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{"title":"Extended-spectrum beta-lactamases resistance in Klebsiella pneumoniae in sub-Saharan Africa: a systematic review and meta-analysis","authors":"Morufat Oluwatosin, 1¥ Olaitan, Oluwatosin Qawiyy, 2¥ Orababa, Bushola Rukayya Shittu, Adams Alabi Oyediran, G. M. Obunukwu, Margaret Toluwalayo Arowolo, A. Kade, Khalid Ibrahim, Yahaya, Rildwan Alaba, Yusuff, M. Olaitan","doi":"10.1101/2024.08.10.24311782","DOIUrl":"https://doi.org/10.1101/2024.08.10.24311782","url":null,"abstract":"Background Extended-spectrum beta-lactamase (ESBL)-producing Klebsiella pneumoniae is a critical priority pathogen for which there is a need for new antimicrobials and poses a great public health threat to many parts of the world including sub-Saharan Africa (SSA). This study aims to determine the prevalence of ESBL-resistant K. pneumoniae in SSA and the predominant ESBL genes in the region. Methods Databases such as PubMed, Scopus, Web of Science, Africa Journal Online, and Google Scholar were searched for eligible articles based on preset eligibility criteria. After screening of titles, abstracts, and full texts, a meta-analysis using a random-effect model was conducted on the eligible studies to determine the overall and subgroup prevalence of ESBL-producing K. pneumoniae in SSA. Findings This meta-analysis included 119 eligible studies from 25 SSA countries in all SSA subregions. The overall prevalence of ESBL-resistant K. pneumoniae in SSA is estimated to be 8.6% [95% CI: 6.4-11]. South Africa (18.5%) and Central Africa (4.6%) subregions have the highest and lowest prevalence of ESBL-producing K. pneumoniae in the region, respectively. Additionally, South Africa (23.3%), Kenya (23%), and Nigeria (11.1%) are countries with the top three prevalence of ESBL-resistant K. pneumoniae in the region. Animal samples were also seen to have the highest prevalence compared to clinical and environmental samples in this study. Lastly, CTX-M-15 was the most reported ESBL gene in SSA. Interpretation Although this study reports a low pooled prevalence of ESBL-resistant K. pneumoniae in SSA, some countries in the region have a high burden of this drug-resistant strain. Additionally, some countries in the region lack data on this drug-resistant strain, thus putting other parts of the region at risk due to the porous borders and immigration between the countries in the region. Funding There was no funding for this study","PeriodicalId":18505,"journal":{"name":"medRxiv","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141919054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Extended-spectrum beta-lactamases resistance in Klebsiella pneumoniae in sub-Saharan Africa: a systematic review and meta-analysis","authors":"Morufat Oluwatosin, 1¥ Olaitan, Oluwatosin Qawiyy, 2¥ Orababa, Bushola Rukayya Shittu, Adams Alabi Oyediran, G. M. Obunukwu, Margaret Toluwalayo Arowolo, A. Kade, Khalid Ibrahim, Yahaya, Rildwan Alaba, Yusuff, M. Olaitan","doi":"10.1101/2024.08.10.24311782","DOIUrl":"https://doi.org/10.1101/2024.08.10.24311782","url":null,"abstract":"Background Extended-spectrum beta-lactamase (ESBL)-producing Klebsiella pneumoniae is a critical priority pathogen for which there is a need for new antimicrobials and poses a great public health threat to many parts of the world including sub-Saharan Africa (SSA). This study aims to determine the prevalence of ESBL-resistant K. pneumoniae in SSA and the predominant ESBL genes in the region. Methods Databases such as PubMed, Scopus, Web of Science, Africa Journal Online, and Google Scholar were searched for eligible articles based on preset eligibility criteria. After screening of titles, abstracts, and full texts, a meta-analysis using a random-effect model was conducted on the eligible studies to determine the overall and subgroup prevalence of ESBL-producing K. pneumoniae in SSA. Findings This meta-analysis included 119 eligible studies from 25 SSA countries in all SSA subregions. The overall prevalence of ESBL-resistant K. pneumoniae in SSA is estimated to be 8.6% [95% CI: 6.4-11]. South Africa (18.5%) and Central Africa (4.6%) subregions have the highest and lowest prevalence of ESBL-producing K. pneumoniae in the region, respectively. Additionally, South Africa (23.3%), Kenya (23%), and Nigeria (11.1%) are countries with the top three prevalence of ESBL-resistant K. pneumoniae in the region. Animal samples were also seen to have the highest prevalence compared to clinical and environmental samples in this study. Lastly, CTX-M-15 was the most reported ESBL gene in SSA. Interpretation Although this study reports a low pooled prevalence of ESBL-resistant K. pneumoniae in SSA, some countries in the region have a high burden of this drug-resistant strain. Additionally, some countries in the region lack data on this drug-resistant strain, thus putting other parts of the region at risk due to the porous borders and immigration between the countries in the region. Funding There was no funding for this study","PeriodicalId":18505,"journal":{"name":"medRxiv","volume":"2 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141919771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Testing of retail cheese, butter, ice cream and other dairy products for highly pathogenic avian influenza in the US","authors":"D. L. Suarez, I. V. Goraichuk, L. Killmaster, E. Spackman, N. J. Clausen, T. Colonius, C. Leonard, M. Metz","doi":"10.1101/2024.08.11.24311811","DOIUrl":"https://doi.org/10.1101/2024.08.11.24311811","url":null,"abstract":"The recent outbreak of highly pathogenic avian influenza (HPAI) in dairy cows has created public health concerns about the potential of consumers being exposed to live virus from commercial dairy products. Previous studies support that pasteurization effectively inactivates avian influenza in milk and an earlier retail milk survey showed viral RNA, but no live virus could be detected in the dairy products tested. Because of the variety of products and processing methods in which milk is used, additional product testing was conducted to determine if HPAI viral RNA could be detected in retail dairy samples, and for positive quantitative real-time RT-PCR (qRT-PCR) samples to be tested for presence of live virus. Revised protocols were developed to extract RNA from solid dairy products including cheese and butter. The solid dairy product was mechanically liquified with garnet and zirconium beads in a bead beater diluted 1 to 4 with BHI media. This pre-processing step was suitable in allowing efficient RNA extraction with standard methods. Trial studies were conducted with different cheese types with spiked in avian influenza virus to show that inoculation of the liquified cheese into embryonating chicken eggs was not toxic to the embryos and allowed virus replication. A total of 167 retail dairy samples, including a variety of cheeses, butter, ice cream, and fluid milk were collected as part of nationwide survey. A total of 17.4% (29/167) of the samples had detectable viral RNA by qRT-PCR targeting the matrix gene, but all samples were negative for live virus after testing with embryonating egg inoculation. The viral RNA was also evaluated by sequencing part of the hemagglutinin gene using a revised protocol optimized to deal with the fragmented viral RNA. The sequence analysis showed all viral RNA positive samples were highly similar to previously reported HPAI dairy cow isolates. Using the revised protocols, it was determined that HPAI viral RNA could be detected in a variety of dairy products, but existing pasteurizations methods effectively inactivate virus assuring consumer safety.","PeriodicalId":18505,"journal":{"name":"medRxiv","volume":"1 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141920058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Educational attainment and mental health conditions: a within-sibship Mendelian randomization study","authors":"M. F. Vinueza Veloz, L. Bhatta, P. R. Jones, M. S. Tesli, G. Davey Smith, N. M. Davies, B. M. Brumpton, O. E. Naess","doi":"10.1101/2024.08.10.24311789","DOIUrl":"https://doi.org/10.1101/2024.08.10.24311789","url":null,"abstract":"Importance: Observational studies have demonstrated consistent protective effects of higher educational attainment (EA) on the risk of suffering mental health conditions (MHC). Determining whether these beneficial effects are causal is challenging given the potential role of dynastic effects and demographic factors (assortative mating and population structure) in this association. Objective: To evaluate to what extent the relationship between EA and various MHC is independent from dynastic effects and demographic factors. Design: Within-sibship Mendelian randomization (MR) study. Setting: One-sample MR analyses included participants data from the Trondelag Health Study (HUNT, Norway) and UK Biobank (United Kingdom). For two-sample MR analyses we used summary statistics from publicly available genome-wide-association-studies. Participants: 61 880 siblings (27 507 sibships). Exposure: Years of education. Main outcomes: Scores for symptoms of anxiety, depression and neuroticism using the Hospital Anxiety Depression Scale (HADS), the 7-item Generalized Anxiety Disorder Scale (GAD-7), the 9-item Patient Health Questionnaire (PHQ-9), and the Eysenck Personality Questionnaire, as well as self-reported consumption of psychotropic medication. Results: One standard deviation (SD) unit increase in years of education was associated with a lower symptom score of anxiety (-0.20 SD [95%CI: -0.26, -0.14]), depression (-0.11 SD [-0.43, 0.22]), neuroticism (-0.30 SD [-0.53, -0.06]), and lower odds of psychotropic medication consumption (OR: 0.60 [0.52, 0.69]). Estimates from the within-sibship MR analyses showed some attenuation, which however were suggestive of a causal association (anxiety: -0.17 SD [-0.33, -0.00]; depression: -0.18 SD [-1.26, 0.89]; neuroticism: -0.29 SD [-0.43, -0.15]); psychotropic medication consumption: OR, 0.52 [0.34, 0.82]). Conclusions and Relevance: Associations between EA and MHC in adulthood, although to some extend explained by dynastic effects and demographic factors, overall remain robust, indicative of a causal effect. However, larger studies are warranted to improve statistical power and further validate our conclusions.","PeriodicalId":18505,"journal":{"name":"medRxiv","volume":"15 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141919064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Estimation of age and sex specific Glomerular Filtration Rate in the Abu Dhabi population and its association with mortality and Atherosclerotic cardiovascular outcome. A Retrospective Cohort Study","authors":"L. Alketbi, Yousef Boobes, N. Nagelkerke, H. Aleissaee, N. AlShamsi, M. Almansoori, Ahmed Hemaid, M. AlDobaee, Noura AlAlawi, R. AlKetbi, T. Fahmawee, B. AlHashaikeh, A. AlAzeezi, F. Shuaib, J. Alnuaimi, E. Mahmoud, N. AlAhbabi, Bachar Afandi, Retrospective Cohort Study","doi":"10.1101/2024.08.10.24311788","DOIUrl":"https://doi.org/10.1101/2024.08.10.24311788","url":null,"abstract":"The impact of abnormal Glomerular Filtration Rate (eGFR) on various adverse outcomes has been well studied; however, the United Arab Emirates (UAE), like many other regions in the world, remains understudied in this area. Method This retrospective cohort study estimates the age and sex-specific Glomerular Filtration Rate (eGFR) in the Abu Dhabi population and its association with mortality and Atherosclerotic cardiovascular (ASCVD) outcomes. The cohort of 8699 participants in a national cardiovascular disease screening from 2011 to 2013. The cohort was reevaluated in 2023 for mortality and cardiovascular outcomes. Reference eGFR percentiles were estimated from subjects without comorbidities using the LMS method. Results The reference percentiles of normal eGFR values showed a marked decrease with age, with small sex differences in the reference percentile distribution. A prognostic definition of renal hyperfiltration (RH) is suggested by the observation that subjects in the 97th percentile had a significantly higher incidence of ASCVD, although not statistically significant, in terms of mortality rate. Older age, female sex, history of ASCVD, history of hypertension, being treated for hypertension, lower diastolic blood pressure, higher systolic blood pressure, lower HDL, higher HA1C, and higher vitamin D were significantly associated with lower eGFR percentiles. Subjects in the two categories within the RH range, the 95th and 97th percentiles, had a significantly higher prevalence of diabetes; they are older smokers with higher BMI, higher HA1C, higher HDL, lower vitamin D, and more likely to be males, with higher physical activity and have a lower prevalence of CHD. Conclusion The distribution of eGFR by age and sex is valuable for clinical decision-making in Abu Dhabi and likely for the Arab population in general. Although the 95th percentile of eGFR in this cohort showed a higher but nonsignificant risk, the 97th percentile is significantly associated with ASCVD, even more than subjects in the less than 10th eGFR percentile. This study provides important insights into the prevalence and risk factors associated with different eGFR percentiles in the Abu Dhabi population. The findings underscore the need for targeted interventions to address modifiable risk factors and prevent the progression of renal damage in this high-risk population.","PeriodicalId":18505,"journal":{"name":"medRxiv","volume":"2 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141920048","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transparency in the secondary use of health data: Assessing the status quo of guidance and best practices","authors":"O. R. van den Akker, R. T. Thibault, J. Ioannidis, S. G. Schorr, D. Strech","doi":"10.1101/2024.08.11.24311808","DOIUrl":"https://doi.org/10.1101/2024.08.11.24311808","url":null,"abstract":"We evaluated what guidance exists in the literature to improve the transparency of studies that make secondary use of health data. To find relevant literature, we searched PubMed and Google Scholar and drafted a list of health organizations based on our personal expertise. We quantitatively and qualitatively coded different types of research transparency: registration, methods reporting, results reporting, data sharing, and code sharing. We found 54 documents that provide recommendations to improve the transparency of studies making secondary use of health data, mainly in relation to study registration (n = 27) and methods reporting (n = 39). Only three documents made recommendations on data sharing or code sharing. Recommendations for study registration and methods reporting mainly came in the form of structured documents like registration templates and reporting guidelines. Aside from the recommendations aimed directly at researchers, we found 31 recommendations aimed at the wider research community, typically on how to improve research infrastructure. Limitations or challenges of improving transparency were rarely mentioned, highlighting the need for more nuance in providing transparency guidance for studies that make secondary use of health data.","PeriodicalId":18505,"journal":{"name":"medRxiv","volume":"1 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141920055","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Directionality of neural activity in and out of the seizure onset zone in focal epilepsy","authors":"H. Karimi-Rouzbahani, A. McGonigal","doi":"10.1101/2024.08.10.24311802","DOIUrl":"https://doi.org/10.1101/2024.08.10.24311802","url":null,"abstract":"Epilepsy affects over 50 million people worldwide, with approximately 30% experiencing drug-resistant forms that may require surgical intervention. Accurate localisation of the epileptogenic zone (EZ) is crucial for effective treatment, but how best to use intracranial EEG data to delineate the EZ remains unclear. Previous studies have used the directionality of neural activities across the brain to investigate seizure dynamics and localise the EZ. However, the different connectivity measures used across studies have often provided inconsistent insights about the direction and the localisation power of signal flow as a biomarker for EZ localisation. In a data-driven approach, this study employs a large set of 13 distinct directed connectivity measures to evaluate neural activity flow in and out the seizure onset zone (SOZ) during interictal and ictal periods. These measures test the hypotheses of sink SOZ (SOZ dominantly receiving neural activities during interictal periods) and source SOZ (SOZ dominantly transmitting activities during ictal periods). While the results were different across connectivity measures, several measures consistently supported higher connectivity directed towards the SOZ in interictal periods and higher connectivity directed away during ictal period. Comparing six distinct metrics of node behaviour in the network, we found that SOZ separates itself from the rest of the network allowing for the metric of eccentricity to localise the SOZ more accurately than any other metrics including in-strength and out-strength. This introduced a novel biomarker for localising the SOZ, leveraging the discriminative power of directed connectivity measures in an explainable machine learning pipeline. By using a comprehensive, objective and data-driven approach, this study addresses previously unresolved questions on the direction of neural activities in seizure organisation, and sheds light on dynamics of interictal and ictal activity in focal epilepsy.","PeriodicalId":18505,"journal":{"name":"medRxiv","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141920041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Efficacy, public health impact and optimal use of the Takeda dengue vaccine","authors":"B. Cracknell Daniels, N. M. Ferguson, I. Dorigatti","doi":"10.1101/2024.08.10.24311393","DOIUrl":"https://doi.org/10.1101/2024.08.10.24311393","url":null,"abstract":"Dengue is the most common arboviral infection, causing substantial morbidity and mortality globally. The licensing of Qdenga, a second-generation vaccine developed by Takeda Pharmaceuticals, is therefore timely, but the potential public health impact of vaccination across transmission settings needs to be evaluated. To address this, we characterised Qdenga's efficacy profile using mathematical models calibrated to published clinical trial data and estimated the public health impact of routine vaccine use. We find that efficacy depends on the infecting serotype, serological status, and age. We estimate that vaccination of children aged over six years in moderate to high dengue transmission settings (seroprevalence at 9 years of age > 60%) could reduce the burden of hospitalised dengue by 10-22% on average over ten years. We find some evidence of a risk of vaccine-induced disease enhancement in seronegative vaccine recipients for dengue serotypes 3 and 4, especially for children under six years of age. Because of this, the benefits of vaccination in lower transmission settings are more uncertain, and more data on the long-term efficacy of Qdenga against serotypes 3 and 4 are needed.","PeriodicalId":18505,"journal":{"name":"medRxiv","volume":"2 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141920049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Directionality of neural activity in and out of the seizure onset zone in focal epilepsy","authors":"H. Karimi-Rouzbahani, A. McGonigal","doi":"10.1101/2024.08.10.24311802","DOIUrl":"https://doi.org/10.1101/2024.08.10.24311802","url":null,"abstract":"Epilepsy affects over 50 million people worldwide, with approximately 30% experiencing drug-resistant forms that may require surgical intervention. Accurate localisation of the epileptogenic zone (EZ) is crucial for effective treatment, but how best to use intracranial EEG data to delineate the EZ remains unclear. Previous studies have used the directionality of neural activities across the brain to investigate seizure dynamics and localise the EZ. However, the different connectivity measures used across studies have often provided inconsistent insights about the direction and the localisation power of signal flow as a biomarker for EZ localisation. In a data-driven approach, this study employs a large set of 13 distinct directed connectivity measures to evaluate neural activity flow in and out the seizure onset zone (SOZ) during interictal and ictal periods. These measures test the hypotheses of sink SOZ (SOZ dominantly receiving neural activities during interictal periods) and source SOZ (SOZ dominantly transmitting activities during ictal periods). While the results were different across connectivity measures, several measures consistently supported higher connectivity directed towards the SOZ in interictal periods and higher connectivity directed away during ictal period. Comparing six distinct metrics of node behaviour in the network, we found that SOZ separates itself from the rest of the network allowing for the metric of eccentricity to localise the SOZ more accurately than any other metrics including in-strength and out-strength. This introduced a novel biomarker for localising the SOZ, leveraging the discriminative power of directed connectivity measures in an explainable machine learning pipeline. By using a comprehensive, objective and data-driven approach, this study addresses previously unresolved questions on the direction of neural activities in seizure organisation, and sheds light on dynamics of interictal and ictal activity in focal epilepsy.","PeriodicalId":18505,"journal":{"name":"medRxiv","volume":"17 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141919052","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Testing of retail cheese, butter, ice cream and other dairy products for highly pathogenic avian influenza in the US","authors":"D. L. Suarez, I. V. Goraichuk, L. Killmaster, E. Spackman, N. J. Clausen, T. Colonius, C. Leonard, M. Metz","doi":"10.1101/2024.08.11.24311811","DOIUrl":"https://doi.org/10.1101/2024.08.11.24311811","url":null,"abstract":"The recent outbreak of highly pathogenic avian influenza (HPAI) in dairy cows has created public health concerns about the potential of consumers being exposed to live virus from commercial dairy products. Previous studies support that pasteurization effectively inactivates avian influenza in milk and an earlier retail milk survey showed viral RNA, but no live virus could be detected in the dairy products tested. Because of the variety of products and processing methods in which milk is used, additional product testing was conducted to determine if HPAI viral RNA could be detected in retail dairy samples, and for positive quantitative real-time RT-PCR (qRT-PCR) samples to be tested for presence of live virus. Revised protocols were developed to extract RNA from solid dairy products including cheese and butter. The solid dairy product was mechanically liquified with garnet and zirconium beads in a bead beater diluted 1 to 4 with BHI media. This pre-processing step was suitable in allowing efficient RNA extraction with standard methods. Trial studies were conducted with different cheese types with spiked in avian influenza virus to show that inoculation of the liquified cheese into embryonating chicken eggs was not toxic to the embryos and allowed virus replication. A total of 167 retail dairy samples, including a variety of cheeses, butter, ice cream, and fluid milk were collected as part of nationwide survey. A total of 17.4% (29/167) of the samples had detectable viral RNA by qRT-PCR targeting the matrix gene, but all samples were negative for live virus after testing with embryonating egg inoculation. The viral RNA was also evaluated by sequencing part of the hemagglutinin gene using a revised protocol optimized to deal with the fragmented viral RNA. The sequence analysis showed all viral RNA positive samples were highly similar to previously reported HPAI dairy cow isolates. Using the revised protocols, it was determined that HPAI viral RNA could be detected in a variety of dairy products, but existing pasteurizations methods effectively inactivate virus assuring consumer safety.","PeriodicalId":18505,"journal":{"name":"medRxiv","volume":"14 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141919284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}