Last data update: May 06, 2024. (Total: 46732 publications since 2009)
Records 1-30 (of 119 Records) |
Query Trace: Chow C[original query] |
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A teenage girl with altered mental status and paraparesis
Miyakawa R , Louie J , Keh C , Chen L , Javid B , Ernst JD , Goswami N , Chow FC . J Clin Tuberc Other Mycobact Dis 2024 35 100425 A teenage girl presented with fever and altered mental status. MRI showed diffuse leptomeningeal enhancement of the brain and spine. She was diagnosed by a positive cerebrospinal fluid (CSF) culture with tuberculous (TB) meningitis and was started on anti-TB medications and corticosteroids. Her mental status improved, but she was noted to have proximal weakness of the lower extremities. In the course of tapering corticosteroids at week 11 of anti-TB therapy, she became acutely confused and febrile. MRI demonstrated interval development of tuberculomas in the brain and a mass lesion in the thoracic spine causing cord compression. Given the clinical picture was suggestive of a paradoxical reaction, the dose of corticosteroids was increased. Infliximab was added when repeat MRI revealed enlargement of the mass lesion in the spine with worsening cord compression. She was successfully tapered off of corticosteroids. Over several months, the patient's motor function recovered fully, and she returned to ambulating without assistance. |
Remote surveillance and detection of SARS-CoV-2 transmission among household members in King County, Washington
Emanuels A , Casto AM , Heimonen J , O'Hanlon J , Chow EJ , Ogokeh C , Rolfes MA , Han PD , Hughes JP , Uyeki TM , Frazar C , Chung E , Starita LM , Englund JA , Chu HY . BMC Infect Dis 2024 24 (1) 309 BACKGROUND: Early during the COVID-19 pandemic, it was important to better understand transmission dynamics of SARS-CoV-2, the virus that causes COVID-19. Household contacts of infected individuals are particularly at risk for infection, but delays in contact tracing, delays in testing contacts, and isolation and quarantine posed challenges to accurately capturing secondary household cases. METHODS: In this study, 346 households in the Seattle region were provided with respiratory specimen collection kits and remotely monitored using web-based surveys for respiratory illness symptoms weekly between October 1, 2020, and June 20, 2021. Symptomatic participants collected respiratory specimens at symptom onset and mailed specimens to the central laboratory in Seattle. Specimens were tested for SARS-CoV-2 using RT-PCR with whole genome sequencing attempted when positive. SARS-CoV-2-infected individuals were notified, and their household contacts submitted specimens every 2 days for 14 days. RESULTS: In total, 1371 participants collected 2029 specimens that were tested; 16 individuals (1.2%) within 6 households tested positive for SARS-CoV-2 during the study period. Full genome sequences were generated from 11 individuals within 4 households. Very little genetic variation was found among SARS-CoV-2 viruses sequenced from different individuals in the same household, supporting transmission within the household. CONCLUSIONS: This study indicates web-based surveillance of respiratory symptoms, combined with rapid and longitudinal specimen collection and remote contact tracing, provides a viable strategy to monitor households and detect household transmission of SARS-CoV-2. TRIAL REGISTRATION IDENTIFIER: NCT04141930, Date of registration 28/10/2019. |
Emergence of zoonotic sporotrichosis in Brazil: a genomic epidemiology study
Ribeiro Dos Santos A , Misas E , Min B , Le N , Bagal UR , Parnell LA , Sexton DJ , Lockhart SR , de Souza Carvalho Melhem M , Takahashi JPF , Oliboni GM , Bonfieti LX , Cappellano P , Sampaio JLM , Araujo LS , Alves Filho HL , Venturini J , Chiller TM , Litvintseva AP , Chow NA . Lancet Microbe 2024 BACKGROUND: Zoonotic sporotrichosis is a neglected fungal disease, whereby outbreaks are primarily driven by Sporothrix brasiliensis and linked to cat-to-human transmission. To understand the emergence and spread of sporotrichosis in Brazil, the epicentre of the current epidemic in South America, we aimed to conduct whole-genome sequencing (WGS) to describe the genomic epidemiology. METHODS: In this genomic epidemiology study, we included Sporothrix spp isolates from sporotrichosis cases from Brazil, Colombia, and the USA. We conducted WGS using Illumina NovaSeq on isolates collected by three laboratories in Brazil from humans and cats with sporotrichosis between 2013 and 2022. All isolates that were confirmed to be Sporothrix genus by internal transcribed spacer or beta-tubulin PCR sequencing were included in this study. We downloaded eight Sporothrix genome sequences from the National Center for Biotechnology Information (six from Brazil, two from Colombia). Three Sporothrix spp genome sequences from the USA were generated by the US Centers for Disease Control and Prevention as part of this study. We did phylogenetic analyses and correlated geographical and temporal case distribution with genotypic features of Sporothrix spp isolates. FINDINGS: 72 Sporothrix spp isolates from 55 human and 17 animal sporotrichosis cases were included: 67 (93%) were from Brazil, two (3%) from Colombia, and three (4%) from the USA. Cases spanned from 1999 to 2022. Most (61 [85%]) isolates were S brasiliensis, and all were reported from Brazil. Ten (14%) were Sporothrix schenckii and were reported from Brazil, USA, and Colombia. For S schenckii isolates, two distinct clades were observed wherein isolates clustered by geography. For S brasiliensis isolates, five clades separated by more than 100 000 single-nucleotide polymorphisms were observed. Among the five S brasiliensis clades, clades A and C contained isolates from both human and cat cases, and clade A contained isolates from six different states in Brazil. Compared with S brasiliensis isolates, larger genetic diversity was observed among S schenckii isolates from animal and human cases within a clade. INTERPRETATION: Our results suggest that the ongoing epidemic driven by S brasiliensis in Brazil represents several, independent emergence events followed by animal-to-animal and animal-to human transmission within and between Brazilian states. These results describe how S brasiliensis can emerge and spread within a country. FUNDING: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Brazil; the São Paulo Research Foundation; Productivity in Research fellowships by the National Council for Scientific and Technological Development, and Ministry of Science and Technology of Brazil. |
Genomic description of acquired fluconazole- and echinocandin-resistance in patients with serial Candida glabrata isolates
Misas E , Seagle E , Jenkins EN , Rajeev M , Hurst S , Nunnally NS , Bentz ML , Lyman MM , Berkow E , Harrison LH , Schaffner W , Markus TM , Pierce R , Farley MM , Chow NA , Lockhart SR , Litvintseva AP . J Clin Microbiol 2024 e0114023 Candida glabrata is one of the most common causes of systemic candidiasis, often resistant to antifungal medications. To describe the genomic context of emerging resistance, we conducted a retrospective analysis of 82 serially collected isolates from 33 patients from population-based candidemia surveillance in the United States. We used whole-genome sequencing to determine the genetic relationships between isolates obtained from the same patient. Phylogenetic analysis demonstrated that isolates from 29 patients were clustered by patient. The median SNPs between isolates from the same patient was 30 (range: 7-96 SNPs), while unrelated strains infected four patients. Twenty-one isolates were resistant to echinocandins, and 24 were resistant to fluconazole. All echinocandin-resistant isolates carried a mutation either in the FKS1 or FKS2 HS1 region. Of the 24 fluconazole-resistant isolates, 17 (71%) had non-synonymous polymorphisms in the PDR1 gene, which were absent in susceptible isolates. In 11 patients, a genetically related resistant isolate was collected after recovering susceptible isolates, indicating in vivo acquisition of resistance. These findings allowed us to estimate the intra-host diversity of C. glabrata and propose an upper boundary of 96 SNPs for defining genetically related isolates, which can be used to assess donor-to-host transmission, nosocomial transmission, or acquired resistance.IMPORTANCEIn our study, mutations associated to azole resistance and echinocandin resistance were detected in Candida glabrata isolates using a whole-genome sequence. C. glabrata is the second most common cause of candidemia in the United States, which rapidly acquires resistance to antifungals, in vitro and in vivo. |
Finding Candida auris in public metagenomic repositories
Mario-Vasquez JE , Bagal UR , Lowe E , Morgulis A , Phan J , Sexton DJ , Shiryev S , Slatkevičius R , Welsh R , Litvintseva AP , Blumberg M , Agarwala R , Chow NA . PLoS One 2024 19 (1) e0291406 Candida auris is a newly emerged multidrug-resistant fungus capable of causing invasive infections with high mortality. Despite intense efforts to understand how this pathogen rapidly emerged and spread worldwide, its environmental reservoirs are poorly understood. Here, we present a collaborative effort between the U.S. Centers for Disease Control and Prevention, the National Center for Biotechnology Information, and GridRepublic (a volunteer computing platform) to identify C. auris sequences in publicly available metagenomic datasets. We developed the MetaNISH pipeline that uses SRPRISM to align sequences to a set of reference genomes and computes a score for each reference genome. We used MetaNISH to scan ~300,000 SRA metagenomic runs from 2010 onwards and identified five datasets containing C. auris reads. Finally, GridRepublic has implemented a prospective C. auris molecular monitoring system using MetaNISH and volunteer computing. |
Outcome and sequelae of autoimmune encephalitis
Kvam KA , Stahl JP , Chow FC , Soldatos A , Tattevin P , Sejvar J , Mailles A . J Clin Neurol 2024 20 (1) 3-22 Autoimmune etiologies are a common cause for encephalitis. The clinical syndromes consistent with autoimmune encephalitis are both distinct and increasingly recognized, but less is known about persisting sequelae or outcomes. We searched PubMed for reports on outcomes after autoimmune encephalitis. Studies assessing validated, quantitative outcomes were included. We performed a narrative review of the published literature of outcomes after autoimmune encephalitis. We found 146 studies that produced outcomes data. The mortality rates were 6%-19% and the relapse risks were 10%-62%. Most patients achieved a good outcome based on a score on the modified Rankin Scale (mRS) of ≤2. Forty-nine studies evaluated outcomes beyond mRS; these studies investigated cognitive outcome, psychiatric sequelae, neurological deficits, global function, and quality-of-life/patient-reported outcomes using various tools at varying time points after the index hospital discharge. These more-detailed assessments revealed that most patients had persistent impairments, with frequent deficits in cognitive function, especially memory and attention. Depression and anxiety were also common. Many of these sequelae continued to improve over months or even years after the acute illness. While we found that lasting impairments were common among survivors of autoimmune encephalitis, additional research is needed to better understand the nature and impact of these sequelae. Standardized evaluation protocols are needed to improve the ability to compare outcomes across studies, guide rehabilitation strategies, and inform outcomes of interest in treatment trials as the field advances. |
Outcome and sequelae of infectious encephalitis
Kvam KA , Stahl JP , Chow FC , Soldatos A , Tattevin P , Sejvar J , Mailles A . J Clin Neurol 2024 20 (1) 23-36 Acute infectious encephalitis is a widely studied clinical syndrome. Although identified almost 100 years ago, its immediate and delayed consequences are still neglected despite their high frequency and possible severity. We reviewed the available data on sequelae and persisting symptoms following infectious encephalitis with the aim of characterizing the clinical picture of these patients at months to years after hospitalization. We searched PubMed for case series involving sequelae after infectious encephalitis. We carried out a narrative review of the literature on encephalitis caused by members of the Herpesviridae family (herpes simplex virus, varicella zoster virus, and human herpesvirus-6), members of the Flaviviridae family (West Nile virus, tick-borne encephalitis virus, and Japanese encephalitis virus), alphaviruses, and Nipah virus. We retrieved 41 studies that yielded original data involving 3,072 adult patients evaluated after infectious encephalitis. At least one of the five domains of cognitive outcome, psychiatric disorders, neurological deficits, global functioning, and quality of life was investigated in the reviewed studies. Various tests were used in the 41 studies and the investigation took place at different times after hospital discharge. The results showed that most patients are discharged with impairments, with frequent deficits in cognitive function such as memory loss or attention disorders. Sequelae tend to improve within several years following flavivirus or Nipah virus infection, but long-term data are scarce for other pathogens. Further research is needed to better understand the extent of sequelae after infectious encephalitis, and to propose a standardized assessment method and assess the rehabilitation efficacy in these patients. |
High-fat Western diet alters crystalline silica-induced airway epithelium ion transport but not airway smooth muscle reactivity
Thompson JA , Kashon ML , McKinney W , Fedan JS . BMC Res Notes 2024 17 (1) 13 OBJECTIVES: Silicosis is an irreversible occupational lung disease resulting from crystalline silica inhalation. Previously, we discovered that Western diet (HFWD)-consumption increases susceptibility to silica-induced pulmonary inflammation and fibrosis. This study investigated the potential of HFWD to alter silica-induced effects on airway epithelial ion transport and smooth muscle reactivity. METHODS: Six-week-old male F344 rats were fed a HFWD or standard rat chow (STD) and exposed to silica (Min-U-Sil 5(®), 15 mg/m(3), 6 h/day, 5 days/week, for 39 d) or filtered air. Experimental endpoints were measured at 0, 4, and 8 weeks post-exposure. Transepithelial potential difference (V(t)), short-circuit current (I(SC)) and transepithelial resistance (R(t)) were measured in tracheal segments and ion transport inhibitors [amiloride, Na(+) channel blocker; NPPB; Cl- channel blocker; ouabain, Na(+), K(+)-pump blocker] identified changes in ion transport pathways. Changes in airway smooth muscle reactivity to methacholine (MCh) were investigated in the isolated perfused trachea preparation. RESULTS: Silica reduced basal I(SC) at 4 weeks and HFWD reduced the I(SC) response to amiloride at 0 week compared to air control. HFWD + silica exposure induced changes in ion transport 0 and 4 weeks after treatment compared to silica or HFWD treatments alone. No effects on airway smooth muscle reactivity to MCh were observed. |
Vaccine value profile for Neisseria gonorrhoeae
Lyu Y , Choong A , Chow EPF , Seib KL , Marshall HS , Unemo M , de Voux A , Wang B , Miranda AE , Gottlieb SL , Mello MB , Wi T , Baggaley R , Marshall C , Abu-Raddad LJ , Abara WE , Chen XS , Ong JJ . Vaccine 2023 Neisseria gonorrhoeae infection (gonorrhoea) is a global public health challenge, causing substantial sexual and reproductive health consequences, such as infertility, pregnancy complications and increased acquisition or transmission of HIV. There is an urgency to controlling gonorrhoea because of increasing antimicrobial resistance to ceftriaxone, the last remaining treatment option, and the potential for gonorrhoea to become untreatable. No licensed gonococcal vaccine is available. Mounting observational evidence suggests that N. meningitidis serogroup B outer membrane vesicle-based vaccines may induce cross-protection against N. gonorrhoeae (estimated 30%-40% effectiveness using the 4CMenB vaccine). Clinical trials to determine the efficacy of the 4CMenB vaccine against N. gonorrhoeae are underway, as are Phase 1/2 studies of a new gonococcal-specific vaccine candidate. Ultimately, a gonococcal vaccine must be accessible, affordable and equitably dispensed, given that those most affected by gonorrhoea are also those who may be most disadvantaged in our societies, and most cases are in less-resourced settings. This vaccine value profile (VVP) provides a high level, holistic assessment of the current data to inform the potential public health, economic and societal value of pipeline vaccines. This was developed by a working group of subject matter experts from academia, non-profit organizations, public private partnerships and multi-lateral organizations. All contributors have extensive expertise on various elements of the N. gonorrhoeae VVP and collectively aimed to identify current research and knowledge gaps. The VVP was developed using published data obtained from peer-reviewed journals or reports. |
A phylogeographic description of histoplasma capsulatum in the United States
Bagal UR , Gade L , Benedict K , Howell V , Christophe N , Gibbons-Burgener S , Hallyburton S , Ireland M , McCracken S , Metobo AK , Signs K , Warren KA , Litvintseva AP , Chow NA . J Fungi (Basel) 2023 9 (9) Histoplasmosis is one of the most under-diagnosed and under-reported endemic mycoses in the United States. Histoplasma capsulatum is the causative agent of this disease. To date, molecular epidemiologic studies detailing the phylogeographic structure of H. capsulatum in the United States have been limited. We conducted genomic sequencing using isolates from histoplasmosis cases reported in the United States. We identified North American Clade 2 (NAm2) as the most prevalent clade in the country. Despite high intra-clade diversity, isolates from Minnesota and Michigan cases were predominately clustered by state. Future work incorporating environmental sampling and veterinary surveillance may further elucidate the molecular epidemiology of H. capsulatum in the United States and how genomic sequencing can be applied to the surveillance and outbreak investigation of histoplasmosis. |
Candida auris: a global pathogen that has taken root in Colombia
Escandón P , Lockhart SR , Chow NA , Chiller TM . Biomedica 2023 43 278-287 Candida auris has been recognized as an emerging multidrug-resistant pathogen with a significant public health burden, causing cases of invasive infection and colonization due to its persistence on inanimate surfaces, ability to colonize skin of some patients, and high transmissibility in healthcare settings. The first sporadic report of the isolation of this species from the ear canal of a patient in Asia was in 2009 and reports from other regions of the world soon followed. However, it was not until 2015 that global epidemiological alerts were communicated as a result of an increasing number of reports of invasive infections caused by C. auris in several countries. Colombia was soon added to this list in 2016 after an unusual increase in the number of C. haemulonii isolates was reported, later confirmed as C. auris. Since the issuing of a national alert by the Colombian National Institute of Health together with the Ministry of Health in 2016, the number of cases reported reached over 2,000 by 2022. Colombian isolates have not shown pan resistance to available antifungals, unlike C. auris strains reported in other regions of the world, which leaves patients in Colombia with therapeutic options for these infections. However, increasing fluconazole resistance is being observed. Whole-genome sequencing of Colombian C. auris isolates has enhanced molecular epidemiological data, grouping Colombian isolates in clade IV together with other South American isolates. |
Public health research priorities for fungal diseases: A multidisciplinary approach to save lives
Smith DJ , Gold JAW , Benedict K , Wu K , Lyman M , Jordan A , Medina N , Lockhart SR , Sexton DJ , Chow NA , Jackson BR , Litvintseva AP , Toda M , Chiller T . J Fungi (Basel) 2023 9 (8) Fungal infections can cause severe disease and death and impose a substantial economic burden on healthcare systems. Public health research requires a multidisciplinary approach and is essential to help save lives and prevent disability from fungal diseases. In this manuscript, we outline the main public health research priorities for fungal diseases, including the measurement of the fungal disease burden and distribution and the need for improved diagnostics, therapeutics, and vaccines. Characterizing the public health, economic, health system, and individual burden caused by fungal diseases can provide critical insights to promote better prevention and treatment. The development and validation of fungal diagnostic tests that are rapid, accurate, and cost-effective can improve testing practices. Understanding best practices for antifungal prophylaxis can optimize prevention in at-risk populations, while research on antifungal resistance can improve patient outcomes. Investment in vaccines may eliminate certain fungal diseases or lower incidence and mortality. Public health research priorities and approaches may vary by fungal pathogen. |
Risk of subsequent respiratory virus detection after primary virus detection in a community household study - King County, Washington 2019-2021
Heimonen J , Chow EJ , Wang Y , Hughes JP , Rogers J , Emanuels A , O'Hanlon J , Han PD , Wolf CR , Logue JK , Ogokeh CE , Rolfes MA , Uyeki TM , Starita L , Englund JA , Chu HY . J Infect Dis 2023 BACKGROUND: The epidemiology of respiratory viral infections is complex. How infection with one respiratory virus affects risk of subsequent infection with the same or another respiratory virus is not well described. METHODS: We retrospectively analyzed data from a longitudinal household cohort study from October 2019-June 2021. Enrolled households completed active surveillance for acute respiratory illness (ARI), and participants with ARI self-collected nasal swabs; after April 2020, participants with ARI or laboratory-confirmed SARS-CoV-2 and their household members self-collected nasal swabs. Specimens were tested via multiplex RT-PCR for respiratory viruses. A Cox regression model with a time-dependent covariate examined risk of subsequent detections following a specific primary viral detection. RESULTS: Rhinovirus was the most frequently detected pathogen in study specimens (n=406, 9.5%). Among 51 participants with multiple viral detections, rhinovirus to seasonal coronavirus (8, 14.8%) was the most common viral detection pairing. Relative to no primary detection, there was a 1.03-2.06-fold increase in risk of subsequent virus detection in the 90 days following primary detection; risk varied by primary virus: parainfluenza, rhinovirus, and respiratory syncytial virus were statistically significant. CONCLUSIONS: Primary virus detection was associated with higher risk of subsequent virus detection within the first 90 days after primary detection. |
Tracing the evolutionary history and global expansion of Candida auris using population genomic analyses (preprint)
Chow NA , Munoz JF , Gade L , Berkow EL , Li X , Welsh RM , Forsberg K , Lockhart SR , Adam R , Alanio A , Alastruey-Izquierdo A , Althawadi S , Arauz AB , Ben-Ami R , Bharat A , Calvo B , Desnos-Ollivier M , Escandon P , Gardam D , Gunturu R , Heath CH , Kurzai O , Martin R , Litvintseva AP , Cuomo CA . bioRxiv 2020 2020.01.06.896548 Candida auris has emerged globally as a multidrug-resistant yeast that can spread via nosocomial transmission. An initial phylogenetic study of isolates from Japan, India, Pakistan, South Africa, and Venezuela revealed four populations (Clades I, II, III, and IV) corresponding to these geographic regions. Since this description, C. auris has been reported in over 30 additional countries. To trace this global emergence, we compared the genomes of 304 C. auris isolates from 19 countries on six continents. We found that four predominant clades persist across wide geographic locations. We observed phylogeographic mixing in most clades; Clade IV, with isolates mainly from South America, demonstrated the strongest phylogeographic substructure. C. auris isolates from two clades with opposite mating types were detected contemporaneously in a single healthcare facility in Kenya. We estimated a Bayesian molecular clock phylogeny and dated the origin of each clade within the last 339 years; outbreak-causing clusters from Clades I, III, and IV originated 34-35 years ago. We observed high rates of antifungal resistance in Clade I, including four isolates resistant to all three major classes of antifungals. Mutations that contribute to resistance varied between the clades, with Y132F in ERG11 as the most widespread mutation associated with azole resistance and S639P in FKS1 for echinocandin resistance. Copy number variants in ERG11 predominantly appeared in Clade III and were associated with fluconazole resistance. These results provide a global context for the phylogeography, population structure, and mechanisms associated with antifungal resistance in C. auris.Importance In less than a decade, C. auris has emerged in healthcare settings worldwide; this species is capable of colonizing skin and causing outbreaks of invasive candidiasis. In contrast to other Candida species, C. auris is unique in its ability to spread via nosocomial transmission and its high rates of drug resistance. As part of the public health response, whole-genome sequencing has played a major role in characterizing transmission dynamics and detecting new C. auris introductions. Through a global collaboration, we assessed genome evolution of isolates of C. auris from 19 countries. Here, we described estimated timing of the expansion of each C. auris clade and of fluconazole resistance, characterized discrete phylogeographic population structure of each clade, and compared genome data to sensitivity measurements to describe how antifungal resistance mechanisms vary across the population. These efforts are critical for a sustained, robust public health response that effectively utilizes molecular epidemiology. |
Genomic basis of multidrug-resistance, mating, and virulence in Candida auris and related emerging species (preprint)
Munoz JF , Gade L , Chow NA , Loparev VN , Juieng P , Berkow EL , Farrer RA , Litvintseva AP , Cuomo CA . bioRxiv 2018 299917 Candida auris is an emergent fungal pathogen of rising public health concern due to increasing reports of outbreaks in healthcare settings and resistance to multiple classes of antifungal drugs. While distantly related to the more common pathogens C. albicans and C. glabrata, C. auris is closely related to three rarely observed and often multidrug-resistant species, C. haemulonii, C. duobushaemulonii and C. pseudohaemulonii. Here, we generated and analyzed near complete genome assemblies and RNA-Seq-guided gene predictions for isolates from each of the four major C. auris clades and for C. haemulonii, C. duobushaemulonii and C. pseudohaemulonii. Our analyses mapped seven chromosomes and revealed chromosomal rearrangements between C. auris clades and related species. We found conservation of genes involved in mating and meiosis and identified both MTLa and MTLα C. auris isolates, suggesting the potential for mating between clades. Gene conservation analysis highlighted that many genes linked to drug resistance and virulence in other pathogenic Candida species are conserved in C. auris and related species including expanded families of transporters and lipases, as well as mutations and copy number variants in ERG11 that confer drug resistance. In addition, we found genetic features of the emerging species that likely underlie differences in virulence and drug response between these and other Candida species, including genes involved in cell wall structure. To begin to characterize the species-specific genes important for antifungal response, we profiled the gene expression of C. auris in response to voriconazole and amphotericin B and found induction of several transporters and metabolic regulators that may play a role in drug resistance. This study provides a comprehensive view of the genomic basis of drug resistance, potential for mating, and virulence in this emerging fungal clade. |
COVID-19 reopening strategies at the county level in the face of uncertainty: Multiple Models for Outbreak Decision Support (preprint)
Shea K , Borchering RK , Probert WJM , Howerton E , Bogich TL , Li S , van Panhuis WG , Viboud C , Aguás R , Belov A , Bhargava SH , Cavany S , Chang JC , Chen C , Chen J , Chen S , Chen Y , Childs LM , Chow CC , Crooker I , Valle SYD , España G , Fairchild G , Gerkin RC , Germann TC , Gu Q , Guan X , Guo L , Hart GR , Hladish TJ , Hupert N , Janies D , Kerr CC , Klein DJ , Klein E , Lin G , Manore C , Meyers LA , Mittler J , Mu K , Núñez RC , Oidtman R , Pasco R , Piontti APY , Paul R , Pearson CAB , Perdomo DR , Perkins TA , Pierce K , Pillai AN , Rael RC , Rosenfeld K , Ross CW , Spencer JA , Stoltzfus AB , Toh KB , Vattikuti S , Vespignani A , Wang L , White L , Xu P , Yang Y , Yogurtcu ON , Zhang W , Zhao Y , Zou D , Ferrari M , Pannell D , Tildesley M , Seifarth J , Johnson E , Biggerstaff M , Johansson M , Slayton RB , Levander J , Stazer J , Salerno J , Runge MC . medRxiv 2020 Policymakers make decisions about COVID-19 management in the face of considerable uncertainty. We convened multiple modeling teams to evaluate reopening strategies for a mid-sized county in the United States, in a novel process designed to fully express scientific uncertainty while reducing linguistic uncertainty and cognitive biases. For the scenarios considered, the consensus from 17 distinct models was that a second outbreak will occur within 6 months of reopening, unless schools and non-essential workplaces remain closed. Up to half the population could be infected with full workplace reopening; non-essential business closures reduced median cumulative infections by 82%. Intermediate reopening interventions identified no win-win situations; there was a trade-off between public health outcomes and duration of workplace closures. Aggregate results captured twice the uncertainty of individual models, providing a more complete expression of risk for decision-making purposes. |
Incidence of SARS-CoV-2 infection and associated risk factors among staff and residents at homeless shelters in King County, Washington: an active surveillance study (preprint)
Rogers JH , Cox SN , Link AC , Nwanne G , Han PD , Pfau B , Chow EJ , Wolf CR , Boeckh M , Hughes JP , Halloran ME , Uyeki TM , Shim MM , Duchin J , Englund JA , Mosites E , Rolfes MA , Starita LA , Chu HY . medRxiv 2023 30 Homeless shelter residents and staff may be at higher risk of SARS-CoV-2 infection. However, SARS-CoV-2 infection estimates in this population have been reliant on cross-sectional or outbreak investigation data. We conducted routine surveillance and outbreak testing in 23 homeless shelters in King County, Washington to estimate the occurrence of laboratory-confirmed SARS-CoV-2 infection and risk factors during 1/1/2020 -5/31/2021. Symptom surveys and nasal swabs were collected for SARS-CoV-2 testing by RT-PCR for residents aged >=3 months and staff. We collected 12,915 specimens from 2,930 unique participants. We identified 4.74 (95% CI 4.00 - 5.58) SARS-CoV-2 infections per 100 individuals (residents: 4.96, 95% CI 4.12 - 5.91; staff: 3.86, 95% CI 2.43 - 5.79). Most infections were asymptomatic at time of detection (74%) and detected during routine surveillance (73%). Outbreak testing yielded higher test positivity compared to routine surveillance (2.7% vs. 0.9%). Among those infected, residents were less likely to report symptoms than staff. Participants who were vaccinated against seasonal influenza and were current smokers had lower odds of having an infection detected. Active surveillance that includes SARS-CoV-2 testing of all persons is essential in ascertaining the true burden of SARS-CoV-2 infections among residents and staff of congregate settings. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. |
Incidence of SARS-CoV-2 infection and associated risk factors among staff and residents at homeless shelters in King County, Washington: an active surveillance study
Rogers JH , Cox SN , Link AC , Nwanne G , Han PD , Pfau B , Chow EJ , Wolf CR , Boeckh M , Hughes JP , Halloran ME , Uyeki TM , Shim MM , Duchin J , Englund JA , Mosites E , Rolfes MA , Starita LA , Chu HY . Epidemiol Infect 2023 151 1-48 Homeless shelter residents and staff may be at higher risk of SARS-CoV-2 infection. However, | 34 SARS-CoV-2 infection estimates in this population have been reliant on cross-sectional or | 35 outbreak investigation data. We conducted routine surveillance and outbreak testing in 23 | 36 homeless shelters in King County, Washington to estimate the occurrence of laboratory37 confirmed SARS-CoV-2 infection and risk factors during 1/1/2020 -5/31/2021. Symptom surveys | 38 and nasal swabs were collected for SARS-CoV-2 testing by RT-PCR for residents aged ≥3 | 39 months and staff. We collected 12,915 specimens from 2,930 unique participants. We identified | 40 4.74 (95% CI 4.00 – 5.58) SARS-CoV-2 infections per 100 individuals (residents: 4.96, 95% CI | 41 4.12 – 5.91; staff: 3.86, 95% CI 2.43 – 5.79). Most infections were asymptomatic at time of | 42 detection (74%) and detected during routine surveillance (73%). Outbreak testing yielded higher | 43 test positivity compared to routine surveillance (2.7% vs. 0.9%). Among those infected, | 44 residents were less likely to report symptoms than staff. Participants who were vaccinated | 45 against seasonal influenza and were current smokers had lower odds of having an infection | 46 detected. Active surveillance that includes SARS-CoV-2 testing of all persons is essential in | 47 ascertaining the true burden of SARS-CoV-2 infections among residents and staff of congregate | 48 settings. |
Streptococcus pneumoniae nasal carriage patterns with and without common respiratory virus detections in households in Seattle, WA, USA before and during the COVID-19 pandemic
Bennett JC , Emanuels A , Heimonen J , O'Hanlon J , Hughes JP , Han PD , Chow EJ , Ogokeh CE , Rolfes MA , Lockwood CM , Pfau B , Uyeki TM , Shendure J , Hoag S , Fay K , Lee J , Sibley TR , Rogers JH , Starita LM , Englund JA , Chu HY . Front Pediatr 2023 11 1198278 BACKGROUND: Respiratory viruses might influence Streptococcus pneumoniae nasal carriage and subsequent disease risk. We estimated the association between common respiratory viruses and semiquantitative S. pneumoniae nasal carriage density in a household setting before and during the COVID-19 pandemic. METHODS: From November 2019-June 2021, we enrolled participants in a remote household surveillance study of respiratory pathogens. Participants submitted weekly reports of acute respiratory illness (ARI) symptoms. Mid-turbinate or anterior nasal swabs were self-collected at enrollment, when ARI occurred, and, in the second year of the study only, from household contacts after SARS-CoV-2 was detected in a household member. Specimens were tested using multiplex reverse-transcription PCR for respiratory pathogens, including S. pneumoniae, rhinovirus, adenovirus, common human coronavirus, influenza A/B virus, respiratory syncytial virus (RSV) A/B, human metapneumovirus, enterovirus, and human parainfluenza virus. We estimated differences in semiquantitative S. pneumoniae nasal carriage density, estimated by the inverse of S. pneumoniae relative cycle threshold (Crt) values, with and without viral detection for any virus and for specific respiratory viruses using linear generalized estimating equations of S. pneumoniae Crt values on virus detection adjusted for age and swab type and accounting for clustering of swabs within households. RESULTS: We collected 346 swabs from 239 individuals in 151 households that tested positive for S. pneumoniae (n = 157 with and 189 without ≥1 viruses co-detected). Difficulty breathing, cough, and runny nose were more commonly reported among individuals with specimens with viral co-detection compared to without (15%, 80% and 93% vs. 8%, 57%, and 51%, respectively) and ear pain and headache were less commonly reported (3% and 26% vs. 16% and 41%, respectively). For specific viruses among all ages, semiquantitative S. pneumoniae nasal carriage density was greater with viral co-detection for enterovirus, RSV A/B, adenovirus, rhinovirus, and common human coronavirus (P < 0.01 for each). When stratified by age, semiquantitative S. pneumoniae nasal carriage density was significantly greater with viral co-detection among children aged <5 (P = 0.002) and 5-17 years (P = 0.005), but not among adults aged 18-64 years (P = 0.29). CONCLUSION: Detection of common respiratory viruses was associated with greater concurrent S. pneumoniae semiquantitative nasal carriage density in a household setting among children, but not adults. |
Previous health care experiences' influence on health care perceptions among residents of six homeless shelters in Seattle, Washington, July-October 2021
Meehan AA , Cox SN , Thuo NB , Rogers JH , Link AC , Martinez MA , Lo NK , Manns BJ , Rolfes MA , Chow EJ , Chu HY , Mosites E , Al Achkar M . J Patient Cent Res Rev 2023 10 (3) 111-120 PURPOSE: The study purpose was to learn and describe 1) where homeless shelter residents receive health care, 2) what contributes to positive or negative health care experiences among shelter residents, and 3) shelter resident perceptions toward health care. METHODS: Semi-structured interviews (SSIs) utilizing purposive sampling and focus group discussions (FGDs) utilizing convenience sampling were conducted at 6 homeless shelters in Seattle-King County, Washington, during July-October 2021. All residents (age ≥18) were eligible to participate. SSIs were conducted with 25 residents, and 8 FGDs were held. Thematic analysis was conducted using Dedoose. RESULTS: Participants received health care in settings ranging from no regular care to primary care providers. Four elements emerged as contributing positively and negatively to health care experiences: 1) ability to access health care financially, physically, and technologically; 2) clarity of communication from providers and staff about appointment logistics, diagnoses, and treatment options; 3) ease of securing timely follow-up services; and 4) respect versus stigma and discrimination from providers and staff. Participants who felt positively toward health care found low- or no-cost care to be widely available and encouraged others to seek care. However, some participants described health care in the United States as greedy, classist, discriminatory, and untrustworthy. Participants reported delaying care and self-medicating in anticipation of discrimination. CONCLUSIONS: Findings demonstrate that while people experiencing homelessness can have positive experiences with health care, many have faced negative interactions with health systems. Improving the patient experience for those experiencing homelessness can increase engagement and improve health outcomes. |
Respiratory syncytial virus and other respiratory virus infections in residents of homeless shelters - King County, Washington, 2019-2021
McCulloch DJ , Rogers JH , Wang Y , Chow EJ , Link AC , Wolf CR , Uyeki TM , Rolfes MA , Mosites E , Sereewit J , Duchin JS , Sugg NK , Greninger AL , Boeckh MJ , Englund JA , Shendure J , Hughes JP , Starita LM , Roychoudhury P , Chu HY . Influenza Other Respir Viruses 2023 17 (6) e13166 Respiratory syncytial virus (RSV) causes disproportionate morbidity and mortality in vulnerable populations. We tested residents of homeless shelters in Seattle, Washington for RSV in a repeated cross-sectional study as part of community surveillance for respiratory viruses. Of 15 364 specimens tested, 35 had RSV detected, compared to 77 with influenza. The most common symptoms for both RSV and influenza were cough and rhinorrhea. Many individuals with RSV (39%) and influenza (58%) reported that their illness significantly impacted their ability to perform their regular activities. RSV and influenza demonstrated similar clinical presentations and burden of illness in vulnerable populations living in congregate settings. |
Multiple models for outbreak decision support in the face of uncertainty
Shea K , Borchering RK , Probert WJM , Howerton E , Bogich TL , Li SL , van Panhuis WG , Viboud C , Aguás R , Belov AA , Bhargava SH , Cavany SM , Chang JC , Chen C , Chen J , Chen S , Chen Y , Childs LM , Chow CC , Crooker I , Del Valle SY , España G , Fairchild G , Gerkin RC , Germann TC , Gu Q , Guan X , Guo L , Hart GR , Hladish TJ , Hupert N , Janies D , Kerr CC , Klein DJ , Klein EY , Lin G , Manore C , Meyers LA , Mittler JE , Mu K , Núñez RC , Oidtman RJ , Pasco R , Pastore YPiontti A , Paul R , Pearson CAB , Perdomo DR , Perkins TA , Pierce K , Pillai AN , Rael RC , Rosenfeld K , Ross CW , Spencer JA , Stoltzfus AB , Toh KB , Vattikuti S , Vespignani A , Wang L , White LJ , Xu P , Yang Y , Yogurtcu ON , Zhang W , Zhao Y , Zou D , Ferrari MJ , Pannell D , Tildesley MJ , Seifarth J , Johnson E , Biggerstaff M , Johansson MA , Slayton RB , Levander JD , Stazer J , Kerr J , Runge MC . Proc Natl Acad Sci U S A 2023 120 (18) e2207537120 Policymakers must make management decisions despite incomplete knowledge and conflicting model projections. Little guidance exists for the rapid, representative, and unbiased collection of policy-relevant scientific input from independent modeling teams. Integrating approaches from decision analysis, expert judgment, and model aggregation, we convened multiple modeling teams to evaluate COVID-19 reopening strategies for a mid-sized United States county early in the pandemic. Projections from seventeen distinct models were inconsistent in magnitude but highly consistent in ranking interventions. The 6-mo-ahead aggregate projections were well in line with observed outbreaks in mid-sized US counties. The aggregate results showed that up to half the population could be infected with full workplace reopening, while workplace restrictions reduced median cumulative infections by 82%. Rankings of interventions were consistent across public health objectives, but there was a strong trade-off between public health outcomes and duration of workplace closures, and no win-win intermediate reopening strategies were identified. Between-model variation was high; the aggregate results thus provide valuable risk quantification for decision making. This approach can be applied to the evaluation of management interventions in any setting where models are used to inform decision making. This case study demonstrated the utility of our approach and was one of several multimodel efforts that laid the groundwork for the COVID-19 Scenario Modeling Hub, which has provided multiple rounds of real-time scenario projections for situational awareness and decision making to the Centers for Disease Control and Prevention since December 2020. |
Comparing genomic variant identification protocols for Candida auris
Li X , Muñoz JF , Gade L , Argimon S , Bougnoux ME , Bowers JR , Chow NA , Cuesta I , Farrer RA , Maufrais C , Monroy-Nieto J , Pradhan D , Uehling J , Vu D , Yeats CA , Aanensen DM , d'Enfert C , Engelthaler DM , Eyre DW , Fisher MC , Hagen F , Meyer W , Singh G , Alastruey-Izquierdo A , Litvintseva AP , Cuomo CA . Microb Genom 2023 9 (4) Genomic analyses are widely applied to epidemiological, population genetic and experimental studies of pathogenic fungi. A wide range of methods are employed to carry out these analyses, typically without including controls that gauge the accuracy of variant prediction. The importance of tracking outbreaks at a global scale has raised the urgency of establishing high-accuracy pipelines that generate consistent results between research groups. To evaluate currently employed methods for whole-genome variant detection and elaborate best practices for fungal pathogens, we compared how 14 independent variant calling pipelines performed across 35 Candida auris isolates from 4 distinct clades and evaluated the performance of variant calling, single-nucleotide polymorphism (SNP) counts and phylogenetic inference results. Although these pipelines used different variant callers and filtering criteria, we found high overall agreement of SNPs from each pipeline. This concordance correlated with site quality, as SNPs discovered by a few pipelines tended to show lower mapping quality scores and depth of coverage than those recovered by all pipelines. We observed that the major differences between pipelines were due to variation in read trimming strategies, SNP calling methods and parameters, and downstream filtration criteria. We calculated specificity and sensitivity for each pipeline by aligning three isolates with chromosomal level assemblies and found that the GATK-based pipelines were well balanced between these metrics. Selection of trimming methods had a greater impact on SAMtools-based pipelines than those using GATK. Phylogenetic trees inferred by each pipeline showed high consistency at the clade level, but there was more variability between isolates from a single outbreak, with pipelines that used more stringent cutoffs having lower resolution. This project generated two truth datasets useful for routine benchmarking of C. auris variant calling, a consensus VCF of genotypes discovered by 10 or more pipelines across these 35 diverse isolates and variants for 2 samples identified from whole-genome alignments. This study provides a foundation for evaluating SNP calling pipelines and developing best practices for future fungal genomic studies. |
Worsening spread of Candida auris in the United States, 2019 to 2021
Lyman M , Forsberg K , Sexton DJ , Chow NA , Lockhart SR , Jackson BR , Chiller T . Ann Intern Med 2023 176 (4) 489-495 BACKGROUND: Candida auris is an emerging fungal threat that has been spreading in the United States since it was first reported in 2016. OBJECTIVE: To describe recent changes in the U.S. epidemiology of C auris occurring from 2019 to 2021. DESIGN: Description of national surveillance data. SETTING: United States. PATIENTS: Persons with any specimen that was positive for C auris. MEASUREMENTS: Case counts reported to the Centers for Disease Control and Prevention by health departments, volume of colonization screening, and antifungal susceptibility results were aggregated and compared over time and by geographic region. RESULTS: A total of 3270 clinical cases and 7413 screening cases of C auris were reported in the United States through 31 December 2021. The percentage increase in clinical cases grew each year, from a 44% increase in 2019 to a 95% increase in 2021. Colonization screening volume and screening cases increased in 2021 by more than 80% and more than 200%, respectively. From 2019 to 2021, 17 states identified their first C auris case. The number of C auris cases that were resistant to echinocandins in 2021 was about 3 times that in each of the previous 2 years. LIMITATION: Identification of screening cases depends on screening that is done on the basis of need and available resources. Screening is not conducted uniformly across the United States, so the true burden of C auris cases may be underestimated. CONCLUSION: C auris cases and transmission have risen in recent years, with a dramatic increase in 2021. The rise in echinocandin-resistant cases and evidence of transmission is particularly concerning because echinocandins are first-line therapy for invasive Candida infections, including C auris. These findings highlight the need for improved detection and infection control practices to prevent spread of C auris. PRIMARY FUNDING SOURCE: None. |
Genomic description of human clinical Aspergillus fumigatus isolates, California, 2020.
Misas E , Deng JZ , Gold JAW , Gade L , Nunnally NS , Georgacopoulos O , Bentz M , Berkow EL , Litvintseva AP , Chiller TM , Klausner JD , Chow NA . Med Mycol 2023 61 (2) Aspergillus fumigatus, an environmental mold, causes life-threatening infections. Studies on the phylogenetic structure of human clinical A. fumigatus isolates are limited. Here, we performed whole-genome sequencing of 24 A. fumigatus isolates collected from 18 patients in U.S. healthcare facilities in California. Single-nucleotide polymorphism (SNP) differences between patient isolates ranged from 187-70 829 SNPs. For five patients with multiple isolates, we calculated the within-host diversities. Three patients had a within-host diversity that ranged from 4-10 SNPs and two patients ranged from 2-16 977 SNPs. Findings revealed highly diverse A. fumigatus strains among patients and two patterns of diversity for isolates that come from the same patient, low and extremely high diversity. | Aspergillus fumigatus is an environmental mold. It can cause a severe infection called aspergillosis in patients with weakened immune systems. We analyzed A. fumigatus DNA from patients at California hospitals. We described genetic diversity between samples from the same patients and among different patients. Our findings provide insight on using genomic sequencing to investigate aspergillosis in hospitals. | eng |
Genomic Epidemiology Linking Nonendemic Coccidioidomycosis to Travel.
Monroy-Nieto J , Gade L , Benedict K , Etienne KA , Litvintseva AP , Bowers JR , Engelthaler DM , Chow NA . Emerg Infect Dis 2023 29 (1) 110-117 Coccidioidomycosis is a fungal infection endemic to hot, arid regions of the western United States, northern Mexico, and parts of Central and South America. Sporadic cases outside these regions are likely travel-associated; alternatively, an infection could be acquired in as-yet unidentified newly endemic locales. A previous study of cases in nonendemic regions with patient self-reported travel history suggested that infections were acquired during travel to endemic regions. We sequenced 19 Coccidioides isolates from patients with known travel histories from that earlier investigation and performed phylogenetic analysis to identify the locations of potential source populations. Our results show that those isolates were phylogenetically linked to Coccidioides subpopulations naturally occurring in 1 of the reported travel locales, confirming that these cases were likely acquired during travel to endemic regions. Our findings demonstrate that genomic analysis is a useful tool for investigating travel-related coccidioidomycosis. |
Genomics and metagenomics of Madurella mycetomatis, a causative agent of black grain mycetoma in Sudan
Litvintseva AP , Bakhiet S , Gade L , Wagner DD , Bagal UR , Batra D , Norris E , Rishishwar L , Beer KD , Siddig EE , Mhmoud NA , Chow NA , Fahal A . PLoS Negl Trop Dis 2022 16 (11) e0010787 Madurella mycetomatis is one of the main causative agents of mycetoma, a debilitating neglected tropical disease. Improved understanding of the genomic diversity of the fungal and bacterial causes of mycetoma is essential to advances in diagnosis and treatment. Here, we describe a high-quality genome assembly of M. mycetomatis and results of the whole genome sequence analysis of 26 isolates from Sudan. We demonstrate evidence of at least seven genetically diverse lineages and extreme clonality among isolates within these lineages. We also performed shotgun metagenomic analysis of DNA extracted from mycetoma grains and showed that M. mycetomatis reads were detected in all sequenced samples with the average of 11,317 reads (s.d. +/- 21,269) per sample. In addition, 10 (12%) of the 81 tested grain samples contained bacterial reads including Streptococcus sp., Staphylococcus sp. and others. |
Human Parainfluenza Virus in Homeless Shelters before and during the COVID-19 Pandemic, Washington, USA.
Chow EJ , Casto AM , Sampoleo R , Mills MG , Han PD , Xie H , Pfau B , Nguyen TV , Sereewit J , Rogers JH , Cox SN , Rolfes MA , Ogokeh C , Mosites E , Uyeki TM , Greninger AL , Hughes JP , Shim MM , Sugg N , Duchin JS , Starita LM , Englund JA , Roychoudhury P , Chu HY . Emerg Infect Dis 2022 28 (11) 2343-2347 To determine the epidemiology of human parainfluenza virus in homeless shelters during the COVID-19 pandemic, we analyzed data and sequences from respiratory specimens collected in 23 shelters in Washington, USA, during 2019-2021. Two clusters in children were genetically similar by shelter of origin. Shelter-specific interventions are needed to reduce these infections. |
Trends and factors associated with change in COVID-19 vaccination intent among residents and staff in six Seattle homeless shelters, March 2020 to August 2021.
Cox SN , Rogers JH , Thuo NB , Meehan A , Link AC , Lo NK , Manns BJ , Chow EJ , Al Achkar M , Hughes JP , Rolfes MA , Mosites E , Chu HY . Vaccine X 2022 12 100232 INTRODUCTION: Achieving high COVID-19 vaccination coverage in homeless shelters is critical in preventing morbidity, mortality, and outbreaks, however, vaccination coverage remains lower among people experiencing homelessness (PEH) than the general population. METHODS: We conducted a cross-sectional study to retrospectively describe attitudes and identify factors associated with change in COVID-19 vaccination intent among shelter residents and staff during March 2020 - August 2021. To identify factors associated with change in COVID-19 vaccine intent becoming more positive overall compared to other attitudes, we utilized a Poisson model to calculate Risk Ratios with robust standard errors, adjusting for confounding by shelter site and demographic variables determined a priori. RESULTS: From July 12 - August 2, 2021, 97 residents and 20 staff participated in surveys across six shelters in Seattle King County, Washington. Intent to be vaccinated against COVID-19 increased from 45.3% (n=53) when recalling attitudes in March 2020 to 74.4% (n=87) as of August 2021, and was similar among residents and staff. Many participants (43.6%, n=51) indicated feeling increasingly accepting about receiving a COVID-19 vaccine since March 2020, while 13.7% (n=16) changed back and forth, 10.3% (n=12) became more hesitant, and 32.5% (n=38) had no change in intent. In the model examining the relationship between becoming more positive about receiving a COVID-19 vaccine compared to all other attitudes (n=116), we found a 57.2% increase in vaccine acceptability (RR 1.57; 95% CI: 1.01, 2.45) among those who reported worsening mental health since the start of the pandemic. CONCLUSIONS: Findings highlight opportunities to improve communication with residents and staff about COVID-19 vaccination and support a need for continued dialogue and a person-centered approach to understanding the sociocultural complexities and dynamism of vaccine attitudes at shelters.Clinical Trial Registry Number: NCT04141917. |
Review of filters for air sampling and chemical analysis in mining workplaces
Chow JC , Watson JG , Wang X , Abbasi B , Reed WR , Parks D . Minerals 2022 12 (10) 1314 This review considers the use of filters to sample air in mining workplace environments for dust concentration measurement and subsequent analysis of hazardous contaminants, especially respirable crystalline silica (RCS) on filters compatible with wearable personal dust monitors (PDM). The review summarizes filter vendors, sizes, costs, chemical and physical properties, and information available on filter modeling, laboratory testing, and field performance. Filter media testing and selection should consider the characteristics required for mass by gravimetry in addition to RCS quantification by Fourier-transform infrared (FTIR) or Raman spectroscopic analysis. For mass determination, the filters need to have high filtration efficiency (≥99% for the most penetrable particle sizes) and a reasonable pressure drop (up to 16.7 kPa) to accommodate high dust loading. Additional requirements include: negligible uptake of water vapor and gaseous volatile compounds; adequate particle adhesion as a function of particle loading; sufficient particle loading capacity to form a stable particle deposit layer during sampling in wet and dusty environments; mechanical strength to withstand vibrations and pressure drops across the filter; and appropriate filter mass compatible with the tapered element oscillating microbalance. FTIR and Raman measurements require filters to be free of spectral interference. Furthermore, because the irradiated area does not completely cover the sample deposit, particles should be uniformly deposited on the filter. |
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