability to infect mammals. The frequent detection of H6 viruses in Vietnamese live bird markets, the high rate of co-infections of birds with different influenza viruses, and the dual receptor-binding specificity of these viruses warrant their close monitoring for potential infection and spread among mammals.

Analysis of a Cohort of 165 Pediatric Patients with Human Bocavirus Infection and Comparison between Mono-Infection and Respiratory Co-Infections: A Retrospective Study.

Human Bocavirus (HBoV) is mainly associated with respiratory tract infections. However, its role as respiratory pathogen is not fully understood for a high co-infection rate in symptomatic patients and a significant HBoV detection rate in asymptomatic subjects. This study aimed to describe a large cohort of children with HBoV infection and to compare HBoV mono-infection and co-infections. We retrospectively reviewed data from 165 children admitted to Meyer Children's Hospital IRCCS from March 2022 to March 2023 with the diagnosis of HBoV infection, detected using Reverse Transcription qPCR from nasal swabs. Thereafter, we compared patients with HBoV mono-infection (Group A) and those with HBoV co-infections (Group B) in terms of disease severity, established by the length of stay (LOS), the requirement of Pediatric Intensive Care Unit (PICU), and advanced respiratory support (ARS). The median age was 1.5 years; 80% of patients presented with respiratory symptoms. The discharge rate from the emergency department (ED) within 24 h was 42.4%. Most cases (57.6%) were hospitalized, and 7.3% were admitted to PICU due to respiratory failure. Group A comprised 69 patients, and Group B 96 children (95% viral co-infections, 2% bacterial, 3% viral and bacterial). Group A and Group B were similar in hospitalization rate but differed significantly in LOS (median 3 vs. 5 days) and requirement of PICU admission (0 vs. 12 patients, p < 0.001). Patients with a respiratory disease history (17.5%) showed significantly longer LOS and more necessity of inhaled bronchodilator therapy. HBoV should be considered a relevant respiratory pathogen especially in viral co-infections. Patients with HBoV co-infections have a higher risk of necessitating advanced respiratory support with more PICU admission and longer LOS; a previous respiratory disease puts them at a higher risk of longer hospitalization.

Clinical features of omicron SARS-CoV-2 variants infection associated with co-infection and ICU-acquired infection in ICU patients.

Although the decreasing rate of hospital admission in the omicron wave has led countries to loosen control, still the patients requires ICU admission. It is common for viral respiratory infections to be co-infected with bacteria. However, the difference between co-infection and ICU-acquired infection on their clinical characteristics and outcomes during the Omicron wave was little reported. Clinical and microbiological data were collected from ICU patients with omicron infection between April 1st, 2022, and May 31th, 2022 and a comprehensive comparative study of the clinical characteristics and endpoint were conducted. The Omicron SARS-CoV-2 variants-infected patients requiring intensive care had high rates of co-infection (42.55%). Additionally, the ICU COVID-19 patients with co-infection showed more severe clinical features compared to those with ICU-acquired infection. Furthermore, Multivariate Cox analysis demonstrated that co-infection (hazard ratio: 4.670, p = 0.018) was a significant risk factor for poor outcomes in ICU patients with COVID-19. Besides, Kaplan-Meier survival curve analysis revealed that COVID-19 patients with co-infection had a significantly shorter 28-Day survival time compared to those with ICU-acquired infection (p < 0.001). Finally, our investigation identified a significant association between the presence of Candida app. in the broncho-alveolar lavage and an elevated risk of mortality (OR: 13.80, p = 0.002) and invasive ventilation (OR: 5.63, p = 0.01). Co-infection is prevalent among patients requiring intensive care and is linked to unfavorable outcomes in the Omicron wave. Consequently, more attention may be needed for the empirical antibacterial treatment in ICU patients within the COVID-19 Omicron variant, especially anti-fungi.

Cases of Monkeypox show highly-overlapping co-infection with HIV and syphilis.

Ongoing Monkeypox (MPX) outbreaks in countries outside Africa have unique characteristics. However, data on cohorts of confirmed cases in China is limited. The study provides important epidemiological, diagnostic, and clinical information about this disease in China. We report a series of Chinese individuals with confirmed MPX infections identified at Beijing Youan Hospital (China) from June 10 to July 15, 2023. Samples were taken from the skin, anus, throat, and blood. An epidemiological questionnaire was used to collect demographic and clinical data. Further, we compared the MPX viral (MPXV) loads across different anatomical sites. 66 samples were collected from 20 patients, all of whom were cisgender men. Median patient age was 29 years. Notably, 19 (95%) patients reported unprotected sexual encounters with men in the preceding month, and 13 (65%) were human immunodeficiency virus (HIV)-positive. Among those with HIV, 12 (92%) were receiving antiretroviral therapy, and 11 (85%) had well-controlled infections (HIV viral load <40/mL). The median CD4+ T cell count was 667 cells/mm3. In the HIV-negative group, three (43%) patients were taking preexposure prophylaxis. Fifteen patients (75%) had concurrent sexually transmitted infections (50% had syphilis and 65% had HIV) and eight (40%) had HIV and syphilis co-infection. MPXV loads were significantly higher in samples from the skin (cycle threshold value [Ct value]: 19·0) and anus (Ct value: 23.0) compared to samples from the throat (Ct value: 31.0) or blood (Ct value: 34.5). All patients had skin lesions (85% of whom presented with anogenital lesions). Common systemic symptoms included fever (85%) and lymphadenopathy (55%). The median incubation period was 8 d [interquartile range (IQR): 6-16 d]. The median time from the onset of skin lesions to scab removal was 14 d (IQR: 10-16 d). No deaths or severe cases were reported. MPXV primarily affects young homosexual men. The high MPXV viral loads in skin and anal lesions indicate that transmission most likely occurs through direct and close body contact. This study also reports high rates of HIV and syphilis co-infection. Therefore, preventive efforts should focus on homosexual men.

Prevalence and Molecular Evolution of Parvovirus in Cats in Eastern Shandong, China, between 2021 and 2022

Feline panleukopenia (FPL) is a highly contagious infectious disease caused by infection with feline parvovirus (FPV) and canine parvovirus type 2 (CPV-2). In recent years, the number of cats with FPL has increased with the expansion of pet cat population in China. The feces of 51 cats with diarrhea symptoms collected from 2021 to 2022 in Eastern Shandong, China, were detected by polymerase chain reaction for parvovirus and other viruses related to feline diarrhea to investigate the prevalence and gene variation of parvovirus in cats. In all the 51 samples, 45.1% (23/51) were positive for at least one viral pathogen, and the positivity of parvovirus was 41.2% (21/51), showing a high prevalence. Multiple-pathogen testing indicated high-coinfection rates of 42.9% (9/21) with other common viruses in parvovirus-positive cats. Most of the coinfections are feline coronavirus (FCoV), followed by feline astrovirus (FAstV) and feline bocavirus (FBoV). The complete VP2 sequences of 21 parvoviruses were obtained. Among them, 20 sequences were identified as FPV, and only one was CPV-2c of Asian origin, which was first detected from cats in Eastern Shandong, China. A phylogenetic tree of the 20 FPVs was constructed together with 698 FPVs (cat/dog host) worldwide on the basis of complete VP2. The 18 FPVs displayed high-sequence identity to one another (99.8%–100%), and they were clustered into FPV-G1 group, whereas the other two were clustered into FPV-G3 group. The FPV-G1 group increased dramatically to become predominant after 2019 in China, contributing to the prevalence of A91S mutation due to 96.07% FPV-G1 with A91S mutation as well as 100% of FPV-G2 and 99.12% of FPV-G3 with 91A in the statistical analysis. This study enriched the understanding of the prevalence, molecular evolution, and cross-species transmission of parvovirus in cats and provided a basis for responding to challenges in the diagnosis and treatment of FPL.

Elevated HIV Viral Load is Associated with Higher Recombination Rate In Vivo.

HIV's exceptionally high recombination rate drives its intrahost diversification, enabling immune escape and multidrug resistance within people living with HIV. While we know that HIV's recombination rate varies by genomic position, we have little understanding of how recombination varies throughout infection or between individuals as a function of the rate of cellular coinfection. We hypothesize that denser intrahost populations may have higher rates of coinfection and therefore recombination. To test this hypothesis, we develop a new approach (recombination analysis via time series linkage decay or RATS-LD) to quantify recombination using autocorrelation of linkage between mutations across time points. We validate RATS-LD on simulated data under short read sequencing conditions and then apply it to longitudinal, high-throughput intrahost viral sequencing data, stratifying populations by viral load (a proxy for density). Among sampled viral populations with the lowest viral loads (<26,800 copies/mL), we estimate a recombination rate of 1.5×10-5 events/bp/generation (95% CI: 7×10-6 to 2.9×10-5), similar to existing estimates. However, among samples with the highest viral loads (>82,000 copies/mL), our median estimate is approximately 6 times higher. In addition to co-varying across individuals, we also find that recombination rate and viral load are associated within single individuals across different time points. Our findings suggest that rather than acting as a constant, uniform force, recombination can vary dynamically and drastically across intrahost viral populations and within them over time. More broadly, we hypothesize that this phenomenon may affect other facultatively asexual populations where spatial co-localization varies.

Clinicopathological Study of Mucormycosis in COVID-19: A Cross-sectional Study from a Tertiary Care Centre in North Kerala, India

Introduction: Mucormycosis is an angioinvasive disease associated with high morbidity and mortality caused by fungi of the order Mucorales. The rise in the incidence of mucormycosis, along with the surge of Coronavirus Disease- 2019 (COVID-19), justifies reassessment of associated risk factors and the susceptible population. The present study aims to highlight the specific clinicopathological features and risk factors of mucormycosis in COVID-19 patients. Aim: To investigate the histopathological features, key clinical findings in mucormycosis, and the predisposing factors associated with mucormycosis in post-COVID-19 patients. Materials and Methods: This descriptive cross-sectional study was conducted at the Department of Pathology, Government Medical College, Manjeri, Malappuram, Kerala, India, in the Department of Pathology. It included all histopathologically proven Mucormycosis specimens from confirmed COVID-19 positive and post-COVID-19 cases in this Medical College from January 1, 2021, to December 31, 2021, amounting to a total of 30 cases. The type of tissue reaction, fungal hyphae, angioinvasion, necrosis, and fungal co-infections were assessed. Histopathologic analysis was performed using routine Haematoxylin and Eosin (H&amp;E) slides, followed by special stains such as Periodic Acid Schiff (PAS) and Grocott Methenamine Silver (GMS). Data was collected using a proforma, and the clinical details were obtained from the request form received along with the biopsy specimen and case sheets. Age, gender, site of involvement, and risk factors were assessed and subjected to descriptive tabulation and analysis. Results: The mean age was 49.5 years with a male-to-female ratio of 1.30:1. The major risk factors observed in the present study were Diabetes Mellitus (DM) and steroid therapy, 30 all cases (100%), along with others such as chronic kidney disease 2 cases (6.67%) immune disorders, and renal transplantation 1 case each (3.33%). The most commonly involved site was sinuses 27 cases (90.00%). Multiple sinuses were affected in 22 cases (73.33%), with the ethmoid sinus being the most common site 24 cases (80.00%), followed by the maxillary sinus 21 cases (70.00%). The most common reaction pattern observed was acute inflammation 15 cases (50.00%). Angioinvasion was noticed in 19 cases (63.33%) and necrosis was present in 28 cases (93.33%). Co-infection with fungal pathogens was observed in 8 cases (26.67%), with aspergillus being the most common co-infection in all except one of the eight cases. Fungal hyphae were visible on H&amp;E slides in 28 cases (93.33%), while the remaining cases were identified only through special stains (PAS and GMS). Conclusion: Mucormycosis infection is strongly associated with DM and steroid therapy. A more even distribution between males and females was noted, deviating from the male predominance described in most studies. The histopathological appearance of angioinvasion was less frequent compared to most studies, consistent with previous studies on the Indian population. Higher rates of co-infection and the presence of granulomatous inflammation were observed. Further studies are needed to explore the relationship between host immunity, morphological patterns, and their influence on prognosis.

Clinical and molecular characterization of children and adults with respiratory bocavirus infection in Mexico: a cross-sectional nested study within the ILI002 prospective observational study

BackgroundHuman Bocaviruses (HBoV) can cause acute respiratory tract infections. High coinfection rates cloud its pathogenicity. This study sought to describe the clinical features of HBoV1 disease in children and adults with Influenza-like illness (ILI), exploring associations between viral load, clinical features, and seasonality. MethodsPatients who tested positive for HBoV1 by polymerase chain reaction, enrolled from April 2010 to March 2014 in the ILI002 prospective observational cohort study were included in this cross-sectional nested study. Participants were included in ILI002 if they presented with signs and/or symptoms suggestive of influenza-like illness. Samples were tested for viral load, and NP1 and VP1/VP2 phylogenetic analyses, except for the samples lacking suitable and viable clinical material for genotyping. FindingsWe identified HBoV1 in 157 (2·8%) of participants. Prevalence was 4·5% in children and 1·8% in adults. Single HBoV1 detection occurred in 41·1% and 46·3% of children and adults, respectively. Children commonly experienced fever (83·3%), cough with sputum (74·4%), and shortness of breath (72·2%). In the multivariate analysis of children, significant positive associations were detected between viral loads and age (0·20 [95%CI: 0·07, 0·33]), and the presence of fever (2·64 [95%CI: 1·35, 3·94]), nasal congestion (1·03 [95%CI: 0·07, 1·99]), dry cough (1·32 [95%CI: 0·42, 2·22]), chest congestion (1·57 [95%CI: 0·33, 2·80]), red eyes (1·25 [95%CI: 0·35, 2·14]), cough with sputum (1·79 [95%CI: 0·80, 2·78]), and other signs and symptoms such as chills, dizziness, and diaphoresis (1·73 [95%CI: 0·19, 3·27]). In contrast, significant negative associations were found between viral loads and percent neutrophils on the blood count (-0·04 [95%CI: -0·06, -0·02]), fatigue (-1·60 [95%CI: -2·46, -0·74]) and the presence of other symptoms or signs, including adenopathy and rash (-1·26 [95%CI: -2·31, -0·21]). Adults commonly experienced sore throat (73·1%), fatigue (77·4%), and headache (73·1%). In the multivariate analysis of adults, significant positive associations were detected between viral load and body mass index (0·13 [95%CI: 0·04, 0·21]), and the presence of confusion (1·54 [95%CI: 0·55, 2·53]), and sore throat (1·03 [95%CI: 0·20, 1·85]), and significant negative associations were detected between viral load and chest congestion (-1·16 [95%CI: -2·07,-0·24]. HBoV1 was detected throughout the year irrespective of season, temperature, and humidity. InterpretationThis study demonstrated the importance of detecting HBoV1 in patients with influenza-like illness either as single infection or co-infection, in both adults and children, and improves the characterization of HBoV1 seasonality, clinical features, and viral load. Phylogenetic analyses show a high conservation.

Characteristics of the Mycoplasma pneumoniae Epidemic from 2019 to 2020 in Korea: Macrolide Resistance and Co-Infection Trends.

Mycoplasma pneumoniae, a major etiological agent of community-acquired pneumonia, exhibits distinct cyclic epidemic patterns recurring every three to five years. Several cases of co-infection with severe acute respiratory syndrome coronavirus 2 have been reported globally, resulting in unfavorable clinical manifestations. This study investigated the epidemiological features of the recent M. pneumoniae outbreak (May 2019-April 2020) using retrospective data from the last five years. Molecular test data for macrolide resistance and co-infection were obtained from the Seegene Medical Foundation. National medical expenditure and hospitalization rates were analyzed using data from The Health Insurance Review and Assessment Service of Korea. The macrolide resistance rate was 69.67%, peaking at 71.30% during the epidemic period, which was considerably higher than the 60.89% rate during non-epidemic periods. The co-infection rate with other respiratory pathogens was 88.49%; macrolide-resistant M. pneumoniae strains showed a 2.33% higher co-infection rate than the susceptible strains. The epidemic period had 15.43% higher hospitalization and 78.27% higher medical budget expenditure per patient than non-epidemic periods. The increased rates of macrolide resistance and co-infection observed in macrolide-resistant M. pneumoniae during the epidemic period highlight the importance of monitoring future outbreaks, especially considering macrolide resistance and the risk of co-infection with other pathogens.

Specific primers for the rapid detection and quantitation of Rhizobium elite strains of common beans in the plant and environment

Tools for adequately detecting and monitoring elite strains used for common bean inoculation are lacking. These tools help evaluate strain competitiveness and nodule occupancy rates and study their ecology in the environment. For this reason, we designed and tested specific primers for three Rhizobium elite strains widely used as common bean inoculants: Rhizobium tropici CIAT 899, R. tropici CPAC H12, and R. freirei PRF 81. Primer specificity was confirmed in PCR assays performed with the target strains and 45 strains of the Rhizobiaceae family. CIAT 899 and CPAC H12 showed an average nucleotide identity of 99.99 %; thus, all further evaluations were performed with CIAT 899 and PRF 81. Primer amplification efficiency, sensitivity, determination coefficients, and dissociation curves were evaluated. In addition, three pairs of primers for each target strain were evaluated for their capacities to quantify their targets in the nodules, rhizosphere, and roots. Eleven and seven strain-specific primer pairs were selected for CIAT 899 and PRF 81, respectively. They amplified DNA isolated from bacterial suspensions, nodules, and nodule extracts used directly in PCR with average amplification efficiencies between 91 % and 105 % and 96 % and 107 % for CIAT 899 and PRF 81 primers and detection limits of 32 and 34 copies of target DNA, respectively. Their use showed that populations increased in the roots and decreased in the rhizospheric soil over 15 days. Nodular occupancy rates were above 90 % when the strains were inoculated individually, and a high co-infection rate was observed upon co-inoculation, with CIAT 899 and PRF 81 detected in 100 % and 73 % of the nodules, respectively. We conclude that the primers and methodologies shown here are suitable for detecting the target strains with high specificity and sensitivity. Our approach also demonstrated that R. tropici CIAT 899 and R. freirei PRF 81 were competitive and effective in infecting common beans under the tested conditions.

Epidemiology of Nontuberculous Mycobacteria in Tuberculosis suspects, Southwest of China, 2017-2022.

This study summarizes the epidemiological characteristics, species distribution, and drug sensitivity of clinical nontuberculous mycobacteria (NTM) isolates at the Public Health Clinical Center of Chengdu, China, from January 2017 to December 2022. We retrospectively analyzed data from patients with clinically isolated NTM strains. Chi-square analysis assessed the rate of Mycobacterium strain isolation over 6 years. The number of samples tested for Mycobacterium tuberculosis (MTB) and/or NTM increased each year, while MTB detection decreased and NTM detection rose significantly each year (P=0.03). The average age of NTM patients was 51 ± 17.53 years, with a 14.1% HIV infection rate. The predominant isolates were Mycobacterium avium-intracellulare (MAC) and M. chelonae/M. abscessus, with 96.4% of cases being of Han ethnicity. Amikacin, moxifloxacin, and clarithromycin were effective against M. avium and M. intracellulare; linezolid, amikacin, and cefoxitin were effective against M. chelonae/M. abscessus. Over 90% of NTM cases originated from the respiratory tract. The NTM isolation rate in Southwest China has risen in recent years, primarily among elderly patients with a high HIV co-infection rate. The main NTM isolates were MAC and M. chelonae/M. abscessus. Amikacin, moxifloxacin, clarithromycin, and linezolid exhibited strong antibacterial activity against SGM, while amikacin and linezolid displayed relatively better antibacterial activity against RGM. The prevalence of NTM infection may be positively associated with regional economic development and health conditions.