Last data update: May 20, 2024. (Total: 46824 publications since 2009)
Records 1-30 (of 33 Records) |
Query Trace: Etienne K[original query] |
---|
Using regional sero-epidemiology SARS-CoV-2 Anti-S antibodies in the Dominican Republic to inform targeted public health response
Mario Martin B , Cadavid Restrepo A , Mayfield HJ , Then Paulino C , De St Aubin M , Duke W , Jarolim P , Zielinski Gutiérrez E , Skewes Ramm R , Dumas D , Garnier S , Etienne MC , Peña F , Abdalla G , Lopez B , de la Cruz L , Henríquez B , Baldwin M , Sartorius B , Kucharski A , Nilles EJ , Lau CL . Trop Med Infect Dis 2023 8 (11) Incidence of COVID-19 has been associated with sociodemographic factors. We investigated variations in SARS-CoV-2 seroprevalence at sub-national levels in the Dominican Republic and assessed potential factors influencing variation in regional-level seroprevalence. Data were collected in a three-stage cross-sectional national serosurvey from June to October 2021. Seroprevalence of antibodies against the SARS-CoV-2 spike protein (anti-S) was estimated and adjusted for selection probability, age, and sex. Multilevel logistic regression was used to estimate the effect of covariates on seropositivity for anti-S and correlates of 80% protection (PT(80)) against symptomatic infection for the ancestral and Delta strains. A total of 6683 participants from 134 clusters in all 10 regions were enrolled. Anti-S, PT80 for the ancestral and Delta strains odds ratio varied across regions, Enriquillo presented significant higher odds for all outcomes compared with Yuma. Compared to being unvaccinated, receiving ≥2 doses of COVID-19 vaccine was associated with a significantly higher odds of anti-S positivity (OR 85.94, [10.95-674.33]) and PT(80) for the ancestral (OR 4.78, [2.15-10.62]) and Delta strains (OR 3.08, [1.57-9.65]) nationally and also for each region. Our results can help inform regional-level public health response, such as strategies to increase vaccination coverage in areas with low population immunity against currently circulating strains. |
Integrated SARS-CoV-2 serological and virological screening across an acute fever surveillance platform to monitor temporal changes in anti-spike antibody levels and risk of infection during sequential waves of variant transmission - Dominican Republic, March 2021 to August 2022 (preprint)
Nilles EJ , Aubin MDSt , Dumas D , Duke W , Etienne MC , Abdalla G , Jarolim P , Oasan T , Garnier S , Iihoshi N , Lopez B , de la Cruz L , Puello YC , Baldwin M , Roberts KW , Pena F , Durski K , Sanchez IM , Gunter SM , Kneubehl AR , Murray KO , Lino A , Strobel S , Baez AA , Lau CL , Kucharski A , Gutierrez EZ , Skewes-Ramm R , Vasquez M , Paulino CT . medRxiv 2022 26 The global SARS-CoV-2 immune landscape and population protection against emerging variants is largely unknown. We assessed SARS-CoV-2 antibody changes in the Dominican Republic and implications for immunological protection against variants of concern. Between March 2021 and August 2022, 2,300 patients with undifferentiated febrile illnesses were prospectively enrolled. Sera was tested for total anti-spike antibodies and simultaneously collected nasopharyngeal samples for acute SARSCoV-2 infection with RT-PCR. Geometric mean anti-spike titers increased from 6.6 BAU/ml (95% CI 5.1-8.7) to 1,332 BAU/ml (1055-1,682). Multivariable binomial odds ratios for acute SARS-CoV-2 infection were 0.55 (0.40-0.74), 0.38 (0.27-0.55), and 0.27 (0.18-0.40) for the second, third, and fourth versus the first anti-S quartile, with similar findings by viral strain. Integrated serological and virological screening can leverage existing acute fever surveillance platforms to monitor population-level immunological markers and concurrently characterize implications for emergent variant transmission in near real-time. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. |
SARS-CoV-2 seroprevalence, cumulative infections, and immunity to symptomatic infection - A multistage national household survey and modelling study, Dominican Republic, June-October 2021.
Nilles EJ , Paulino CT , de St Aubin M , Restrepo AC , Mayfield H , Dumas D , Finch E , Garnier S , Etienne MC , Iselin L , Duke W , Jarolim P , Oasan T , Yu J , Wan H , Peña F , Iihoshi N , Abdalla G , Lopez B , Cruz L , Henríquez B , Espinosa-Bode A , Puello YC , Durski K , Baldwin M , Baez AA , Merchant RC , Barouch DH , Skewes-Ramm R , Gutiérrez EZ , Kucharski A , Lau CL . Lancet Reg Health Am 2022 16 100390 BACKGROUND: Population-level SARS-CoV-2 immunological protection is poorly understood but can guide vaccination and non-pharmaceutical intervention priorities. Our objective was to characterise cumulative infections and immunological protection in the Dominican Republic. METHODS: Household members ≥5 years were enrolled in a three-stage national household cluster serosurvey in the Dominican Republic. We measured pan-immunoglobulin antibodies against the SARS-CoV-2 spike (anti-S) and nucleocapsid glycoproteins, and pseudovirus neutralising activity against the ancestral and B.1.617.2 (Delta) strains. Seroprevalence and cumulative prior infections were weighted and adjusted for assay performance and seroreversion. Binary classification machine learning methods and pseudovirus neutralising correlates of protection were used to estimate 50% and 80% protection against symptomatic infection. FINDINGS: Between 30 Jun and 12 Oct 2021 we enrolled 6683 individuals from 3832 households. We estimate that 85.0% (CI 82.1-88.0) of the ≥5 years population had been immunologically exposed and 77.5% (CI 71.3-83) had been previously infected. Protective immunity sufficient to provide at least 50% protection against symptomatic SARS-CoV-2 infection was estimated in 78.1% (CI 74.3-82) and 66.3% (CI 62.8-70) of the population for the ancestral and Delta strains respectively. Younger (5-14 years, OR 0.47 [CI 0.36-0.61]) and older (≥75-years, 0.40 [CI 0.28-0.56]) age, working outdoors (0.53 [0.39-0.73]), smoking (0.66 [0.52-0.84]), urban setting (1.30 [1.14-1.49]), and three vs no vaccine doses (18.41 [10.69-35.04]) were associated with 50% protection against the ancestral strain. INTERPRETATION: Cumulative infections substantially exceeded prior estimates and overall immunological exposure was high. After controlling for confounders, markedly lower immunological protection was observed to the ancestral and Delta strains across certain subgroups, findings that can guide public health interventions and may be generalisable to other settings and viral strains. FUNDING: This study was funded by the US CDC. |
Monitoring temporal changes in SARS-CoV-2 spike antibody levels and variant-specific risk for infection, Dominican Republic, March 2021-August 2022
Nilles EJ , de St Aubin M , Dumas D , Duke W , Etienne MC , Abdalla G , Jarolim P , Oasan T , Garnier S , Iihoshi N , Lopez B , de la Cruz L , Puello YC , Baldwin M , Roberts KW , Peña F , Durski K , Sanchez IM , Gunter SM , Kneubehl AR , Murray KO , Lino A , Strobel S , Baez AA , Lau CL , Kucharski A , Gutiérrez EZ , Skewes-Ramm R , Vasquez M , Paulino CT . Emerg Infect Dis 2023 29 (4) 723-733 To assess changes in SARS-CoV-2 spike binding antibody prevalence in the Dominican Republic and implications for immunologic protection against variants of concern, we prospectively enrolled 2,300 patients with undifferentiated febrile illnesses in a study during March 2021-August 2022. We tested serum samples for spike antibodies and tested nasopharyngeal samples for acute SARS-CoV-2 infection using a reverse transcription PCR nucleic acid amplification test. Geometric mean spike antibody titers increased from 6.6 (95% CI 5.1-8.7) binding antibody units (BAU)/mL during March-June 2021 to 1,332 (95% CI 1,055-1,682) BAU/mL during May-August 2022. Multivariable binomial odds ratios for acute infection were 0.55 (95% CI 0.40-0.74), 0.38 (95% CI 0.27-0.55), and 0.27 (95% CI 0.18-0.40) for the second, third, and fourth versus the first anti-spike quartile; findings were similar by viral strain. Combining serologic and virologic screening might enable monitoring of discrete population immunologic markers and their implications for emergent variant transmission. |
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. |
Of masks and methylene blue-The use of methylene blue photochemical treatment to decontaminate surgical masks contaminated with a tenacious small nonenveloped norovirus.
Wielick Constance , Fries Allyson , Dams Lorène , Razafimahefa Ravo M , Heyne Belinda , Harcourt Brian H , Lendvay Thomas S , Willaert Jean-François , de Jaeger Simon , Haubruge Eric , Thiry Etienne , Ludwig-Begall Louisa F . Am J Infect Control 2022 50 (8) 871-877 PPE reuse necessitates reliable respiratory and oral human pathogen decontamination. Equitable decontamination technologies must be available in low-resource settings. Methylene blue photochemical treatment decontaminates noroviruses on surgical masks. Norovirus inactivation predicts inactivation of any less resistant viral contaminant. Role of low-cost – low-tech photochemical decontamination in pandemic preparedness. In the context of the SARS-CoV-2 pandemic, reuse of personal protective equipment, specifically that of medical face coverings, has been recommended. The reuse of these typically single-use only items necessitates procedures to inactivate contaminating human respiratory and gastrointestinal pathogens. We previously demonstrated decontamination of surgical masks and respirators contaminated with infectious SARS-CoV-2 and various animal coronaviruses via low concentration- and short exposure methylene blue photochemical treatment (10 µM methylene blue, 30 minutes of 12,500-lux red light or 50,000 lux white light exposure). Here, we describe the adaptation of this protocol to the decontamination of a more resistant, non-enveloped gastrointestinal virus and demonstrate efficient photodynamic inactivation of murine norovirus, a human norovirus surrogate. Methylene blue photochemical treatment (100 µM methylene blue, 30 minutes of 12,500-lux red light exposure) of murine norovirus-contaminated masks reduced infectious viral titers by over four orders of magnitude on surgical mask surfaces. Inactivation of a norovirus, the most difficult to inactivate of the respiratory and gastrointestinal human viruses, can predict the inactivation of any less resistant viral mask contaminant. The protocol developed here thus solidifies the position of methylene blue photochemical decontamination as an important tool in the package of practical pandemic preparedness. |
Genomic Diversity of Azole-Resistant Aspergillus fumigatus in the United States.
Etienne KA , Berkow EL , Gade L , Nunnally N , Lockhart SR , Beer K , Jordan IK , Rishishwar L , Litvintseva AP . mBio 2021 12 (4) e0180321 Azole resistance in pathogenic Aspergillus fumigatus has become a global public health issue threatening the use of medical azoles. The environmentally occurring resistance mutations, TR(34)/L98H (TR(34)) and TR(46)/Y121F/T289A (TR(46)), are widespread across multiple continents and emerging in the United States. We used whole-genome single nucleotide polymorphism (SNP) analysis on 179 nationally represented clinical and environmental A. fumigatus genomes from the United States along with 18 non-U.S. genomes to evaluate the genetic diversity and foundation of the emergence of azole resistance in the United States. We demonstrated the presence of clades of A. fumigatus isolates: clade A (17%) comprised a global collection of clinical and environmental azole-resistant strains, including all strains with the TR(34)/L98H allele from India, The Netherlands, the United Kingdom, and the United States, and clade B (83%) consisted of isolates without this marker mainly from the United States. The TR(34)/L98H polymorphism was shared among azole-resistant A. fumigatus strains from India, The Netherlands, the United Kingdom, and the United States, suggesting the common origin of this resistance mechanism. Six percent of azole-resistant A. fumigatus isolates from the United States with the TR(34) resistance marker had a mixture of clade A and clade B alleles, suggestive of recombination. Additionally, the presence of equal proportions of both mating types further suggests the ongoing presence of recombination. This study demonstrates the genetic background for the emergence of azole resistance in the United States, supporting a single introduction and subsequent propagation, possibly through recombination of environmentally driven resistance mutations. IMPORTANCE Aspergillus fumigatus is one of the most common causes of invasive mold infections in patients with immune deficiencies and has also been reported in patients with severe influenza and severe acute respiratory syndrome coronavirus 2 (SARs-CoV-2). Triazole drugs are the first line of therapy for this infection; however, their efficacy has been compromised by the emergence of azole resistance in A. fumigatus, which was proposed to be selected for by exposure to azole fungicides in the environment [P. E. Verweij, E. Snelders, G. H. J. Kema, E. Mellado, et al., Lancet Infect Dis 9:789-795, 2009, https://doi.org/10.1016/S1473-3099(09)70265-8]. Isolates with environmentally driven resistance mutations, TR(34)/L98H (TR(34)) and TR(46)/Y121F/T289A (TR(46)), have been reported worldwide. Here, we used genomic analysis of a large sample of resistant and susceptible A. fumigatus isolates to demonstrate a single introduction of TR(34) in the United States and suggest its ability to spread into the susceptible population is through recombination between resistant and susceptible isolates. |
Addressing personal protective equipment (PPE) decontamination: Methylene blue and light inactivates severe acute respiratory coronavirus virus 2 (SARS-CoV-2) on N95 respirators and medical masks with maintenance of integrity and fit.
Lendvay TS , Chen J , Harcourt BH , Scholte FE , Lin YL , Kilinc-Balci FS , Lamb MM , Homdayjanakul K , Cui Y , Price A , Heyne B , Sahni J , Kabra KB , Lin YC , Evans D , Mores CN , Page K , Chu LF , Haubruge E , Thiry E , Ludwig-Begall LF , Wielick C , Clark T , Wagner T , Timm E , Gallagher T , Faris P , Macia N , Mackie CJ , Simmons SM , Reader S , Malott R , Hope K , Davies JM , Tritsch SR , Dams L , Nauwynck H , Willaert JF , De Jaeger S , Liao L , Zhao M , Laperre J , Jolois O , Smit SJ , Patel AN , Mayo M , Parker R , Molloy-Simard V , Lemyre JL , Chu S , Conly JM , Chu MC . Infect Control Hosp Epidemiol 2021 43 (7) 1-83 OBJECTIVE: The coronavirus disease 2019 (COVID-19) pandemic has resulted in shortages of personal protective equipment (PPE) underscoring the urgent need for simple, efficient, and inexpensive methods to decontaminate SARS-CoV-2-exposed masks and respirators. We hypothesized that methylene blue (MB) photochemical treatment, which has various clinical applications, could decontaminate PPE contaminated with coronavirus. DESIGN: The two arms of the study included: 1) PPE inoculation with coronaviruses followed by MB with light (MBL) decontamination treatment, and 2) PPE treatment with MBL for 5 cycles of decontamination (5CD) to determine maintenance of PPE performance. METHODS: MBL treatment was used to inactivate coronaviruses on three N95 filtering facepiece respirator (FFR) and two medical mask (MM) models. We inoculated FFR and MM materials with three coronaviruses, including SARS-CoV-2, and treated with 10 µM MB and exposed to 50,000 lux of white light or 12,500 lux of red light for 30 minutes. In parallel, integrity was assessed after 5CD using multiple US and international test methods and compared to the FDA-authorized vaporized hydrogen peroxide plus ozone (VHP+O3) decontamination method. RESULTS: Overall, MBL robustly and consistently inactivated all three coronaviruses with 99.8 - to >99.9% virus inactivation across all FFRs and MMs tested. FFR and MM integrity was maintained after 5 cycles of MBL treatment, whereas one FFR model failed after 5 cycles of VHP+O3. CONCLUSIONS: MBL treatment decontaminated respirators and masks by inactivating three tested coronaviruses without compromising integrity through 5CD. MBL decontamination is effective, low-cost and does not require specialized equipment, making it applicable in all-resource settings. |
Recommendations on the measurement and theclinical useof vitamin D metabolites and vitamin D binding protein - A position paper from the IFCC Committee on Bone Metabolism.
Makris K , Bhattoa HP , Cavalier E , Phinney K , Sempos CT , Ulmer CZ , Vasikaran SD , Vesper H , Heijboer AC . Clin Chim Acta 2021 517 171-197 Vitamin D, an important hormone with a central role in calcium and phosphate homeostasis, is required for bone and muscle development as well as preservation of musculoskeletal function. The most abundant vitamin D metabolite is 25-hydroxyvitamin D [25(OH)D], which is currently considered the best marker to evaluate overall vitamin D status. 25(OH)D is therefore the most commonly measured metabolite in clinical practice. However, several other metabolites, although not broadly measured, are useful in certain clinical situations. Vitamin D and all its metabolites are circulating in blood bound to vitamin D binding protein, (VDBP). This highly polymorphic protein is not only the major transport protein which, along with albumin, binds over 99% of the circulating vitamin D metabolites, but also participates in the transport of the 25(OH)D into the cell via a megalin/cubilin complex. The accurate measurement of 25(OH)D has proved a difficult task. Although a reference method and standardization program are available for 25(OH)D, the other vitamin D metabolites still lack this. Interpretation of results, creation of clinical supplementation, and generation of therapeutic guidelines require not only accurate measurements of vitamin D metabolites, but also the accurate measurements of several other "molecules" related with bone metabolism. IFCC understood this priority and a committee has been established with the task to support and continue the standardization processes of vitamin D metabolites along with other bone-related biomarkers. In this review, we present the position of this IFCC Committee on Bone Metabolism on the latest developments concerning the measurement and standardization of vitamin D metabolites and its binding protein, as well as clinical indications for their measurement and interpretation of the results. |
Parenting in a time of COVID-19.
Cluver L , Lachman JM , Sherr L , Wessels I , Krug E , Rakotomalala S , Blight S , Hillis S , Bachman G , Green O , Butchart A , Tomlinson M , Ward CL , Doubt J , McDonald K . Lancet 2020 395 (10231) e64 Coronavirus disease 2019 (COVID-19) is changing family life. The United Nations Educational, Scientific and Cultural Organization estimates 1·38 billion children are out of school or child care, without access to group activities, team sports, or playgrounds. Parents and caregivers are attempting to work remotely or unable to work, while caring for children, with no clarity on how long the situation will last. For many people, just keeping children busy and safe at home is a daunting prospect. For those living in low-income and crowded households, these challenges are exacerbated. |
In vitro activity of ibrexafungerp, a novel glucan synthase inhibitor against Candida glabrata isolates with FKS mutations
Nunnally NS , Etienne KA , Angulo D , Lockhart SR , Berkow EL . Antimicrob Agents Chemother 2019 63 (11) Ibrexafungerp is a first in class glucan-synthase inhibitor. In vitro activity was determined for 89 Candida glabrata isolates with molecularly identified FKS1 or FKS2 mutations conferring resistance to the echinocandins. All isolates were resistant to at least one echinocandin (i.e., anidulafungin, caspofungin, and micafungin) by broth microdilution. Results for ibrexafungerp were compared to those for each echinocandin. Ibrexafungerp had good activity against all echinocandin-resistant Candida glabrata isolates. |
Utility of Whole-Genome Sequencing to Ascertain Locally Acquired Cases of Coccidioidomycosis, Washington, USA.
Oltean HN , Etienne KA , Roe CC , Gade L , McCotter OZ , Engelthaler DM , Litvintseva AP . Emerg Infect Dis 2019 25 (3) 501-506 Coccidioidomycosis is an emerging fungal infection in Washington, USA, and the epidemiology of the disease in this state is poorly understood. We used whole-genome sequencing to differentiate locally acquired cases in Washington on the basis of the previously identified phylogeographic population structure of Coccidioides spp. Clinical isolates from coccidioidomycosis cases involving possible Washington soil exposure were included. Of 17 human infections with epidemiologic evidence of possible local acquisition, 4 were likely locally acquired infections and 13 were likely acquired outside Washington. Isolates from locally acquired cases clustered within the previously established Washington clade of C. immitis. Genetic differences among these strains suggest multiple environmental reservoirs of C. immitis in the state. |
Challenges in identifying Candida auris in hospital clinical laboratories: a need for hospital and public health laboratory collaboration in rapid identification of an emerging pathogen
Durante AJ , Maloney MH , Leung VH , Razeq JH , Banach DB . Infect Control Hosp Epidemiol 2018 39 (8) 1-2 Candida auris is an emerging fungus that poses a considerable threat to US healthcare facilities and their patients. Patients exposed to C. auris can develop invasive infection, which can be fatal,Reference Lockhart, Etienne and Vallabhaneni 1 or can become colonized, which poses long-term transmission risks. Once introduced into a healthcare facility, C. auris can spread through contact with affected patients and contaminated surfaces.Reference Tsay, Welsh and Adams 2 The organism can persist in the environment,Reference Welsh, Bentz and Shams 3 and quaternary ammonium disinfectants demonstrate poor activity against it.Reference Cadnum, Shaikh, Piedrahita and Sankar 4 Candida auris is often multidrug-resistant,Reference Lockhart, Etienne and Vallabhaneni 1 , Reference Cadnum, Shaikh, Piedrahita and Sankar4 and its detection is challenging because it can be misidentified by some biochemically based identification methods. For example, the API 20 C (bioMerieux, Marcy-l’Etoile, France) can misidentify C. auris as C. sake or Rhodotorula glutinis, and the Vitek 2 (bioMerieux) can misidentify C. auris as C. haemulonii or C. duobushaemulonii.Reference Mizusawa, Miller and Green 5 Rapid and accurate C. auris detection would help hospitals to guide infection control activities intended to prevent the spread of the fungus within and between facilities and to properly plan antifungal treatment. We surveyed laboratories that serve Connecticut’s acute-care hospitals to assess their capability to identify C. auris. The information was collected to guide statewide hospital prevention efforts. |
Surveillance of carbon monoxide-related incidents - implications for prevention of related illnesses and injuries, 2005-2014
Mukhopadhyay S , Hirsch A , Etienne S , Melnikova N , Wu J , Sircar K , Orr M . Am J Emerg Med 2018 36 (10) 1837-1844 BACKGROUND: Carbon monoxide (CO) is an insidious gas responsible for approximately 21,000 emergency department visits, 2300 hospitalizations, and 500 deaths in the United States annually. We analyzed 10 combined years of data from two Agency for Toxic Substances and Disease Registry acute hazardous substance release surveillance programs to evaluate CO incident-related injuries. METHODS: Seventeen states participated in these programs during 2005-2014. RESULTS: In those 10years, the states identified 1795 CO incidents. Our analysis focused on 897 CO incidents having injured persons. Of the 3414 CO injured people, 61.0% were classified as general public, 27.7% were employees, 7.6% were students, and 2.2% were first responders. More than 78% of CO injured people required hospital or pre-hospital treatment and 4.3% died. The location for most injured people (39.9%) were homes or apartments, followed by educational facilities (10.0%). Educational services had a high number of people injured per incident (16.3%). The three most common sources of CO were heating, ventilation, and air conditioning systems; generators; and motor vehicles. Equipment failure was the primary contributing factor for most CO incidents. CONCLUSIONS: States have used the data to evaluate trends in CO poisoning and develop targeted public health outreach. Surveillance data are useful for setting new policies or supporting existing policy such as making CO poisoning a reportable condition at the state level and requiring CO alarms in all schools and housing. Public health needs to remain vigilant to the sources and causes of CO to help reduce this injury and death. |
Public Health Progress in Haiti
Lowrance DW , Tappero JW , Poncelet JL , Etienne C , Frieden TR , Delsoins D . Am J Trop Med Hyg 2017 97 1-3 Although the attention of the Haitian public and international community has understandably turned to the recurrent political challenges facing the country and recovery from Hurricane Mathew, it is important that public health stakeholders take stock of progress made, remaining gaps, and fundamental public health priorities. In the past year, the global community has assessed progress toward the Millennium Development Goals (MDGs) and established new health targets under the Sustainable Development Goals framework.1 Haiti has made progress toward the MDGs and many of the objectives established in the aftermath of the earthquake.1–7 Important lessons regarding the association between various global health emergency responses, such as to human immunodeficiency virus (HIV), tuberculosis (TB), Ebola (Haitian public health professionals deployed to Guinea), and health sector resiliency have been identified.8,9 Yet much remains to be done to increase health service access and to reduce morbidity and mortality from preventable causes in the country. Although the public health system in Haiti has been improved since the earthquake, emergency response and health recovery funding has largely focused on new and acute threats such as Zika virus.10 Moreover, the health-care delivery infrastructure remains fragile, with limited coverage of primary care services, suboptimal health-care performance, and excessive health risk and vulnerability for the Haitian population. It is in this context that the Supplement, entitled “Public Health Progress in Haiti,” was developed. The reports enclosed span HIV, TB, malaria, cholera, immunizations, rabies, water, sanitation and hygiene, and lymphatic filariasis, and also address notifiable disease surveillance reporting and national laboratory capacity.11–20 Collectively, they appraise some of the key programs and services that have been the focus of postearthquake response and recovery planning and which have central roles informing current and future strengthening and prioritization within the health sector. |
Virus genomes reveal factors that spread and sustained the Ebola epidemic.
Dudas G , Carvalho LM , Bedford T , Tatem AJ , Baele G , Faria NR , Park DJ , Ladner JT , Arias A , Asogun D , Bielejec F , Caddy SL , Cotten M , D'Ambrozio J , Dellicour S , Caro AD , Diclaro JW , Duraffour S , Elmore MJ , Fakoli LS , Faye O , Gilbert ML , Gevao SM , Gire S , Gladden-Young A , Gnirke A , Goba A , Grant DS , Haagmans BL , Hiscox JA , Jah U , Kugelman JR , Liu D , Lu J , Malboeuf CM , Mate S , Matthews DA , Matranga CB , Meredith LW , Qu J , Quick J , Pas SD , Phan MV , Pollakis G , Reusken CB , Sanchez-Lockhart M , Schaffner SF , Schieffelin JS , Sealfon RS , Simon-Loriere E , Smits SL , Stoecker K , Thorne L , Tobin EA , Vandi MA , Watson SJ , West K , Whitmer S , Wiley MR , Winnicki SM , Wohl S , Wolfel R , Yozwiak NL , Andersen KG , Blyden SO , Bolay F , Carroll MW , Dahn B , Diallo B , Formenty P , Fraser C , Gao GF , Garry RF , Goodfellow I , Gunther S , Happi CT , Holmes EC , Kargbo B , Keita S , Kellam P , Koopmans MP , Kuhn JH , Loman NJ , Magassouba N , Naidoo D , Nichol ST , Nyenswah T , Palacios G , Pybus OG , Sabeti PC , Sall A , Stroher U , Wurie I , Suchard MA , Lemey P , Rambaut A . Nature 2017 544 (7650) 309-315 The 2013-2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genomes, which represent over 5% of the known cases. We test the association of geography, climate and demography with viral movement among administrative regions, inferring a classic 'gravity' model, with intense dispersal between larger and closer populations. Despite attenuation of international dispersal after border closures, cross-border transmission had already sown the seeds for an international epidemic, rendering these measures ineffective at curbing the epidemic. We address why the epidemic did not spread into neighbouring countries, showing that these countries were susceptible to substantial outbreaks but at lower risk of introductions. Finally, we reveal that this large epidemic was a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help to inform interventions in future epidemics. |
Genetic Assessment of African Swine Fever Isolates Involved in Outbreaks in the Democratic Republic of Congo between 2005 and 2012 Reveals Co-Circulation of p72 Genotypes I, IX and XIV, Including 19 Variants.
Mulumba-Mfumu LK , Achenbach JE , Mauldin MR , Dixon LK , Tshilenge CG , Thiry E , Moreno N , Blanco E , Saegerman C , Lamien CE , Diallo A . Viruses 2017 9 (2) African swine fever (ASF) is a devastating disease of domestic pigs. It is a socioeconomically important disease, initially described from Kenya, but subsequently reported in most Sub-Saharan countries. ASF spread to Europe, South America and the Caribbean through multiple introductions which were initially eradicated-except for Sardinia-followed by reintroduction into Europe in 2007. In this study of ASF within the Democratic Republic of the Congo, 62 domestic pig samples, collected between 2005-2012, were examined for viral DNA and sequencing at multiple loci: C-terminus of the B646L gene (p72 protein), central hypervariable region (CVR) of the B602L gene, and the E183L gene (p54 protein). Phylogenetic analyses identified three circulating genotypes: I (64.5% of samples), IX (32.3%), and XIV (3.2%). This is the first evidence of genotypes IX and XIV within this country. Examination of the CVR revealed high levels of intra-genotypic variation, with 19 identified variants. |
Simultaneous Emergence of Multidrug-Resistant Candida auris on 3 Continents Confirmed by Whole-Genome Sequencing and Epidemiological Analyses.
Lockhart SR , Etienne KA , Vallabhaneni S , Farooqi J , Chowdhary A , Govender NP , Colombo AL , Calvo B , Cuomo CA , Desjardins CA , Berkow EL , Castanheira M , Magobo RE , Jabeen K , Asghar RJ , Meis JF , Jackson B , Chiller T , Litvintseva AP . Clin Infect Dis 2016 64 (2) 134-140 BACKGROUND: Candida auris, a multidrug-resistant yeast that causes invasive infections, was first described in 2009 in Japan and has since been reported from several countries. METHODS: To understand the global emergence and epidemiology of C. auris, we obtained isolates from 54 patients with C. auris infection from Pakistan, India, South Africa, and Venezuela during 2012-2015 and the type specimen from Japan. Patient information was available for 41 of the isolates. We conducted antifungal susceptibility testing and whole-genome sequencing (WGS). RESULTS: Available clinical information revealed that 41% of patients had diabetes mellitus, 51% had undergone recent surgery, 73% had a central venous catheter, and 41% were receiving systemic antifungal therapy when C. auris was isolated. The median time from admission to infection was 19 days (interquartile range, 9-36 days), 61% of patients had bloodstream infection, and 59% died. Using stringent break points, 93% of isolates were resistant to fluconazole, 35% to amphotericin B, and 7% to echinocandins; 41% were resistant to 2 antifungal classes and 4% were resistant to 3 classes. WGS demonstrated that isolates were grouped into unique clades by geographic region. Clades were separated by thousands of single-nucleotide polymorphisms, but within each clade isolates were clonal. Different mutations in ERG11 were associated with azole resistance in each geographic clade. CONCLUSIONS: C. auris is an emerging healthcare-associated pathogen associated with high mortality. Treatment options are limited, due to antifungal resistance. WGS analysis suggests nearly simultaneous, and recent, independent emergence of different clonal populations on 3 continents. Risk factors and transmission mechanisms need to be elucidated to guide control measures. |
An integrated genomic and transcriptomic survey of mucormycosis-causing fungi.
Chibucos MC , Soliman S , Gebremariam T , Lee H , Daugherty S , Orvis J , Shetty AC , Crabtree J , Hazen TH , Etienne KA , Kumari P , O'Connor TD , Rasko DA , Filler SG , Fraser CM , Lockhart SR , Skory CD , Ibrahim AS , Bruno VM . Nat Commun 2016 7 12218 Mucormycosis is a life-threatening infection caused by Mucorales fungi. Here we sequence 30 fungal genomes, and perform transcriptomics with three representative Rhizopus and Mucor strains and with human airway epithelial cells during fungal invasion, to reveal key host and fungal determinants contributing to pathogenesis. Analysis of the host transcriptional response to Mucorales reveals platelet-derived growth factor receptor B (PDGFRB) signaling as part of a core response to divergent pathogenic fungi; inhibition of PDGFRB reduces Mucorales-induced damage to host cells. The unique presence of CotH invasins in all invasive Mucorales, and the correlation between CotH gene copy number and clinical prevalence, are consistent with an important role for these proteins in mucormycosis pathogenesis. Our work provides insight into the evolution of this medically and economically important group of fungi, and identifies several molecular pathways that might be exploited as potential therapeutic targets. |
Whole-Genome Sequencing to Determine Origin of Multinational Outbreak of Sarocladium kiliense Bloodstream Infections.
Etienne KA , Roe CC , Smith RM , Vallabhaneni S , Duarte C , Escadon P , Castaneda E , Gomez BL , de Bedout C , Lopez LF , Salas V , Hederra LM , Fernandez J , Pidal P , Hormazabel JC , Otaiza F , Vannberg FO , Gillece J , Lemmer D , Driebe EM , Englethaler DM , Litvintseva AP . Emerg Infect Dis 2016 22 (3) 476-81 We used whole-genome sequence typing (WGST) to investigate an outbreak of Sarocladium kiliense bloodstream infections (BSI) associated with receipt of contaminated antinausea medication among oncology patients in Colombia and Chile during 2013-2014. Twenty-five outbreak isolates (18 from patients and 7 from medication vials) and 11 control isolates unrelated to this outbreak were subjected to WGST to elucidate a source of infection. All outbreak isolates were nearly indistinguishable (<5 single-nucleotide polymorphisms), and >21,000 single-nucleotide polymorphisms were identified from unrelated control isolates, suggesting a point source for this outbreak. S. kiliense has been previously implicated in healthcare-related infections; however, the lack of available typing methods has precluded the ability to substantiate point sources. WGST for outbreak investigation caused by eukaryotic pathogens without reference genomes or existing genotyping methods enables accurate source identification to guide implementation of appropriate control and prevention measures. |
The genome sequence of four isolates from the family Lichtheimiaceae.
Chibucos MC , Etienne KA , Orvis J , Lee H , Daugherty S , Lockhart SR , Ibrahim AS , Bruno VM . Pathog Dis 2015 73 (5) This study reports the release of draft genome sequences of two isolates of Lichtheimia corymbifera and two isolates of Lichtheimia ramosa. Phylogenetic analyses indicate that the two L. corymbifera strains (CDC-B2541 and 008-049) are closely related to the previously sequenced L. corymbifera isolate (FSU 9682) while our two L. ramosa strains CDC-B5399 and CDC-B5792 cluster apart from them. These genome sequences will further the understanding of intra-species and inter-species genetic variation within the Mucoraceae family of pathogenic fungi. |
Dengue virus infections among Haitian and expatriate non-governmental organization workers - Leogane and Port-au-Prince, Haiti, 2012
Salyer SJ , Ellis EM , Salomon C , Bron C , Juin S , Hemme RR , Hunsperger E , Jentes ES , Magloire R , Tomashek KM , Desormeaux AM , Munoz-Jordan JL , Etienne L , Beltran M , Sharp TM , Moffett D , Tappero J , Margolis HS , Katz MA . PLoS Negl Trop Dis 2014 8 (10) e3269 In October 2012, the Haitian Ministry of Health and the US CDC were notified of 25 recent dengue cases, confirmed by rapid diagnostic tests (RDTs), among non-governmental organization (NGO) workers. We conducted a serosurvey among NGO workers in Leogane and Port-au-Prince to determine the extent of and risk factors for dengue virus infection. Of the total 776 staff from targeted NGOs in Leogane and Port-au-Prince, 173 (22%; 52 expatriates and 121 Haitians) participated. Anti-dengue virus (DENV) IgM antibody was detected in 8 (15%) expatriates and 9 (7%) Haitians, and DENV non-structural protein 1 in one expatriate. Anti-DENV IgG antibody was detected in 162 (94%) participants (79% of expatriates; 100% of Haitians), and confirmed by microneutralization testing as DENV-specific in 17/34 (50%) expatriates and 42/42 (100%) Haitians. Of 254 pupae collected from 68 containers, 65% were Aedes aegypti; 27% were Ae. albopictus. Few NGO workers reported undertaking mosquito-avoidance action. Our findings underscore the risk of dengue in expatriate workers in Haiti and Haitians themselves. |
Real-time PCR assays for genotyping of Cryptococcus gattii in North America
Kelley EJ , Driebe EM , Etienne K , Brandt ME , Schupp JM , Gillece JD , Trujillo JS , Lockhart SR , Deak E , Keim PS , Engelthaler DM . BMC Microbiol 2014 14 (1) 125 BACKGROUND: Cryptococcus gattii has been the cause of an ongoing outbreak starting in 1999 on Vancouver Island, British Columbia and spreading to mainland Canada and the US Pacific Northwest. In the course of the outbreak, C. gattii has been identified outside of its previously documented climate, habitat, and host disease. Genotyping of C. gattii is essential to understand the ecological and geographical expansion of this emerging pathogen. METHODS: We developed and validated a mismatch amplification mutation assay (MAMA) real-time PCR panel for genotyping C. gattii molecular types VGI-VGIV and VGII subtypes a,b,c. Subtype assays were designed based on whole-genome sequence of 20 C. gattii strains. Publically available multilocus sequence typing (MLST) data from a study of 202 strains was used for the molecular type (VGI-VGIV) assay design. All assays were validated across DNA from 112 strains of diverse international origin and sample types, including animal, environmental and human. RESULTS: Validation revealed each assay on the panel is 100% sensitive, specific and concordant with MLST. The assay panel can detect down to 0.5 picograms of template DNA. CONCLUSIONS: The (MAMA) real-time PCR panel for C. gattii accurately typed a collection of 112 diverse strains and demonstrated high sensitivity. This is a time and cost efficient method of genotyping C. gattii best suited for application in large-scale epidemiological studies. |
Draft Genome Sequence of Mortierella alpina Isolate CDC-B6842.
Etienne KA , Chibucos MC , Su Q , Orvis J , Daugherty S , Ott S , Sengamalay NA , Fraser CM , Lockhart SR , Bruno VM . Genome Announc 2014 2 (1) We report the draft genome sequence of Mortierella alpina isolate CDC-B6842. M. alpina is a nonpathogenic member of the Mucoromycotina subphylum of fungi that is an important model for understanding the molecular mechanisms of lipid production and metabolism. |
Cholera elimination in Hispaniola
Etienne CF , Tappero JW , Marston BJ , Frieden TR , Kenyon TA , Andrus JK . Am J Trop Med Hyg 2013 89 (4) 615-616 A catastrophic confluence of factors contributed to the rapid spread of cholera in Haiti following its introduction in late 2010. The outbreak is now the largest in modern history to affect a single country1; cases from Haiti comprised nearly half of the cholera cases reported worldwide in 2012.2 Although cases of cholera related to this outbreak have occurred in the Dominican Republic, the United States,3 and possibly in Cuba and other countries,4,5 spread in these other countries has been nil or limited. The factors responsible for rapid spread in Haiti include: long-standing water and sanitary inadequacies in Haiti; the further disruptions to water and sanitary systems imposed by the earthquake; above average rainfall; high water and ambient temperatures; and insufficient capacity of the government infrastructure to respond to the crisis. | | In 2008, before the earthquake, 63% of Haitians had access to improved sources of drinking water, and only 17% of the population had access to improved sanitation.6 To address these inadequacies, in January 2012 the Pan American Health Organization (PAHO), the United States Centers for Disease Control and Prevention (CDC), and the United Nations Children's Fund (UNICEF) put forward a call to action for international partners to support the governments of Haiti and the Dominican Republic with their long-term vision to strengthen water, sanitation, and hygiene (WASH) conditions in their respective countries.7 The same group supported the development of national plans for the elimination of cholera transmission on the Island of Hispaniola. In Haiti, the National Plan outlined a 10-year strategy to strengthen and sustain broad efforts for prevention and control of cholera infection, including water and sanitation infrastructure, surveillance, health promotion, and treatment measures.8 Plans in the Dominican Republic focused on bridging gaps in WASH access, and improving surveillance, health communication, and treatment. Partners were asked to assist the National governments to finance and implement these plans. |
Trichosporon asahii among intensive care unit patients at a medical center in Jamaica
Fanfair RN , Heslop O , Etienne K , Rainford L , Roy M , Gade L , Peterson J , O'Connell H , Noble-Wang J , Balajee SA , Brandt ME , Lindo JF , Park BJ . Infect Control Hosp Epidemiol 2013 34 (6) 638-41 We investigated an increase in Trichosporon asahii isolates among inpatients. We identified 63 cases; 4 involved disseminated disease. Trichosporon species was recovered from equipment cleaning rooms, washbasins, and fomites, which suggests transmission through washbasins. Patient washbasins should be single-patient use only; adherence to appropriate hospital disinfection guidelines was recommended. |
Necrotizing cutaneous mucormycosis after a tornado in Joplin, Missouri, in 2011
Fanfair RN , Benedict K , Bos J , Bennett SD , Lo YC , Adebanjo T , Etienne K , Deak E , Derado G , Shieh WJ , Drew C , Zaki S , Sugerman D , Gade L , Thompson EH , Sutton DA , Engelthaler DM , Schupp JM , Brandt ME , Harris JR , Lockhart SR , Turabelidze G , Park BJ . N Engl J Med 2012 367 (23) 2214-25 BACKGROUND: Mucormycosis is a fungal infection caused by environmentally acquired molds. We investigated a cluster of cases of cutaneous mucormycosis among persons injured during the May 22, 2011, tornado in Joplin, Missouri. METHODS: We defined a case as a soft-tissue infection in a person injured during the tornado, with evidence of a mucormycete on culture or immunohistochemical testing plus DNA sequencing. We conducted a case-control study by reviewing medical records and conducting interviews with case patients and hospitalized controls. DNA sequencing and whole-genome sequencing were performed on clinical specimens to identify species and assess strain-level differences, respectively. RESULTS: A total of 13 case patients were identified, 5 of whom (38%) died. The patients had a median of 5 wounds (range, 1 to 7); 11 patients (85%) had at least one fracture, 9 (69%) had blunt trauma, and 5 (38%) had penetrating trauma. All case patients had been located in the zone that sustained the most severe damage during the tornado. On multivariate analysis, infection was associated with penetrating trauma (adjusted odds ratio for case patients vs. controls, 8.8; 95% confidence interval [CI], 1.1 to 69.2) and an increased number of wounds (adjusted odds ratio, 2.0 for each additional wound; 95% CI, 1.2 to 3.2). Sequencing of the D1-D2 region of the 28S ribosomal DNA yielded Apophysomyces trapeziformis in all 13 case patients. Whole-genome sequencing showed that the apophysomyces isolates were four separate strains. CONCLUSIONS: We report a cluster of cases of cutaneous mucormycosis among Joplin tornado survivors that were associated with substantial morbidity and mortality. Increased awareness of fungi as a cause of necrotizing soft-tissue infections after a natural disaster is warranted. |
Whole genome sequence typing to investigate the Apophysomyces outbreak following a tornado in Joplin, Missouri, 2011.
Etienne KA , Gillece J , Hilsabeck R , Schupp JM , Colman R , Lockhart SR , Gade L , Thompson EH , Sutton DA , Neblett-Fanfair R , Park BJ , Turabelidze G , Keim P , Brandt ME , Deak E , Engelthaler DM . PLoS One 2012 7 (11) e49989 Case reports of Apophysomyces spp. in immunocompetent hosts have been a result of traumatic deep implantation of Apophysomyces spp. spore-contaminated soil or debris. On May 22, 2011 a tornado occurred in Joplin, MO, leaving 13 tornado victims with Apophysomyces trapeziformis infections as a result of lacerations from airborne material. We used whole genome sequence typing (WGST) for high-resolution phylogenetic SNP analysis of 17 outbreak Apophysomyces isolates and five additional temporally and spatially diverse Apophysomyces control isolates (three A. trapeziformis and two A. variabilis isolates). Whole genome SNP phylogenetic analysis revealed three clusters of genotypically related or identical A. trapeziformis isolates and multiple distinct isolates among the Joplin group; this indicated multiple genotypes from a single or multiple sources. Though no linkage between genotype and location of exposure was observed, WGST analysis determined that the Joplin isolates were more closely related to each other than to the control isolates, suggesting local population structure. Additionally, species delineation based on WGST demonstrated the need to reassess currently accepted taxonomic classifications of phylogenetic species within the genus Apophysomyces. |
Molecular sub-typing suggests that the environment of rehabilitation centers may be a potential source of Aspergillus fumigatus infecting rehabilitating seabirds
Burco JD , Etienne KA , Massey JG , Ziccardi MH , Balajee SA . Med Mycol 2012 50 (1) 91-98 Aspergillosis remains a major cause of infection-related avian mortality in birds that are debilitated and undergoing rehabilitation for release into the wild. This study was designed to understand the source of avian aspergillosis in seabirds undergoing rehabilitation at selected northern California aquatic bird rehabilitation centers. Air, surface and water sampling was performed between August 2007 and July 2008 in three such centers and selected natural seabird loafing sites. Average air Aspergillus fumigatus counts were at least nine times higher in samples obtained from the rehabilitation sites (M = 7.34, SD = 9.78 CFU/m(3)), when compared to those found at natural sites (M = 0.76, SD = 2.24 CFU/m(3)), t (205) = -5.99, P < 0.001. A total of 37 A. fumigatus isolates from birds with confirmed aspergillosis and 42 isolates from environmental samples were identified using both morphological and molecular methods, and subsequently sub-typed using an eight-locus microsatellite panel with the neighbor joining algorithm. Results of the study demonstrated the presence of five clonal groups, 13 genotypically related clusters, and 59 distinct genotypes. Six of the 13 genotypically related clusters contained matching genotypes between clinical isolates and local environmental isolates from the rehabilitation center in which these birds were housed. We present evidence that the environment of rehabilitation centers may be a source for A. fumigatus infection in rehabilitated seabirds. (2012 ISHAM.) |
Investigation of a cluster of cutaneous aspergillosis in a neonatal intensive care unit
Etienne KA , Subudhi CP , Chadwick PR , Settle P , Moise J , Magill SS , Chiller T , Balajee SA . J Hosp Infect 2011 79 (4) 344-8 Between December 2007 and July 2008, three neonates in a neonatal intensive care unit (NICU) in Salford, UK, were diagnosed with primary cutaneous aspergillosis (PCA) due to Aspergillus fumigatus. The first PCA case, in December 2007, developed multi-organ failure leading to death within a short time frame: the other two cases survived after treatment with intravenous antifungal therapy followed by oral posaconazole. Air, surface, and water samples were collected within the NICU and from the incubators that were occupied by the neonates. All recovered fungal isolates were confirmed as A. fumigatus by sequencing the beta-tubulin region. Microsatellite strain typing demonstrated genotypically related A. fumigatus isolates from the neonates and the humidity chambers (HCs) of the neonates' incubators, suggesting that the source of the infection may have been the HCs/incubators used in the NICU. Aspergillus strain typing may be a useful tool in clinical outbreak settings to help understand the source of exposure and to design targeted environmental interventions to prevent future infections. |
- Page last reviewed:Feb 1, 2024
- Page last updated:May 20, 2024
- Content source:
- Powered by CDC PHGKB Infrastructure