Alejandro Pezzulo - Academia.edu (original) (raw)
Papers by Alejandro Pezzulo
RNA sequencing enables high-contents/high-complexity measurements in small molecule screens perfo... more RNA sequencing enables high-contents/high-complexity measurements in small molecule screens performed on biological samples. Whereas the costs of DNA sequencing and the complexity of RNA-seq library preparation and analysis have decreased consistently, RNA extraction remains a significant bottleneck for RNA-seq of hundreds of samples in parallel. Direct use of cell lysate for RNA-seq library prep is common in single cell RNA-seq but not in bulk RNA-seq protocols. Recently published protocols suggest that direct lysis is compatible with simplified RNA-seq library prep. Here, we evaluate the performance of a bulk RNA-seq library prep protocol optimized for analysis of many samples of adherent cultured cells in parallel. We combine a low-cost direct lysis buffer compatible with cDNA synthesis (“in-lysate cDNA synthesis”) with Smart-3SEQ and examine the effects of calmidazolium and fludrocortisone-induced perturbation of primary human dermal fibroblasts. We compared this method to norma...
ABSTRACTMeasles virus (MeV) is the most contagious human virus, but we do not fully understand wh... more ABSTRACTMeasles virus (MeV) is the most contagious human virus, but we do not fully understand why. Unlike most respiratory viruses, MeV does not infect the airway epithelium immediately. MeV traverses the epithelium within immune cells that carry it to lymphatic organs where amplification occurs. Infected immune cells then synchronously deliver large amounts of virus to the airways. However, our understanding of MeV replication in airway epithelia is limited. To model it, we use well-differentiated primary cultures of human airway epithelial cells (HAE) from lung donors. In HAE, MeV spreads directly cell-to-cell forming infectious centers that grow for ∼3-5 days, are stable for a few days, and then disappear. Transepithelial electrical resistance remains intact during the entire course of HAE infection, thus we hypothesized that MeV infectious centers may slough off while preserving epithelial function. After documenting by confocal microscopy that infectious centers progressively ...
bioRxiv, 2021
The small airways of humans are affected early in several lung diseases. However, because they ar... more The small airways of humans are affected early in several lung diseases. However, because they are relatively inaccessible, little is known about the epithelial cells that line these airways. We performed a single cell RNA-seq census of small and large airways of wild-type pigs and pigs with disrupted cystic fibrosis transmembrane conductance regulator (CFTR) gene. The sequencing data showed that small airway epithelia had similar major cell types as large airways but no ionocytes; moreover, lack of CFTR expression had minimal effect on the transcriptome. Small airway epithelial cells expressed a different transcriptome than large airway cells. Quantitative immunohistochemistry showed that small airway basal cells participate in epithelial barrier function. Finally, sequencing data and in vitro electrophysiologic studies suggest that small airway epithelia have a water and ion transport advantage. Our data highlight the archetypal nature of basal, secretory, and ciliated airway cell...
Antimicrobial Stewardship & Healthcare Epidemiology, 2021
Background: COVID-19 in hospitalized patients may be the result of community acquisition or in-ho... more Background: COVID-19 in hospitalized patients may be the result of community acquisition or in-hospital transmission. Molecular epidemiology can help confirm hospital COVID-19 transmission and outbreaks. We describe large COVID-19 clusters identified in our hospital and apply molecular epidemiology to confirm outbreaks. Methods: The University of Iowa Hospitals and Clinics is an 811-bed academic medical center. We identified large clusters involving patients with hospital onset COVID-19 detected during March–October 2020. Large clusters included ≥10 individuals (patients, visitors, or HCWs) with a laboratory confirmed COVID-19 diagnosis (RT-PCR) and an epidemiologic link. Epidemiologic links were defined as hospitalization, work, or visiting in the same unit during the incubation or infectious period for the index case. Hospital onset was defined as a COVID-19 diagnosis ≥14 days from admission date. Admission screening has been conducted since May 2020 and serial testing (every 5 da...
Goblet cell metaplasia and mucus hyper-production are key features of chronic muco-obstructive lu... more Goblet cell metaplasia and mucus hyper-production are key features of chronic muco-obstructive lung diseases such as asthma, chronic bronchitis, and cystic fibrosis. Various mechanisms lead to goblet cell metaplasia in the airways; the driving mechanism for goblet cell metaplasia in a specific patient may be unknown. We recently found that heat shock protein 90 (HSP90) is important for both IL-13- and IL-17- induced airway goblet cell metaplasia. HSP90 interacts with multiple clients that are important in goblet cell metaplasia including Akt, Jak/STAT, IRS, Notch, and various kinases involved in NFκB signaling. Here, we used a targeted phospho-proteomic approach to identify candidate HSP90 clients modulated by the HSP90-inhibitor geldanamycin. NFκB family members were enriched amongst the top candidate targets of HSP90 inhibition in IL-13 an organotypic model of human airway epithelia. We hypothesized that HSP90 inhibition modulated goblet cell metaplasia by interfering with NFκB si...
Proceedings of the National Academy of Sciences, 2010
People with cystic fibrosis (CF) exhibit growth defects. That observation has been attributed, in... more People with cystic fibrosis (CF) exhibit growth defects. That observation has been attributed, in part, to decreased insulin-like growth factor 1 (IGF1) levels, and the reduction has been blamed on malnutrition and pulmonary inflammation. However, patients with CF already have a reduced weight at birth, a manifestation not likely secondary to poor nutrition or inflammation. We found that, like humans, CF pigs were smaller than non-CF littermates and had lower IGF1 levels. To better understand the basis of IGF1 reduction, we studied newborn pigs and found low IGF1 levels within 12 h of birth. Moreover, humerus length and bone mineral content were decreased, consistent with less IGF1 activity in utero. These findings led us to test newborn humans with CF, and we found that they also had reduced IGF1 levels. Discovering lower IGF1 levels in newborn pigs and humans indicates that the decrease is not solely a consequence of malnutrition or pulmonary inflammation and that loss of cystic f...
Antimicrobial Stewardship & Healthcare Epidemiology
Background: Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrom... more Background: Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 RNA can be detected by real-time reverse-transcription polymerase chain reaction (RT-PCR) for several weeks after infection. Discerning persistent RT-PCR positivity versus reinfection is challenging and the frequency of COVID-19 reinfections is unknown. We aimed to determine the frequency of clinically suspected reinfection in our center and confirm reinfection using viral whole-genome sequencing (WGS). Methods: The University of Iowa Hospitals and Clinics (UIHC) is an 811-bed academic medical center. Patients with respiratory complaints undergo COVID-19 RT-PCR using nasopharyngeal swabs. The RT-PCR (TaqPath COVID-19 Combo kit) uses 3 targets (ORF1ab, S gene, and N gene). We identified patients with previous laboratory-confirmed COVID-19 who sought care for new respiratory complaints and underwent a repeated SARS-CoV-2 test at least 45 days from t...
Rationale: Methicillin resistant Staphylococcus aureus (MRSA) is prevalent and consequential in c... more Rationale: Methicillin resistant Staphylococcus aureus (MRSA) is prevalent and consequential in cystic fibrosis (CF). Whole genome sequencing (WGS) could reveal genomic differences in MRSA associated with poorer outcomes or detect MRSA transmission. Objectives: To identify MRSA genes associated with low lung function and identify potential MRSA transmission in CF. Methods: We collected 97 MRSA isolates from 74 individuals with CF from 2017 and performed short-read WGS. We determined sequence type (ST) and the phylogenetic relationship between isolates. We aligned accessory genes from 25 reference genomes to genome assemblies. We classified the MRSA by accessory gene content and correlated the accessory genome to clinical outcomes. Results: The most prevalent ST were ST5 (N=55), ST105 (N=14), and ST8 (N=14). Closely related MRSA strains were shared by family members with CF, but rarely between unrelated individuals. Three distinct clusters of MRSA were identified by accessory genome ...
Infection Control and Hospital Epidemiology, 2021
Miguel E. Ortiz MD1a , Takaaki Kobayashi MD1a, Katherine Imborek MD1, Mohammed Alsuhaibani MBBS1,... more Miguel E. Ortiz MD1a , Takaaki Kobayashi MD1a, Katherine Imborek MD1, Mohammed Alsuhaibani MBBS1, Stephanie Holley MBA1, Alexandra Trannel MS1, Alexandre R. Marra MD, PhD12, William Etienne MD1, Kyle E. Jenn BSN1, Oluchi J. Abosi MBChB, MPH1, Holly MeachamMSN1, Lorinda Sheeler PhD1, Angelique Dains BSN1, Mary E. Kukla BSN1, Paul B. McCrayJr MD1, Stanley PerlmanMD, PhD1, Bradley FordMD, PhD1, Daniel J. DiekemaMD1, Melanie Wellington MD, PhD1, Alejandro A. Pezzulo MD1b and Jorge L. Salinas MD1b 1University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, Iowa, United States and 2Instituto Israelita de Ensino e Pesquisa Albert Einstein, Hospital Israelita Albert Einstein, São Paulo, Brazil
Background: The COVID-19 pandemic has created personal protective equipment (PPE) shortages, part... more Background: The COVID-19 pandemic has created personal protective equipment (PPE) shortages, particularly ofN95 respirators. Institutions have used decontamination strategies including vaporous hydrogen peroxide (VHP) to augment respirator supplies. VHP can be used to decontaminate nonporous surfaceswithout compromisingmaterial integrity.However, little is known about its impact on N95 respirator efficacy. We assessed whether repeated VHP reprocessing altered 4 key respirator efficacy qualities: quantitative fit, qualitative fit, seal check, and filtration rate. Methods: We conducted a prospective cohort study from June 15 to August 31, 2020. In total, 7 participants were fitted to a 3M 1860 small or regular N95 respirator basedonqualitativeandquantitative fit testing.Respiratorsunderwent25disinfection cycles with the Bioquell BQ-50 VHP generator. After each cycle, participants donned and doffed respirators and performed a seal check. Participants were given 2 attempts to pass their...
![Research paper thumbnail of [Effect of hypocapnia/alkalosis on the fluid filtration rate in isolated and perfused rabbit lungs]](https://attachments.academia-assets.com/80947084/thumbnails/1.jpg)
](Hypocapnia/alkalosis is a consequence of several lung and metabolic pathologies. The aim of this ... more Hypocapnia/alkalosis is a consequence of several lung and metabolic pathologies. The aim of this study was to determine whether the increase of fluid filtration rate (FFR) that occurs during Hypocapnia/alkalosis circumstances is determined by hypocapnia, alkalosis or both. 7 groups were formed (N=36) using isolated rabbit lungs. Group 1: Control (PCO2 6%, pH: 7.35-7.45); Group 2 (n=6): Hypocapnia/Alkalosis (CO2 1%, pH: 7.9); Group 3 (n=6): Hypocapnia/Normo-pH (CO2 1% pH 7.35-7.45), Group 4 (n=6) Normocapnia/Alcalosis (CO2 6%, pH: 7.9). Fenoterol, papaverine and hydrocortisone were added to Groups 5, 6 and 7 (n=4) respectively, all under Normocapnia/Alkalosis. FFR and Pulmonary Arterial Pressure (Pap) were considerably higher in group 2 than in control (FFR: 1.92g/min +/- 0.6 vs 0.0 g/min +/- 0.006). A strong influence exerted by pH was observed when Group 3 and group 4 were compared (FFR: 0.02 g/min +/- 0.009 vs 2.3 g/min +/- 0.9) and (Pap: 13.5 cmH2O +/- 1.4 vs 90 cmH2O +/- 15). A ...
The use of Positive end-expiratory pressure (PEEP) as a strategy of mechanical ventilation offers... more The use of Positive end-expiratory pressure (PEEP) as a strategy of mechanical ventilation offers its advantages, such as improved oxygenation, without causing alveolar overstretching and barotrauma. We aim to investigate the effect of several levels of PEEP on barotrauma and, whether an optimal level of PEEP exists. Forty-eight New Zealand rabbits (2.5-3.5 kg) were divided into four groups with PEEP settings of 0, 4, 8 and 12 cmH2O, at increasing levels of inspiratory volume (IV). This was done in blood perfused rabbit lungs and in lungs perfused with a Buffer-Albumin Solution. We observed that lungs ventilated with PEEP 0 cmH2O suffered pulmonary rupture at high IV (300cc), with significant increases of Pap (Pulmonary artery pressure) and FFR (Fluid filtration rate). Lungs ventilated with PEEP 8 and 12 suffered pulmonary rupture at lower IV (200cc and 150cc vs. 300cc respectively) On the other hand, lungs ventilated with PEEP 4 cmH2O reached the highest IV (400cc), in addition, th...
![Research paper thumbnail of [Vasoconstriction is required for edema of contralateral lung after reperfusion injury of one lung]](https://attachments.academia-assets.com/80947082/thumbnails/1.jpg)
](Ischemia-reperfusion (IR) lung injury is a significant cause of morbidity and mortality in certai... more Ischemia-reperfusion (IR) lung injury is a significant cause of morbidity and mortality in certain clinical scenarios that include transplantation, thromboendarterectomy and reexpansion injury of the lung. Edema of the contralateral lung after IR injury of one lung has been reported and this study was aimed to clarify the pathophysiology of this phenomenon. One-lung ischemia/hypoxia followed by reperfusion with either blood or an acellular plasma substitute was achieved in an isolated rabbit lung model by hilum clamping. After reperfusion, we studied the isolated effects of vasoconstriction and inflammation on contralateral lung injury by using papaverine or hydrocortisone as vasodilator and anti-inflammatory, respectively. We observed that IR of one lung induces edema of the contralateral lung. Absence of leukocytes and platelets in the perfusate or use of hydrocortisone completely inhibits IR injury. Moreover, papaverine suppresses edema of the contralateral, but not that of the r...
Scientific Reports
RNA sequencing enables high-content/high-complexity measurements in small molecule screens. Where... more RNA sequencing enables high-content/high-complexity measurements in small molecule screens. Whereas the costs of DNA sequencing and RNA-seq library preparation have decreased consistently, RNA extraction remains a significant bottleneck to scalability. We evaluate the performance of a bulk RNA-seq library prep protocol optimized for analysis of many samples of adherent cultured cells in parallel. We combined a low-cost direct lysis buffer compatible with cDNA synthesis (in-lysate cDNA synthesis) with Smart-3SEQ and examine the effects of calmidazolium and fludrocortisone-induced perturbation of primary human dermal fibroblasts. We compared this method to normalized purified RNA inputs from matching samples followed by Smart-3SEQ or Illumina TruSeq library prep. Our results show the minimal effect of RNA loading normalization on data quality, measurement of gene expression patterns, and generation of differentially expressed gene lists. We found that in-lysate cDNA synthesis combined...
Clinical transplantation, Jan 10, 2017
Idiopathic hyperammonemia syndrome (IHS) is an uncommon, often deadly complication of solid organ... more Idiopathic hyperammonemia syndrome (IHS) is an uncommon, often deadly complication of solid organ transplantation. IHS cases in solid organ transplantation seem to occur predominantly in lung transplant (LTx) recipients. However, to the best of our knowledge, the occurrence of IHS has not been systematically evaluated. We set out to identify all reported cases of IHS following nonliver solid organ transplantations. Retrospective review of our institutional experience and systematic review of the literature. At our institution six cases (of 844 nonliver solid organ transplants) of IHS were identified: five occurred following LTx (incidence 3.9% [lung] vs 0.1% [nonlung], P=.004). In the systematic review, 16 studies met inclusion criteria, reporting on 32 cases of IHS. The majority of IHS cases in the literature (81%) were LTx-recipients. The average peak reported ammonia level was 1039 μmol/L occurring on average 14.7 days post-transplant. Mortality in previously reported IHS cases w...
Annals of the American Thoracic Society, 2016
A 32-year-old man was admitted to the intensive care unit for emergent management of acute decomp... more A 32-year-old man was admitted to the intensive care unit for emergent management of acute decompensated liver failure, an enlarging pleural effusion, and hemorrhagic shock caused by variceal bleeding. He had a history of alcoholic cirrhosis and rightsided hepatic hydrothorax, managed medically. After volume resuscitation and banding of esophageal varices, the patient’s blood pressure normalized, serum lactate cleared, and mental status improved. Over the next 12 hours, he again became hypotensive, with cool extremities, encephalopathy, dyspnea, and rising lactic acid levels. There was no overt gastrointestinal bleeding or obvious infection. His blood pressure did not respond to intravenous fluids. Point-of-care ultrasound was used to evaluate the cause of shock, as illustrated in the parasternal long-axis (Video 1), apical four-chamber (Video 2), and subcostal views (Video 3).
![Research paper thumbnail of [Effect of changes in airway pressure and the inspiratory volume on the fluid filtration rate and pulmonary artery pressure in isolated rabbit lungs perfused with blood and acellular solution]](https://attachments.academia-assets.com/80947083/thumbnails/1.jpg)
](Investigacion Clinica, 2007
Efec to de los cam bios de pre sión de vía aé rea, vo lu men ins pi ra to rio y fe no te rol so b... more Efec to de los cam bios de pre sión de vía aé rea, vo lu men ins pi ra to rio y fe no te rol so bre la tasa de fil tra ción de lí qui dos y la pre sión de ar te ria pul mo nar en pul mo nes de co ne jos ais la dos y per fun di dos con san gre y con so lu ción ace lu lar.
Amer J Respir Crit Care Med, 2010
David K. Meyerholz 1 , David A. Stoltz 2 , Eman Namati 2,8 , Shyam Ramachandran 3 , Alejandro A. ... more David K. Meyerholz 1 , David A. Stoltz 2 , Eman Namati 2,8 , Shyam Ramachandran 3 , Alejandro A. ... Pezzulo 2 , Amanda R. Smith 2 , Michael V. Rector 2 , Melissa J. Suter 8 , Simon Kao 4 , Geoffrey ... McLennan 2,4,5 , Guillermo J. Tearney 8 , Joseph Zabner 2 , Paul B. ...
RNA sequencing enables high-contents/high-complexity measurements in small molecule screens perfo... more RNA sequencing enables high-contents/high-complexity measurements in small molecule screens performed on biological samples. Whereas the costs of DNA sequencing and the complexity of RNA-seq library preparation and analysis have decreased consistently, RNA extraction remains a significant bottleneck for RNA-seq of hundreds of samples in parallel. Direct use of cell lysate for RNA-seq library prep is common in single cell RNA-seq but not in bulk RNA-seq protocols. Recently published protocols suggest that direct lysis is compatible with simplified RNA-seq library prep. Here, we evaluate the performance of a bulk RNA-seq library prep protocol optimized for analysis of many samples of adherent cultured cells in parallel. We combine a low-cost direct lysis buffer compatible with cDNA synthesis (“in-lysate cDNA synthesis”) with Smart-3SEQ and examine the effects of calmidazolium and fludrocortisone-induced perturbation of primary human dermal fibroblasts. We compared this method to norma...
ABSTRACTMeasles virus (MeV) is the most contagious human virus, but we do not fully understand wh... more ABSTRACTMeasles virus (MeV) is the most contagious human virus, but we do not fully understand why. Unlike most respiratory viruses, MeV does not infect the airway epithelium immediately. MeV traverses the epithelium within immune cells that carry it to lymphatic organs where amplification occurs. Infected immune cells then synchronously deliver large amounts of virus to the airways. However, our understanding of MeV replication in airway epithelia is limited. To model it, we use well-differentiated primary cultures of human airway epithelial cells (HAE) from lung donors. In HAE, MeV spreads directly cell-to-cell forming infectious centers that grow for ∼3-5 days, are stable for a few days, and then disappear. Transepithelial electrical resistance remains intact during the entire course of HAE infection, thus we hypothesized that MeV infectious centers may slough off while preserving epithelial function. After documenting by confocal microscopy that infectious centers progressively ...
bioRxiv, 2021
The small airways of humans are affected early in several lung diseases. However, because they ar... more The small airways of humans are affected early in several lung diseases. However, because they are relatively inaccessible, little is known about the epithelial cells that line these airways. We performed a single cell RNA-seq census of small and large airways of wild-type pigs and pigs with disrupted cystic fibrosis transmembrane conductance regulator (CFTR) gene. The sequencing data showed that small airway epithelia had similar major cell types as large airways but no ionocytes; moreover, lack of CFTR expression had minimal effect on the transcriptome. Small airway epithelial cells expressed a different transcriptome than large airway cells. Quantitative immunohistochemistry showed that small airway basal cells participate in epithelial barrier function. Finally, sequencing data and in vitro electrophysiologic studies suggest that small airway epithelia have a water and ion transport advantage. Our data highlight the archetypal nature of basal, secretory, and ciliated airway cell...
Antimicrobial Stewardship & Healthcare Epidemiology, 2021
Background: COVID-19 in hospitalized patients may be the result of community acquisition or in-ho... more Background: COVID-19 in hospitalized patients may be the result of community acquisition or in-hospital transmission. Molecular epidemiology can help confirm hospital COVID-19 transmission and outbreaks. We describe large COVID-19 clusters identified in our hospital and apply molecular epidemiology to confirm outbreaks. Methods: The University of Iowa Hospitals and Clinics is an 811-bed academic medical center. We identified large clusters involving patients with hospital onset COVID-19 detected during March–October 2020. Large clusters included ≥10 individuals (patients, visitors, or HCWs) with a laboratory confirmed COVID-19 diagnosis (RT-PCR) and an epidemiologic link. Epidemiologic links were defined as hospitalization, work, or visiting in the same unit during the incubation or infectious period for the index case. Hospital onset was defined as a COVID-19 diagnosis ≥14 days from admission date. Admission screening has been conducted since May 2020 and serial testing (every 5 da...
Goblet cell metaplasia and mucus hyper-production are key features of chronic muco-obstructive lu... more Goblet cell metaplasia and mucus hyper-production are key features of chronic muco-obstructive lung diseases such as asthma, chronic bronchitis, and cystic fibrosis. Various mechanisms lead to goblet cell metaplasia in the airways; the driving mechanism for goblet cell metaplasia in a specific patient may be unknown. We recently found that heat shock protein 90 (HSP90) is important for both IL-13- and IL-17- induced airway goblet cell metaplasia. HSP90 interacts with multiple clients that are important in goblet cell metaplasia including Akt, Jak/STAT, IRS, Notch, and various kinases involved in NFκB signaling. Here, we used a targeted phospho-proteomic approach to identify candidate HSP90 clients modulated by the HSP90-inhibitor geldanamycin. NFκB family members were enriched amongst the top candidate targets of HSP90 inhibition in IL-13 an organotypic model of human airway epithelia. We hypothesized that HSP90 inhibition modulated goblet cell metaplasia by interfering with NFκB si...
Proceedings of the National Academy of Sciences, 2010
People with cystic fibrosis (CF) exhibit growth defects. That observation has been attributed, in... more People with cystic fibrosis (CF) exhibit growth defects. That observation has been attributed, in part, to decreased insulin-like growth factor 1 (IGF1) levels, and the reduction has been blamed on malnutrition and pulmonary inflammation. However, patients with CF already have a reduced weight at birth, a manifestation not likely secondary to poor nutrition or inflammation. We found that, like humans, CF pigs were smaller than non-CF littermates and had lower IGF1 levels. To better understand the basis of IGF1 reduction, we studied newborn pigs and found low IGF1 levels within 12 h of birth. Moreover, humerus length and bone mineral content were decreased, consistent with less IGF1 activity in utero. These findings led us to test newborn humans with CF, and we found that they also had reduced IGF1 levels. Discovering lower IGF1 levels in newborn pigs and humans indicates that the decrease is not solely a consequence of malnutrition or pulmonary inflammation and that loss of cystic f...
Antimicrobial Stewardship & Healthcare Epidemiology
Background: Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrom... more Background: Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 RNA can be detected by real-time reverse-transcription polymerase chain reaction (RT-PCR) for several weeks after infection. Discerning persistent RT-PCR positivity versus reinfection is challenging and the frequency of COVID-19 reinfections is unknown. We aimed to determine the frequency of clinically suspected reinfection in our center and confirm reinfection using viral whole-genome sequencing (WGS). Methods: The University of Iowa Hospitals and Clinics (UIHC) is an 811-bed academic medical center. Patients with respiratory complaints undergo COVID-19 RT-PCR using nasopharyngeal swabs. The RT-PCR (TaqPath COVID-19 Combo kit) uses 3 targets (ORF1ab, S gene, and N gene). We identified patients with previous laboratory-confirmed COVID-19 who sought care for new respiratory complaints and underwent a repeated SARS-CoV-2 test at least 45 days from t...
Rationale: Methicillin resistant Staphylococcus aureus (MRSA) is prevalent and consequential in c... more Rationale: Methicillin resistant Staphylococcus aureus (MRSA) is prevalent and consequential in cystic fibrosis (CF). Whole genome sequencing (WGS) could reveal genomic differences in MRSA associated with poorer outcomes or detect MRSA transmission. Objectives: To identify MRSA genes associated with low lung function and identify potential MRSA transmission in CF. Methods: We collected 97 MRSA isolates from 74 individuals with CF from 2017 and performed short-read WGS. We determined sequence type (ST) and the phylogenetic relationship between isolates. We aligned accessory genes from 25 reference genomes to genome assemblies. We classified the MRSA by accessory gene content and correlated the accessory genome to clinical outcomes. Results: The most prevalent ST were ST5 (N=55), ST105 (N=14), and ST8 (N=14). Closely related MRSA strains were shared by family members with CF, but rarely between unrelated individuals. Three distinct clusters of MRSA were identified by accessory genome ...
Infection Control and Hospital Epidemiology, 2021
Miguel E. Ortiz MD1a , Takaaki Kobayashi MD1a, Katherine Imborek MD1, Mohammed Alsuhaibani MBBS1,... more Miguel E. Ortiz MD1a , Takaaki Kobayashi MD1a, Katherine Imborek MD1, Mohammed Alsuhaibani MBBS1, Stephanie Holley MBA1, Alexandra Trannel MS1, Alexandre R. Marra MD, PhD12, William Etienne MD1, Kyle E. Jenn BSN1, Oluchi J. Abosi MBChB, MPH1, Holly MeachamMSN1, Lorinda Sheeler PhD1, Angelique Dains BSN1, Mary E. Kukla BSN1, Paul B. McCrayJr MD1, Stanley PerlmanMD, PhD1, Bradley FordMD, PhD1, Daniel J. DiekemaMD1, Melanie Wellington MD, PhD1, Alejandro A. Pezzulo MD1b and Jorge L. Salinas MD1b 1University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, Iowa, United States and 2Instituto Israelita de Ensino e Pesquisa Albert Einstein, Hospital Israelita Albert Einstein, São Paulo, Brazil
Background: The COVID-19 pandemic has created personal protective equipment (PPE) shortages, part... more Background: The COVID-19 pandemic has created personal protective equipment (PPE) shortages, particularly ofN95 respirators. Institutions have used decontamination strategies including vaporous hydrogen peroxide (VHP) to augment respirator supplies. VHP can be used to decontaminate nonporous surfaceswithout compromisingmaterial integrity.However, little is known about its impact on N95 respirator efficacy. We assessed whether repeated VHP reprocessing altered 4 key respirator efficacy qualities: quantitative fit, qualitative fit, seal check, and filtration rate. Methods: We conducted a prospective cohort study from June 15 to August 31, 2020. In total, 7 participants were fitted to a 3M 1860 small or regular N95 respirator basedonqualitativeandquantitative fit testing.Respiratorsunderwent25disinfection cycles with the Bioquell BQ-50 VHP generator. After each cycle, participants donned and doffed respirators and performed a seal check. Participants were given 2 attempts to pass their...
Hypocapnia/alkalosis is a consequence of several lung and metabolic pathologies. The aim of this ... more Hypocapnia/alkalosis is a consequence of several lung and metabolic pathologies. The aim of this study was to determine whether the increase of fluid filtration rate (FFR) that occurs during Hypocapnia/alkalosis circumstances is determined by hypocapnia, alkalosis or both. 7 groups were formed (N=36) using isolated rabbit lungs. Group 1: Control (PCO2 6%, pH: 7.35-7.45); Group 2 (n=6): Hypocapnia/Alkalosis (CO2 1%, pH: 7.9); Group 3 (n=6): Hypocapnia/Normo-pH (CO2 1% pH 7.35-7.45), Group 4 (n=6) Normocapnia/Alcalosis (CO2 6%, pH: 7.9). Fenoterol, papaverine and hydrocortisone were added to Groups 5, 6 and 7 (n=4) respectively, all under Normocapnia/Alkalosis. FFR and Pulmonary Arterial Pressure (Pap) were considerably higher in group 2 than in control (FFR: 1.92g/min +/- 0.6 vs 0.0 g/min +/- 0.006). A strong influence exerted by pH was observed when Group 3 and group 4 were compared (FFR: 0.02 g/min +/- 0.009 vs 2.3 g/min +/- 0.9) and (Pap: 13.5 cmH2O +/- 1.4 vs 90 cmH2O +/- 15). A ...
The use of Positive end-expiratory pressure (PEEP) as a strategy of mechanical ventilation offers... more The use of Positive end-expiratory pressure (PEEP) as a strategy of mechanical ventilation offers its advantages, such as improved oxygenation, without causing alveolar overstretching and barotrauma. We aim to investigate the effect of several levels of PEEP on barotrauma and, whether an optimal level of PEEP exists. Forty-eight New Zealand rabbits (2.5-3.5 kg) were divided into four groups with PEEP settings of 0, 4, 8 and 12 cmH2O, at increasing levels of inspiratory volume (IV). This was done in blood perfused rabbit lungs and in lungs perfused with a Buffer-Albumin Solution. We observed that lungs ventilated with PEEP 0 cmH2O suffered pulmonary rupture at high IV (300cc), with significant increases of Pap (Pulmonary artery pressure) and FFR (Fluid filtration rate). Lungs ventilated with PEEP 8 and 12 suffered pulmonary rupture at lower IV (200cc and 150cc vs. 300cc respectively) On the other hand, lungs ventilated with PEEP 4 cmH2O reached the highest IV (400cc), in addition, th...
Ischemia-reperfusion (IR) lung injury is a significant cause of morbidity and mortality in certai... more Ischemia-reperfusion (IR) lung injury is a significant cause of morbidity and mortality in certain clinical scenarios that include transplantation, thromboendarterectomy and reexpansion injury of the lung. Edema of the contralateral lung after IR injury of one lung has been reported and this study was aimed to clarify the pathophysiology of this phenomenon. One-lung ischemia/hypoxia followed by reperfusion with either blood or an acellular plasma substitute was achieved in an isolated rabbit lung model by hilum clamping. After reperfusion, we studied the isolated effects of vasoconstriction and inflammation on contralateral lung injury by using papaverine or hydrocortisone as vasodilator and anti-inflammatory, respectively. We observed that IR of one lung induces edema of the contralateral lung. Absence of leukocytes and platelets in the perfusate or use of hydrocortisone completely inhibits IR injury. Moreover, papaverine suppresses edema of the contralateral, but not that of the r...
Scientific Reports
RNA sequencing enables high-content/high-complexity measurements in small molecule screens. Where... more RNA sequencing enables high-content/high-complexity measurements in small molecule screens. Whereas the costs of DNA sequencing and RNA-seq library preparation have decreased consistently, RNA extraction remains a significant bottleneck to scalability. We evaluate the performance of a bulk RNA-seq library prep protocol optimized for analysis of many samples of adherent cultured cells in parallel. We combined a low-cost direct lysis buffer compatible with cDNA synthesis (in-lysate cDNA synthesis) with Smart-3SEQ and examine the effects of calmidazolium and fludrocortisone-induced perturbation of primary human dermal fibroblasts. We compared this method to normalized purified RNA inputs from matching samples followed by Smart-3SEQ or Illumina TruSeq library prep. Our results show the minimal effect of RNA loading normalization on data quality, measurement of gene expression patterns, and generation of differentially expressed gene lists. We found that in-lysate cDNA synthesis combined...
Clinical transplantation, Jan 10, 2017
Idiopathic hyperammonemia syndrome (IHS) is an uncommon, often deadly complication of solid organ... more Idiopathic hyperammonemia syndrome (IHS) is an uncommon, often deadly complication of solid organ transplantation. IHS cases in solid organ transplantation seem to occur predominantly in lung transplant (LTx) recipients. However, to the best of our knowledge, the occurrence of IHS has not been systematically evaluated. We set out to identify all reported cases of IHS following nonliver solid organ transplantations. Retrospective review of our institutional experience and systematic review of the literature. At our institution six cases (of 844 nonliver solid organ transplants) of IHS were identified: five occurred following LTx (incidence 3.9% [lung] vs 0.1% [nonlung], P=.004). In the systematic review, 16 studies met inclusion criteria, reporting on 32 cases of IHS. The majority of IHS cases in the literature (81%) were LTx-recipients. The average peak reported ammonia level was 1039 μmol/L occurring on average 14.7 days post-transplant. Mortality in previously reported IHS cases w...
Annals of the American Thoracic Society, 2016
A 32-year-old man was admitted to the intensive care unit for emergent management of acute decomp... more A 32-year-old man was admitted to the intensive care unit for emergent management of acute decompensated liver failure, an enlarging pleural effusion, and hemorrhagic shock caused by variceal bleeding. He had a history of alcoholic cirrhosis and rightsided hepatic hydrothorax, managed medically. After volume resuscitation and banding of esophageal varices, the patient’s blood pressure normalized, serum lactate cleared, and mental status improved. Over the next 12 hours, he again became hypotensive, with cool extremities, encephalopathy, dyspnea, and rising lactic acid levels. There was no overt gastrointestinal bleeding or obvious infection. His blood pressure did not respond to intravenous fluids. Point-of-care ultrasound was used to evaluate the cause of shock, as illustrated in the parasternal long-axis (Video 1), apical four-chamber (Video 2), and subcostal views (Video 3).
Investigacion Clinica, 2007
Efec to de los cam bios de pre sión de vía aé rea, vo lu men ins pi ra to rio y fe no te rol so b... more Efec to de los cam bios de pre sión de vía aé rea, vo lu men ins pi ra to rio y fe no te rol so bre la tasa de fil tra ción de lí qui dos y la pre sión de ar te ria pul mo nar en pul mo nes de co ne jos ais la dos y per fun di dos con san gre y con so lu ción ace lu lar.
Amer J Respir Crit Care Med, 2010
David K. Meyerholz 1 , David A. Stoltz 2 , Eman Namati 2,8 , Shyam Ramachandran 3 , Alejandro A. ... more David K. Meyerholz 1 , David A. Stoltz 2 , Eman Namati 2,8 , Shyam Ramachandran 3 , Alejandro A. ... Pezzulo 2 , Amanda R. Smith 2 , Michael V. Rector 2 , Melissa J. Suter 8 , Simon Kao 4 , Geoffrey ... McLennan 2,4,5 , Guillermo J. Tearney 8 , Joseph Zabner 2 , Paul B. ...