FEMS microbesPub Date : 2022-10-16eCollection Date: 2022-01-01DOI: 10.1093/femsmc/xtac026
Anne Stahlfeld, Laura R Glick, Isabel M Ott, Samuel B Craft, Devyn Yolda-Carr, Christina A Harden, Maura Nakahata, Shelli F Farhadian, Lindsay R Grant, Ronika Alexander-Parrish, Adriano Arguedas, Bradford D Gessner, Daniel M Weinberger, Anne L Wyllie
{"title":"Detection of pneumococcus during hospitalization for SARS-CoV-2.","authors":"Anne Stahlfeld, Laura R Glick, Isabel M Ott, Samuel B Craft, Devyn Yolda-Carr, Christina A Harden, Maura Nakahata, Shelli F Farhadian, Lindsay R Grant, Ronika Alexander-Parrish, Adriano Arguedas, Bradford D Gessner, Daniel M Weinberger, Anne L Wyllie","doi":"10.1093/femsmc/xtac026","DOIUrl":"10.1093/femsmc/xtac026","url":null,"abstract":"<p><strong>Background: </strong>Infections with respiratory viruses [e.g. influenza and respiratory syncytial virus (RSV)] can increase the risk of severe pneumococcal infections. Likewise, pneumococcal coinfection is associated with poorer outcomes in viral respiratory infection. However, there are limited data describing the frequency of pneumococcus and SARS-CoV-2 coinfection and the role of coinfection in influencing COVID-19 severity. We, therefore, investigated the detection of pneumococcus in COVID-19 inpatients during the early pandemic period.</p><p><strong>Methods: </strong>The study included patients aged 18 years and older, admitted to the Yale-New Haven Hospital who were symptomatic for respiratory infection and tested positive for SARS-CoV-2 during March-August 2020. Patients were tested for pneumococcus through culture-enrichment of saliva followed by RT-qPCR (to identify carriage) and serotype-specific urine antigen detection (UAD) assays (to identify presumed lower respiratory tract pneumococcal disease).</p><p><strong>Results: </strong>Among 148 subjects, the median age was 65 years; 54.7% were male; 50.7% had an ICU stay; 64.9% received antibiotics; and 14.9% died while admitted. Pneumococcal carriage was detected in 3/96 (3.1%) individuals tested by saliva RT-qPCR. Additionally, pneumococcus was detected in 14/127 (11.0%) individuals tested by UAD, and more commonly in severe than moderate COVID-19 [OR: 2.20; 95% CI: (0.72, 7.48)]; however, the numbers were small with a high degree of uncertainty. None of the UAD-positive individuals died.</p><p><strong>Conclusions: </strong>Pneumococcal lower respiratory tract infection (LRTI), as detected by positive UAD, occurred in patients hospitalized with COVID-19. Moreover, pneumococcal LRTI was more common in those with more serious COVID-19 outcomes. Future studies should assess how pneumococcus and SARS-CoV-2 interact to influence COVID-19 severity in hospitalized patients.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac026"},"PeriodicalIF":0.0,"publicationDate":"2022-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/8a/cd/xtac026.PMC10117745.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9661872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
FEMS microbesPub Date : 2022-09-24eCollection Date: 2022-01-01DOI: 10.1093/femsmc/xtac024
William Johnson, Katelyn Reeves, Jennifer Liebig, Antonio Feula, Claire Butler, Michaela Alkire, Samiha Singh, Shelby Litton, Kerry O'Conor, Keaton Jones, Nikolas Ortega, Trace Shimek, Julia Witteman, Kristen K Bjorkman, Cresten Mansfeldt
{"title":"Effectiveness of building-level sewage surveillance during both community-spread and sporadic-infection phases of SARS-CoV-2 in a university campus population.","authors":"William Johnson, Katelyn Reeves, Jennifer Liebig, Antonio Feula, Claire Butler, Michaela Alkire, Samiha Singh, Shelby Litton, Kerry O'Conor, Keaton Jones, Nikolas Ortega, Trace Shimek, Julia Witteman, Kristen K Bjorkman, Cresten Mansfeldt","doi":"10.1093/femsmc/xtac024","DOIUrl":"10.1093/femsmc/xtac024","url":null,"abstract":"<p><p>Pathogen surveillance within wastewater rapidly progressed during the SARS-CoV-2 pandemic and informed public health management. In addition to the successful monitoring of entire sewer catchment basins at the treatment facility scale, subcatchment or building-level monitoring enabled targeted support of resource deployment. However, optimizing the temporal and spatial resolution of these monitoring programs remains complex due to population dynamics and within-sewer physical, chemical, and biological processes. To address these limitations, this study explores the advancement of the building-scale network that monitored the on-campus residential population at the University of Colorado Boulder between August 2020 and May 2021 through a daily SARS-CoV-2 surveillance campaign. During the study period, SARS-CoV-2 infection prevalence transitioned from robust community spread in Fall 2020 to sporadic infections in Spring 2021. Temporally, these distinct phases enabled investigating the effectiveness of resource commitment by exploring subsets of the original daily sampling data. Spatially, select sampling sites were installed along the flow path of the pipe network, enabling the exploration of the conservation of viral concentrations within the wastewater. Infection prevalence and resource commitment for informed action displayed an inverted relationship: higher temporal and spatial resolution surveillance is more imperative during sporadic infection phases than during high prevalence periods. This relationship was reinforced when norovirus (two minor clusters) and influenza (primarily absent) were additionally surveilled at a weekly frequency. Overall, resource commitment should scale to meet the objectives of the monitoring campaign-providing a general prevalence estimate requires fewer resources than an early-warning and targeted-action monitoring framework.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac024"},"PeriodicalIF":0.0,"publicationDate":"2022-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117889/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9661876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
FEMS microbesPub Date : 2022-07-25eCollection Date: 2022-01-01DOI: 10.1093/femsmc/xtac022
Amanda P Smith, Lindey C Lane, Ivan Ramirez Zuniga, David M Moquin, Peter Vogel, Amber M Smith
{"title":"Increased virus dissemination leads to enhanced lung injury but not inflammation during influenza-associated secondary bacterial infection.","authors":"Amanda P Smith, Lindey C Lane, Ivan Ramirez Zuniga, David M Moquin, Peter Vogel, Amber M Smith","doi":"10.1093/femsmc/xtac022","DOIUrl":"10.1093/femsmc/xtac022","url":null,"abstract":"<p><p>Secondary bacterial infections increase influenza-related morbidity and mortality, particularly if acquired after 5-7 d from the viral onset. Synergistic host responses and direct pathogen-pathogen interactions are thought to lead to a state of hyperinflammation, but the kinetics of the lung pathology have not yet been detailed, and identifying the contribution of different mechanisms to disease is difficult because these may change over time. To address this gap, we examined host-pathogen and lung pathology dynamics following a secondary bacterial infection initiated at different time points after influenza within a murine model. We then used a mathematical approach to quantify the increased virus dissemination in the lung, coinfection time-dependent bacterial kinetics, and virus-mediated and postbacterial depletion of alveolar macrophages. The data showed that viral loads increase regardless of coinfection timing, which our mathematical model predicted and histomorphometry data confirmed was due to a robust increase in the number of infected cells. Bacterial loads were dependent on the time of coinfection and corresponded to the level of IAV-induced alveolar macrophage depletion. Our mathematical model suggested that the additional depletion of these cells following the bacterial invasion was mediated primarily by the virus. Contrary to current belief, inflammation was not enhanced and did not correlate with neutrophilia. The enhanced disease severity was correlated to inflammation, but this was due to a nonlinearity in this correlation. This study highlights the importance of dissecting nonlinearities during complex infections and demonstrated the increased dissemination of virus within the lung during bacterial coinfection and simultaneous modulation of immune responses during influenza-associated bacterial pneumonia.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac022"},"PeriodicalIF":0.0,"publicationDate":"2022-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/32/6e/xtac022.PMC10117793.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9653269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
FEMS microbesPub Date : 2022-06-17eCollection Date: 2022-01-01DOI: 10.1093/femsmc/xtac017
Brittany L Kmush, David Monk, Hyatt Green, Darcy A Sachs, Teng Zeng, David A Larsen
{"title":"Comparability of 24-hour composite and grab samples for detection of SARS-2-CoV RNA in wastewater.","authors":"Brittany L Kmush, David Monk, Hyatt Green, Darcy A Sachs, Teng Zeng, David A Larsen","doi":"10.1093/femsmc/xtac017","DOIUrl":"10.1093/femsmc/xtac017","url":null,"abstract":"<p><p>Wastewater surveillance is a cost-effective way to monitor pathogen prevalence and transmission patterns in the entire community. Here, we compare 24-hour composite and grab samples collected during September 2020 from several municipalities in New York State to detect SARS-CoV-2. A total of 45 paired samples (90 total samples) from three counties and 14 wastewater treatment plants were available for analysis. The categorical comparison (SARS-CoV-2 genetic material detected and quantifiable, genetic material detected but below the limits of quantification, and genetic material not detected) between the grab and composite samples was quite strong, with 91.1% agreement (kappa <i>P</i>-value < .001). The correlations among the quantifiable grab and composite samples were statistically significant yet modest for SARS2-CoV RNA (Pearson correlation = 0.44, <i>P</i> = .02), crAssphage cDNA (Pearson correlation = 0.36, <i>P</i> = .02), and crAssphage DNA (Pearson correlation = 0.46, <i>P</i> = .002). We found good comparison between grab and 24-hour composite samples for detecting SARS-CoV-2 RNA from municipal wastewater treatment plants. Grab sampling is an efficient and cost-effective method to monitor for the presence of SARS-CoV-2 in the entire community.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac017"},"PeriodicalIF":0.0,"publicationDate":"2022-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117866/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9660447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
FEMS microbesPub Date : 2022-05-13eCollection Date: 2022-01-01DOI: 10.1093/femsmc/xtac016
Christiaan D M Wijers, Ly Pham, Martin V Douglass, Eric P Skaar, Lauren D Palmer, Michael J Noto
{"title":"Gram-negative bacteria act as a reservoir for aminoglycoside antibiotics that interact with host factors to enhance bacterial killing in a mouse model of pneumonia.","authors":"Christiaan D M Wijers, Ly Pham, Martin V Douglass, Eric P Skaar, Lauren D Palmer, Michael J Noto","doi":"10.1093/femsmc/xtac016","DOIUrl":"10.1093/femsmc/xtac016","url":null,"abstract":"<p><p><i>In vitro</i> exposure of multiple Gram-negative bacteria to an aminoglycoside (AG) antibiotic has previously been demonstrated to result in bacterial alterations that interact with host factors to suppress Gram-negative pneumonia. However, the mechanisms resulting in suppression are not known. Here, the hypothesis that Gram-negative bacteria bind and retain AGs, which are introduced into the lung and interact with host defenses to affect bacterial killing, was tested. Following <i>in vitro</i> exposure of one of several, pathogenic Gram-negative bacteria to the AG antibiotics kanamycin or gentamicin, AGs were detected in bacterial cell pellets (up to 208 μg/mL). Using inhibitors of AG binding and internalization, the bacterial outer membrane was implicated as the predominant kanamycin and gentamicin reservoir. Following intranasal administration of gentamicin-bound bacteria or gentamicin solution at the time of infection with live, AG-naïve bacteria, gentamicin was detected in the lungs of infected mice (up to 8 μg/g). Co-inoculation with gentamicin-bound bacteria resulted in killing of AG-naïve bacteria by up to 3-log<sub>10</sub>, mirroring the effects of intranasal gentamicin treatment. <i>In vitro</i> killing of AG-naïve bacteria mediated by kanamycin-bound bacteria required the presence of detergents or pulmonary surfactant, suggesting that increased bacterial killing inside the murine lung is facilitated by the detergent component of pulmonary surfactant. These findings demonstrate that Gram-negative bacteria bind and retain AGs that can interact with host-derived pulmonary surfactant to enhance bacterial killing in the lung. This may help explain why AGs appear to have unique efficacy in the lung and might expand their clinical utility.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac016"},"PeriodicalIF":0.0,"publicationDate":"2022-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9326624/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9188579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
FEMS microbesPub Date : 2022-05-07eCollection Date: 2022-01-01DOI: 10.1093/femsmc/xtac015
Christopher Owen, Dorothy Wright-Foulkes, Prisila Alvarez, Haidy Delgado, Eva C Durance, George F Wells, Rachel Poretsky, Abhilasha Shrestha
{"title":"Reduction and discharge of SARS-CoV-2 RNA in Chicago-area water reclamation plants.","authors":"Christopher Owen, Dorothy Wright-Foulkes, Prisila Alvarez, Haidy Delgado, Eva C Durance, George F Wells, Rachel Poretsky, Abhilasha Shrestha","doi":"10.1093/femsmc/xtac015","DOIUrl":"10.1093/femsmc/xtac015","url":null,"abstract":"<p><p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA is commonly excreted in the feces and urine of infected individuals and is, therefore, detected in wastewaters where infection is present in the surrounding population. Water reclamation plants (WRPs) that treat these wastewaters commonly discharge treated effluents into the surrounding environment, yet little is known about the removal or persistence of SARS-CoV-2 RNA through wastewater treatment systems and potential for eventual release into the environment. We collected 361 24-hour composite influent and effluent samples from seven WRPs in the Greater Chicago Area in Illinois. Samples were collected over a period of 21 weeks for three large WRPs (with design max flows of 1.89-2.32 billion gallons per day and serving a combined population of 4.62 million people) and 11 weeks for four smaller WRPs (with design max flows of 96.3-186 million gallons per day and serving a combined population of >0.5 million people). A total of two of the larger WRPs implemented seasonal disinfection (using UV light or chlorination/dechlorination) for 8 weeks of this sampling period. SARS-CoV-2 RNA was quantified in the influent and effluent samples by reverse-transcription quantitative PCR (RT-qPCR) of the N1 and N2 targets of the nucleocapsid (N) gene. Although SARS-CoV-2 RNA was regularly detected in influent and effluent from all WRPs, viral RNA concentrations in the effluent samples were considerably lower, with mean effluent: influent gene copy concentration ratios ranging from 1:160 to 1:2.95 between WRPs. Samples collected while disinfection was active vs. inactive did not show any significant difference in the portion of RNA persisting through the treatment process (<i>P</i> > .05).</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac015"},"PeriodicalIF":0.0,"publicationDate":"2022-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ba/aa/xtac015.PMC10117756.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9661877","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
FEMS microbesPub Date : 2022-04-18eCollection Date: 2022-01-01DOI: 10.1093/femsmc/xtac012
Paris S Salazar-Hamm, Jennifer J Marshall Hathaway, Ara S Winter, Nicole A Caimi, Debbie C Buecher, Ernest W Valdez, Diana E Northup
{"title":"Great diversity of KS<i>α</i> sequences from bat-associated microbiota suggests novel sources of uncharacterized natural products.","authors":"Paris S Salazar-Hamm, Jennifer J Marshall Hathaway, Ara S Winter, Nicole A Caimi, Debbie C Buecher, Ernest W Valdez, Diana E Northup","doi":"10.1093/femsmc/xtac012","DOIUrl":"10.1093/femsmc/xtac012","url":null,"abstract":"<p><p>Polyketide synthases (PKSs) are multidomain enzymes in microorganisms that synthesize complex, bioactive molecules. PKS II systems are iterative, containing only a single representative of each domain: ketosynthase alpha (KS[Formula: see text]), ketosynthase beta and the acyl carrier protein. Any gene encoding for one of these domains is representative of an entire PKS II biosynthetic gene cluster (BGC). Bat skin surfaces represent an extreme environment prolific in Actinobacteria that may constitute a source for bioactive molecule discovery. KS[Formula: see text] sequences were obtained from culturable bacteria from bats in the southwestern United States. From 467 bat bacterial isolates, we detected 215 (46%) had KS[Formula: see text] sequences. Sequencing yielded 210 operational taxonomic units, and phylogenetic placement found 45 (21%) shared <85% homology to characterized metabolites. Additionally, 16 Actinobacteria genomes from the bat microbiome were analyzed for biosynthetic capacity. A range of 69-93% of the BGCs were novel suggesting the bat microbiome may contain valuable uncharacterized natural products. Documenting and characterizing these are important in understanding the susceptibility of bats to emerging infectious diseases, such as white-nose syndrome. Also noteworthy was the relationship between KS [Formula: see text] homology and total BGC novelty within each fully sequenced strain. We propose amplification and detection of KS[Formula: see text] could predict a strain's global biosynthetic capacity.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac012"},"PeriodicalIF":0.0,"publicationDate":"2022-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/95/40/xtac012.PMC9097503.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9644478","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
FEMS microbesPub Date : 2022-03-17eCollection Date: 2022-01-01DOI: 10.1093/femsmc/xtac008
Michelle Landstrom, Evan Braun, Ellen Larson, Merrill Miller, Geoffrey H Holm
{"title":"Efficacy of SARS-CoV-2 wastewater surveillance for detection of COVID-19 at a residential private college.","authors":"Michelle Landstrom, Evan Braun, Ellen Larson, Merrill Miller, Geoffrey H Holm","doi":"10.1093/femsmc/xtac008","DOIUrl":"10.1093/femsmc/xtac008","url":null,"abstract":"<p><p>Many colleges and universities utilized wastewater surveillance testing for SARS-CoV-2 RNA as a tool to help monitor and mitigate the COVID-19 pandemic on campuses across the USA during the 2020-2021 academic year. We sought to assess the efficacy of one such program by analyzing data on relative wastewater RNA levels from residential buildings in relation to SARS-CoV-2 cases identified through individual surveillance testing, conducted largely independent of wastewater results. Almost 80% of the cases on campus were associated with positive wastewater tests, resulting in an overall positive predictive value of 79% (Chi square 48.1, Df = 1, <i>P</i> < 0.001). However, half of the positive wastewater samples occurred in the two weeks following the return of a student to the residence hall following the 10-day isolation period, and therefore were not useful in predicting new infections. When these samples were excluded, the positive predictive value of a positive wastewater sample was 54%. Overall, we conclude that the continued shedding of viral RNA by patients past the time of potential transmission confounds the identification of new cases using wastewater surveillance, and decreases its effectiveness in managing SARS-CoV-2 infections on a residential college campus.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac008"},"PeriodicalIF":0.0,"publicationDate":"2022-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117736/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9660444","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
FEMS microbesPub Date : 2022-03-04eCollection Date: 2022-01-01DOI: 10.1093/femsmc/xtac007
Karina Mueller Brown, Valerie Le Sage, Andrea J French, Jennifer E Jones, Gabriella H Padovani, Annika J Avery, Stacey Schultz-Cherry, Jason W Rosch, N Luisa Hiller, Seema S Lakdawala
{"title":"Secondary infection with <i>Streptococcus pneumoniae</i> decreases influenza virus replication and is linked to severe disease.","authors":"Karina Mueller Brown, Valerie Le Sage, Andrea J French, Jennifer E Jones, Gabriella H Padovani, Annika J Avery, Stacey Schultz-Cherry, Jason W Rosch, N Luisa Hiller, Seema S Lakdawala","doi":"10.1093/femsmc/xtac007","DOIUrl":"10.1093/femsmc/xtac007","url":null,"abstract":"<p><p>Secondary bacterial infection is a common complication in severe influenza virus infections. During the H1N1 pandemic of 2009, increased mortality was observed among healthy young adults due to secondary bacterial pneumonia, one of the most frequent bacterial species being <i>Streptococcus pneumoniae</i> (Spn). Previous studies in mice and ferrets have suggested a synergistic relationship between Spn and influenza viruses. In this study, the ferret model was used to examine whether secondary Spn infection (strains BHN97 and D39) influence replication and airborne transmission of the 2009 pandemic H1N1 virus (H1N1pdm09). Secondary infection with Spn after H1N1pdm09 infection consistently resulted in a significant decrease in viral titers in the ferret nasal washes. While secondary Spn infection appeared to negatively impact influenza virus replication, animals precolonized with Spn were equally susceptible to H1N1pdm09 airborne transmission. In line with previous work, ferrets with preceding H1N1pdm09 and secondary Spn infection had increased bacterial loads and more severe clinical symptoms as compared to animals infected with H1N1pdm09 or Spn alone. Interestingly, the donor animals that displayed the most severe clinical symptoms had reduced airborne transmission of H1N1pdm09. Based on these data, we propose an asymmetrical relationship between these two pathogens, rather than a synergistic one, since secondary bacterial infection enhances Spn colonization and pathogenesis but decreases viral titers.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac007"},"PeriodicalIF":4.0,"publicationDate":"2022-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/d6/ea/xtac007.PMC8981988.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9641973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
FEMS microbesPub Date : 2022-03-03eCollection Date: 2022-01-01DOI: 10.1093/femsmc/xtac006
Zandra Fagernäs, Domingo C Salazar-García, María Haber Uriarte, Azucena Avilés Fernández, Amanda G Henry, Joaquín Lomba Maurandi, Andrew T Ozga, Irina M Velsko, Christina Warinner
{"title":"Understanding the microbial biogeography of ancient human dentitions to guide study design and interpretation.","authors":"Zandra Fagernäs, Domingo C Salazar-García, María Haber Uriarte, Azucena Avilés Fernández, Amanda G Henry, Joaquín Lomba Maurandi, Andrew T Ozga, Irina M Velsko, Christina Warinner","doi":"10.1093/femsmc/xtac006","DOIUrl":"10.1093/femsmc/xtac006","url":null,"abstract":"<p><p>The oral cavity is a heterogeneous environment, varying in factors such as pH, oxygen levels, and salivary flow. These factors affect the microbial community composition and distribution of species in dental plaque, but it is not known how well these patterns are reflected in archaeological dental calculus. In most archaeological studies, a single sample of dental calculus is studied per individual and is assumed to represent the entire oral cavity. However, it is not known if this sampling strategy introduces biases into studies of the ancient oral microbiome. Here, we present the results of a shotgun metagenomic study of a dense sampling of dental calculus from four Chalcolithic individuals from the southeast Iberian peninsula (ca. 4500-5000 BP). Interindividual differences in microbial composition are found to be much larger than intraindividual differences, indicating that a single sample can indeed represent an individual in most cases. However, there are minor spatial patterns in species distribution within the oral cavity that should be taken into account when designing a study or interpreting results. Finally, we show that plant DNA identified in the samples is likely of postmortem origin, demonstrating the importance of including environmental controls or additional lines of biomolecular evidence in dietary interpretations.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac006"},"PeriodicalIF":0.0,"publicationDate":"2022-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117714/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9653273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}