Last data update: Apr 29, 2024. (Total: 46658 publications since 2009)
Records 1-30 (of 118 Records) |
Query Trace: Bernard B[original query] |
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Cryogenic air supply feasibility for a confined space: Underground refuge alternative case study
Yan L , Yantek DS , DeGennaro CR , Srednicki JR , Lambie B , Carr J . ASME J Heat Mass Transf 2024 146 (3) A breathable air source is required for a confined space such as an underground refuge alternative (RA) when it is occupied. To minimize the risk of suffocation, federal regulations require that mechanisms be provided and procedures be included so that, within the refuge alternative, the oxygen concentration is maintained at levels between 18.5% and 23% for 96 h. The regulation also requires that, during use of the RA, the concentration of carbon dioxide should not exceed 1%, and the concentration of carbon monoxide should not exceed 25 ppm. The National Institute for Occupational Safety and Health (NIOSH) evaluated the cryogenic air supply's ability to provide breathable air for a refuge alternative. A propane smoker was used to simulate human breathing by burning propane gas which will consume O(2) and generate CO(2) and H(2)O. The rate of propane burned at the smoker was controlled to represent the O(2) consumption rate for the breathing of a certain number of people. Two 96-h tests were conducted in a sealed shipping container, which was used as a surrogate for a refuge alternative. While burning propane gas to simulate human oxygen consumption, cryogenic air was provided to the shipping container to determine if the cryogenic air supply would keep the O(2) level above 18.5% and CO(2) level below 1% inside the shipping container as required by the federal regulations pertaining to refuge alternatives. Both of the 96-h tests simulated the breathing of 21 persons. The first test used the oxygen consumption rate (1.32 cu ft of pure oxygen per hour per person) specified in federal regulations, while the second test used the oxygen consumption rate specified by (Bernard et al. 2018, "Estimation of Metabolic Heat Input for Refuge Alternative Thermal Testing and Simulation," Min. Eng., 70(8), pp. 50-54) (0.67 cu ft of pure oxygen per hour per person). The test data shows that during both 96-h tests, the oxygen level was maintained within a 21-23% range, and the CO(2) level was maintained below 1% (0.2-0.45%). The information in this paper could be useful when applying a cryogenic air supply as a breathable air source for an underground refuge alternative or other confined space. [DOI: 10.1115/1.4064062]. |
The U.S. President's Malaria Initiative's support for improving the quality of malaria case management services: Fifteen years of progress and learning
Barat LM , Whitehurst N , Venkatesan M , Connolly K , Yamo E , Psychas P , Bernard YM . Am J Trop Med Hyg 2023 Since its launch in 2005, the U.S. President's Malaria Initiative's (PMI) investment in malaria case management has evolved based on lessons learned from its support to countries. An initial focus on updating malaria treatment policies to adopt artemisinin-based combination therapies achieved limited success, in part because of the poor quality of diagnostic and treatment services in targeted countries. In response, the PMI supported the development, refinement, and expansion of Outreach Training and Supportive Supervision (OTSS), a quality improvement approach that combines structured, competency-based supervision with corrective measures, including on-the-job training, coaching, troubleshooting, action planning, and timely follow-up. With 15 years of experience, the OTSS approach has been adopted by more than a dozen countries, and its effectiveness in improving the quality of malaria case management services has been documented. Through the PMI Impact Malaria Project, launched in 2018, the OTSS approach was expanded beyond case management of uncomplicated malaria to support quality improvement of inpatient management of severe malaria and malaria in pregnancy services delivered through antenatal care clinics. The OTSS platform also enabled targeted countries to respond rapidly to the COVID-19 pandemic by adding modules related to clinical management and laboratory diagnosis of suspected cases. The OTSS approach has been established as an effective approach to improve the quality of clinical malaria services and can be expanded to cover other health priorities. Further innovations to improve the quality of inpatient and community-based services, and further integration and institutionalization of OTSS into country health systems are needed. |
The relationship between the intestinal microbiome and body mass index in children with cystic fibrosis
Bernard R , Shilts MH , Strickland BA , Boone HH , Payne DC , Brown RF , Edwards K , Das SR , Nicholson MR . J Cyst Fibros 2023 BACKGROUND: The nutritional status of children with cystic fibrosis (CF), as assessed by their body mass index percentile (BMIp), is a critical determinant of long-term health outcomes. While the intestinal microbiome plays an important role in nutrition, little is known regarding the relationship of the microbiome and BMIp in children with CF. METHODS: Pediatric patients (< 18 years old) with CF and healthy comparison patients (HCs) were enrolled in the study and stool samples obtained. BMIp was categorized as Green Zone (BMIp > 50th), Yellow Zone (BMIp 25th-49th) and Red Zone (BMIp < 25th). Intestinal microbiome assessment was performed via 16S rRNA gene sequencing; microbial richness, diversity, and differential species abundance were assessed. RESULTS: Stool samples were collected from 107 children with CF and 50 age-matched HCs. Compared to HCs, children with CF were found to have lower bacterial richness, alpha-diversity, and a different microbial composition. When evaluating them by their BMIp color zone, richness and alpha-diversity were lowest in those in the Red Zone. In addition, an unclassified amplicon sequence variant (ASV) of Blautia, a known butyrate-producing anaerobe, was of lowest abundance in children in the Red Zone. CONCLUSION: Children with CF have a dysbiotic intestinal microbiome with specific changes that accompany changes in BMIp. Longitudinal assessments of the microbiome and its metabolic activities over time are needed to better understand how improvements in the microbiome may improve nutrition and enhance long-term survival in children with CF. |
Relationships of p16 Immunohistochemistry and Other Biomarkers With Diagnoses of Cervical Abnormalities: Implications for LAST Terminology
Castle PE , Adcock R , Cuzick J , Wentzensen N , Torrez-Martinez NE , Torres SM , Stoler MH , Ronnett BM , Joste NE , Darragh TM , Gravitt PE , Schiffman M , Hunt WC , Kinney WK , Wheeler CM , New Mexico HPV Pap Registry Steering Committee and for the p16 IHC Study Panel , Bernard Vicki , Unger Elizabeth . Arch Pathol Lab Med 2020 144 (6) 725-734 CONTEXT.—: Lower Anogenital Squamous Terminology (LAST) standardization recommended p16(INK4a) immunohistochemistry (p16 IHC) for biopsies diagnosed morphologically as cervical intraepithelial neoplasia (CIN) grade 2 (CIN2) to classify them as low-grade or high-grade squamous intraepithelial lesions (HSILs). OBJECTIVE.—: To describe the relationships of p16 IHC and other biomarkers associated with cervical cancer risk with biopsy diagnoses. DESIGN.—: A statewide, stratified sample of cervical biopsies diagnosed by community pathologists (CPs), including 1512 CIN2, underwent a consensus, expert pathologist panel (EP) review (without p16 IHC results), p16 IHC interpretation by a third pathology group, and human papillomavirus (HPV) genotyping, results of which were grouped hierarchically according to cancer risk. Antecedent cytologic interpretations were also available. RESULTS.—: Biopsies were more likely to test p16 IHC positive with increasing severity of CP diagnoses, overall (P(trend) ≤ .001) and within each HPV risk group (P(trend) ≤ .001 except for low-risk HPV [P(trend) < .010]). All abnormal grades of CP-diagnosed biopsies were more likely to test p16 IHC positive with a higher HPV risk group (P(trend) < .001), and testing p16 IHC positive was associated with higher HPV risk group than testing p16 IHC negative for each grade of CP-diagnosed biopsies (P < .001). p16 IHC-positive, CP-diagnosed CIN2 biopsies were less likely than CP-diagnosed CIN3 biopsies to test HPV16 positive, have an antecedent HSIL(+) cytology, or to be diagnosed as CIN3(+) by the EP (P < .001 for all). p16 IHC-positive, CP-diagnosed CIN1 biopsies had lower HPV risk groups than p16 IHC-negative, CP-diagnosed CIN2 biopsies (P < .001). CONCLUSIONS.—: p16 IHC-positive, CP-diagnosed CIN2 appears to be lower cancer risk than CP-diagnosed CIN3. LAST classification of "HSIL" diagnosis, which includes p16 IHC-positive CIN2, should annotate the morphologic diagnosis (CIN2 or CIN3) to inform all management decisions, which is especially important for young (<30 years) women diagnosed with CIN2 for whom surveillance rather than treatment is recommended. |
Causes of severe pneumonia requiring hospital admission in children without HIV infection from Africa and Asia: the PERCH multi-country case-control study
Pneumonia Etiology Research for Child Health Study Group , O'Brien Katherine L , Levine Orin S , Knoll Maria Deloria , Feikin Daniel R , DeLuca Andrea N , Driscoll Amanda J , Fancourt Nicholas , Fu Wei , Haddix Meredith , Hammitt Laura L , Higdon Melissa M , Kagucia E Wangeci , Karron Ruth A , Li Mengying , Park Daniel E , Prosperi Christine , Shi Qiyuan , Wu Zhenke , Zeger Scott L , Watson Nora L , Crawley Jane , Murdoch David R , Brooks W Abdullah , Endtz Hubert P , Zaman Khalequ , Goswami Doli , Hossain Lokman , Jahan Yasmin , Chisti Mohammod Jobayer , Howie Stephen R C , Ebruke Bernard E , Antonio Martin , McLellan Jessica L , Machuka Eunice M , Shamsul Arifin , Zaman Syed M A , Mackenzie Grant , Scott J Anthony G , Awori Juliet O , Morpeth Susan C , Kamau Alice , Kazungu Sidi , Ominde Micah Silaba , Kotloff Karen L , Tapia Milagritos D , Sow Samba O , Sylla Mamadou , Tamboura Boubou , Onwuchekwa Uma , Kourouma Nana , Toure Aliou , Sissoko Seydou , Madhi Shabir A , Moore David P , Adrian Peter V , Baillie Vicky L , Kuwanda Locadiah , Mudau Azwifarwi , Groome Michelle J , Mahomed Nasreen , Simões Eric A F , Baggett Henry C , Thamthitiwat Somsak , Maloney Susan A , Bunthi Charatdao , Rhodes Julia , Sawatwong Pongpun , Akarasewi Pasakorn , Thea Donald M , Mwananyanda Lawrence , Chipeta James , Seidenberg Phil , Mwansa James , Somwe Somwe Wa , Kwenda Geoffrey , Anderson Trevor P , Mitchell Joanne L . Lancet 2019 394 (10200) 757-779 BACKGROUND: Pneumonia is the leading cause of death among children younger than 5 years. In this study, we estimated causes of pneumonia in young African and Asian children, using novel analytical methods applied to clinical and microbiological findings. METHODS: We did a multi-site, international case-control study in nine study sites in seven countries: Bangladesh, The Gambia, Kenya, Mali, South Africa, Thailand, and Zambia. All sites enrolled in the study for 24 months. Cases were children aged 1-59 months admitted to hospital with severe pneumonia. Controls were age-group-matched children randomly selected from communities surrounding study sites. Nasopharyngeal and oropharyngeal (NP-OP), urine, blood, induced sputum, lung aspirate, pleural fluid, and gastric aspirates were tested with cultures, multiplex PCR, or both. Primary analyses were restricted to cases without HIV infection and with abnormal chest x-rays and to controls without HIV infection. We applied a Bayesian, partial latent class analysis to estimate probabilities of aetiological agents at the individual and population level, incorporating case and control data. FINDINGS: Between Aug 15, 2011, and Jan 30, 2014, we enrolled 4232 cases and 5119 community controls. The primary analysis group was comprised of 1769 (41·8% of 4232) cases without HIV infection and with positive chest x-rays and 5102 (99·7% of 5119) community controls without HIV infection. Wheezing was present in 555 (31·7%) of 1752 cases (range by site 10·6-97·3%). 30-day case-fatality ratio was 6·4% (114 of 1769 cases). Blood cultures were positive in 56 (3·2%) of 1749 cases, and Streptococcus pneumoniae was the most common bacteria isolated (19 [33·9%] of 56). Almost all cases (98·9%) and controls (98·0%) had at least one pathogen detected by PCR in the NP-OP specimen. The detection of respiratory syncytial virus (RSV), parainfluenza virus, human metapneumovirus, influenza virus, S pneumoniae, Haemophilus influenzae type b (Hib), H influenzae non-type b, and Pneumocystis jirovecii in NP-OP specimens was associated with case status. The aetiology analysis estimated that viruses accounted for 61·4% (95% credible interval [CrI] 57·3-65·6) of causes, whereas bacteria accounted for 27·3% (23·3-31·6) and Mycobacterium tuberculosis for 5·9% (3·9-8·3). Viruses were less common (54·5%, 95% CrI 47·4-61·5 vs 68·0%, 62·7-72·7) and bacteria more common (33·7%, 27·2-40·8 vs 22·8%, 18·3-27·6) in very severe pneumonia cases than in severe cases. RSV had the greatest aetiological fraction (31·1%, 95% CrI 28·4-34·2) of all pathogens. Human rhinovirus, human metapneumovirus A or B, human parainfluenza virus, S pneumoniae, M tuberculosis, and H influenzae each accounted for 5% or more of the aetiological distribution. We observed differences in aetiological fraction by age for Bordetella pertussis, parainfluenza types 1 and 3, parechovirus-enterovirus, P jirovecii, RSV, rhinovirus, Staphylococcus aureus, and S pneumoniae, and differences by severity for RSV, S aureus, S pneumoniae, and parainfluenza type 3. The leading ten pathogens of each site accounted for 79% or more of the site's aetiological fraction. INTERPRETATION: In our study, a small set of pathogens accounted for most cases of pneumonia requiring hospital admission. Preventing and treating a subset of pathogens could substantially affect childhood pneumonia outcomes. FUNDING: Bill & Melinda Gates Foundation. |
Investigation of a Candida auris outbreak in a Skilled Nursing Facility - Virginia, United States, October 2020-June 2021.
Waters A , Chommanard C , Baltozer S , Angel LC , Abdelfattah R , Lyman M , Forsberg K , Misas E , Litvintseva AP , Fields V , Lineberger S , Bernard S . Am J Infect Control 2022 51 (4) 472-474 Candida auris, an emerging multi-drug resistant organism (MDRO), is an urgent public health threat. We report on a C. auris outbreak investigation at a Virginia ventilator skilled nursing facility (vSNF). During October 2020-June 2021, we identified 28 cases among residents in the ventilator unit. Genomic evidence suggested ≥2 distinct C. auris introductions to the facility. We identified multiple infection and prevention control challenges, highlighting the importance of strengthening MDRO prevention efforts at vSNFs. |
Prognostic indicators and outcomes of hospitalised COVID-19 patients with neurological disease: An individual patient data meta-analysis.
Singh B , Lant S , Cividini S , Cattrall JWS , Goodwin LC , Benjamin L , Michael BD , Khawaja A , Matos AMB , Alkeridy W , Pilotto A , Lahiri D , Rawlinson R , Mhlanga S , Lopez EC , Sargent BF , Somasundaran A , Tamborska A , Webb G , Younas K , Al Sami Y , Babu H , Banks T , Cavallieri F , Cohen M , Davies E , Dhar S , Fajardo Modol A , Farooq H , Harte J , Hey S , Joseph A , Karthikappallil D , Kassahun D , Lipunga G , Mason R , Minton T , Mond G , Poxon J , Rabas S , Soothill G , Zedde M , Yenkoyan K , Brew B , Contini E , Cysique L , Zhang X , Maggi P , van Pesch V , Lechien J , Saussez S , Heyse A , Brito Ferreira ML , Soares CN , Elicer I , Eugenín-von Bernhardi L , Ñancupil Reyes W , Yin R , Azab MA , Abd-Allah F , Elkady A , Escalard S , Corvol JC , Delorme C , Tattevin P , Bigaut K , Lorenz N , Hornuss D , Hosp J , Rieg S , Wagner D , Knier B , Lingor P , Winkler AS , Sharifi-Razavi A , Moein ST , SeyedAlinaghi S , JamaliMoghadamSiahkali S , Morassi M , Padovani A , Giunta M , Libri I , Beretta S , Ravaglia S , Foschi M , Calabresi P , Primiano G , Servidei S , Biagio Mercuri N , Liguori C , Pierantozzi M , Sarmati L , Boso F , Garazzino S , Mariotto S , Patrick KN , Costache O , Pincherle A , Klok FA , Meza R , Cabreira V , Valdoleiros SR , Oliveira V , Kaimovsky I , Guekht A , Koh J , Fernández Díaz E , Barrios-López JM , Guijarro-Castro C , Beltrán-Corbellini Á , Martínez-Poles J , Diezma-Martín AM , Morales-Casado MI , García García S , Breville G , Coen M , Uginet M , Bernard-Valnet R , Du Pasquier R , Kaya Y , Abdelnour LH , Rice C , Morrison H , Defres S , Huda S , Enright N , Hassell J , D'Anna L , Benger M , Sztriha L , Raith E , Chinthapalli K , Nortley R , Paterson R , Chandratheva A , Werring DJ , Dervisevic S , Harkness K , Pinto A , Jillella D , Beach S , Gunasekaran K , Rocha Ferreira Da Silva I , Nalleballe K , Santoro J , Scullen T , Kahn L , Kim CY , Thakur KT , Jain R , Umapathi T , Nicholson TR , Sejvar JJ , Hodel EM , Tudur Smith C , Solomon T . PLoS One 2022 17 (6) e0263595 BACKGROUND: Neurological COVID-19 disease has been reported widely, but published studies often lack information on neurological outcomes and prognostic risk factors. We aimed to describe the spectrum of neurological disease in hospitalised COVID-19 patients; characterise clinical outcomes; and investigate factors associated with a poor outcome. METHODS: We conducted an individual patient data (IPD) meta-analysis of hospitalised patients with neurological COVID-19 disease, using standard case definitions. We invited authors of studies from the first pandemic wave, plus clinicians in the Global COVID-Neuro Network with unpublished data, to contribute. We analysed features associated with poor outcome (moderate to severe disability or death, 3 to 6 on the modified Rankin Scale) using multivariable models. RESULTS: We included 83 studies (31 unpublished) providing IPD for 1979 patients with COVID-19 and acute new-onset neurological disease. Encephalopathy (978 [49%] patients) and cerebrovascular events (506 [26%]) were the most common diagnoses. Respiratory and systemic symptoms preceded neurological features in 93% of patients; one third developed neurological disease after hospital admission. A poor outcome was more common in patients with cerebrovascular events (76% [95% CI 67-82]), than encephalopathy (54% [42-65]). Intensive care use was high (38% [35-41]) overall, and also greater in the cerebrovascular patients. In the cerebrovascular, but not encephalopathic patients, risk factors for poor outcome included breathlessness on admission and elevated D-dimer. Overall, 30-day mortality was 30% [27-32]. The hazard of death was comparatively lower for patients in the WHO European region. INTERPRETATION: Neurological COVID-19 disease poses a considerable burden in terms of disease outcomes and use of hospital resources from prolonged intensive care and inpatient admission; preliminary data suggest these may differ according to WHO regions and country income levels. The different risk factors for encephalopathy and stroke suggest different disease mechanisms which may be amenable to intervention, especially in those who develop neurological symptoms after hospital admission. |
Prospective Analysis of Minimum Pricing Policies to Reduce Excessive Alcohol Use and Related Harms in U.S. States
LeClercq J , Bernard S , Mucciaccio F , Esser MB . J Stud Alcohol Drugs 2021 82 (6) 710-719 OBJECTIVE: Increasing the price of alcohol is an effective strategy for reducing excessive consumption and alcohol-related harms. Limited research is available on how the establishment of a minimum price for alcoholic beverages might be an effective strategy to reduce this health risk behavior and what impact that might have in the United States. This study describes alcohol minimum pricing (MP) policy options for consideration in the United States, assesses implementation feasibility and effectiveness, and discusses implications for implementation. METHOD: Three alcohol pricing policy options for reducing excessive drinking were compared in this prospective analysis: alcohol taxation (status quo in states), minimum unit pricing (MUP) by unit of alcohol (e.g., 0.6 oz. [14 g] of pure alcohol), and MP by specified amount of an alcoholic beverage type (e.g., liter of beer). For each policy, five implementation-related domains were analyzed: political feasibility, public acceptability, implementation cost, health equity, and legal feasibility. Effectiveness was also evaluated based on literature. RESULTS: Alcohol MP policies, particularly MUP, could be feasible to implement and cost-efficient for reducing excessive alcohol consumption and related harms in the United States. MP policies are likely to have modest public acceptability in the United States. Although the political feasibility of MP policies is uncertain and would likely vary across states, international research suggests that MP might be a feasible pricing strategy that can be used in conjunction with alcohol taxes. CONCLUSIONS: Alcohol MP can be part of a comprehensive approach for reducing excessive drinking and related harms; however, factors such as state-level differences in alcohol control regulation may influence policy implementation. |
Serotyping and antibiotic susceptibility of invasive Streptococcus agalactiae in Egyptian patients with or without diabetes mellitus
El-Gendy AA , Hassan Shmet , Gertz B , Bernard B , Ahmed MM , Elzohry HA , El Tawab GA , El-Sayed ME , Kamel SY , Zakaria H , Mahros AM , Ahmed MH , Tahoon MA , Sakr MA , Gadallah AA , Ahmed FE , Elgazzar MF . Am J Trop Med Hyg 2021 105 (6) 1684-1689 Streptococcus agalactiae serotype distribution and its antibiotic susceptibility affect disease prevention strategies, but the serotype distribution varies among patient groups. The objectives of this study were to establish the group B Streptococcus (GBS) serotype distribution in patients from Egypt and to assess antibiotic sensitivity of invasive GBS isolates. A total of 490 patients participated in this multicenter study; 160 had urinary tract infection, 115 complained of diabetic foot ulcers, 125 men had genital tract infections, and 30 women females had genital tract infections. Others had bronchopneumonia, otitis media, synovitis, or meningitis. Serotyping of the isolated GBS was performed at the CDC in the United States. Antibiotic sensitivity patterns were determined using the disk diffusion method. In men, the most common serotypes were II, III, and V, whereas types Ia, II, III, and V were isolated from women. Macrolides (erythromycin) resistance occurred in 4.1% of the isolates; 10.2% were resistant to both clindamycin and inducible resistance of macrolides, lincomycin, and streptogramin; 17.3% were resistant to quinolones; and 95.9% were resistant to tetracyclines. GBS primarily infected the urinary tract, skin, soft tissue, and genital tract in both genders. Isolates were sensitive to beta-lactam drugs, vancomycin, and linezolid; 14.0% were resistant to macrolides with or without clindamycin. Only 6.0% of the strains were sensitive to tetracyclines. Although GBS causes invasive infections in Egyptian adults, it rarely causes neonatal meningitis or sepsis. Future studies should determine whether GBS isolates are transmitted sexually, by performing a follow-up study of the partner of the infected patient. |
Patterns of antibiotic nonsusceptibility among invasive group A Streptococcus infections-United States, 2006-2017.
Fay K , Onukwube J , Chochua S , Schaffner W , Cieslak P , Lynfield R , Muse A , Smelser C , Harrison LH , Farley M , Petit S , Alden N , Apostal M , Vagnone PS , Nanduri S , Beall B , Van Beneden CA . Clin Infect Dis 2021 73 (11) 1957-1964 BACKGROUND: Treatment of severe group A streptococcal infections requires timely and appropriate antibiotic therapy. We describe the epidemiology of antimicrobial-resistant invasive group A streptococcal (iGAS) infections in the U.S. METHODS: We analyzed population-based iGAS surveillance data at 10 U.S. sites from 2006-2017. Cases were defined as infection with GAS isolated from normally sterile sites or wounds in patients with necrotizing fasciitis or streptococcal toxic shock syndrome. GAS isolates were emm typed. Antimicrobial susceptibility was determined using broth microdilution or whole genome sequencing. We compared characteristics among patients infected with erythromycin nonsusceptible (EryNS) and clindamycin nonsusceptible (CliNS) strains to those with susceptible infections. We analyzed proportions of EryNS and CliNS among isolates by site, year, risk factors and emm type. RESULTS: Overall, 17,179 iGAS cases were reported; 14.5% were EryNS. Among isolates tested for both inducible and constitutive CliNS (2011-2017), 14.6% were CliNS. Most (99.8%) CliNS isolates were EryNS. Resistance was highest in 2017 (EryNS: 22.8%; CliNS: 22.0%). All isolates were susceptible to beta-lactams. EryNS and CliNS infections were most frequent among persons aged 18-34 years and in persons residing in long-term care facilities, experiencing homelessness, incarcerated, or who injected drugs. Patterns varied by site. Patients with nonsusceptible infections were significantly less likely to die. Emm types with >30% EryNS or CliNS included: 77, 58, 11, 83, 92. CONCLUSION: Increasing prevalence of EryNS and CliNS iGAS infections in the U.S. is predominantly due to expansion of several emm types. Clinicians should consider local resistance patterns when treating iGAS infections. |
Serotype-Switch Variant of Multidrug-Resistant Streptococcus pneumoniae Sequence Type 271.
Scherer EM , Beall B , Metcalf B . Emerg Infect Dis 2021 27 (6) 1689-1692 We discovered 3 invasive, multidrug-resistant Streptococcus pneumoniae isolates of vaccine-refractory capsular serotype 3 that recently arose within the successful sequence type 271 complex through a serotype switch recombination event. Mapping genomic recombination sites within the serotype 3/sequence type 271 progeny revealed a 55.9-kb donated fragment that encompassed cps3, pbp1a, and additional virulence factors. |
Multisectoral cost analysis of a human and livestock anthrax outbreak in Songwe Region, Tanzania (December 2018-January 2019), using a novel Outbreak Costing Tool
Bodenham RF , Mtui-Malamsha N , Gatei W , Woldetsadik MA , Cassell CH , Salyer SJ , Halliday JEB , Nonga HE , Swai ES , Makungu S , Mwakapeje E , Bernard J , Bebay C , Makonnen YJ , Fasina FO . One Health 2021 13 100259 OBJECTIVES: We applied a novel Outbreak Costing Tool (OCT), developed by the US Centers for Disease Control and Prevention (CDC), to estimate the costs of investigating and responding to an anthrax outbreak in Tanzania. We also evaluated the OCT's overall utility in its application to a multisectoral outbreak response. METHODS: We collected data on direct costs associated with a human and animal anthrax outbreak in Songwe Region (December 2018 to January 2019) using structured questionnaires from key-informants. We performed a cost analysis by entering direct costs data into the OCT, grouped into seven cost categories: labor, office, travel and transport, communication, laboratory support, medical countermeasures, and consultancies. RESULTS: The total cost for investigating and responding to this outbreak was estimated at 102,232 United States dollars (USD), with travel and transport identified as the highest cost category (62,536 USD) and communication and consultancies as the lowest, with no expenditure, for the combined human and animal health sectors. CONCLUSIONS: Multisectoral investigation and response may become complex due to coordination challenges, thus allowing escalation of public health impacts. A standardized framework for collecting and analysing cost data is vital to understanding the nature of outbreaks, in anticipatory planning, in outbreak investigation and in reducing time to intervention. Pre-emptive use of the OCT will also reduce overall and specific (response period) intervention costs for the disease. Additional aggregation of the costs by government ministries, departments and tiers will improve the use of the tool to enhance sectoral budget planning for disease outbreaks in a multisectoral response. |
Legionella antibiotic susceptibility testing: is it time for international standardization and evidence-based guidance
Portal E , Descours G , Ginevra C , Mentasti M , Afshar B , Chand M , Day J , Echahidi F , Franzin L , Gaia V , Lück C , Meghraoui A , Moran-Gilad J , Ricci ML , Lina G , Uldum S , Winchell J , Howe R , Bernard K , Spiller OB , Chalker VJ , Jarraud S . J Antimicrob Chemother 2021 76 (5) 1113-1116 Legionella pneumophila, a Gram-negative bacillus, is the causative agent of Legionnaire's disease, a form of severe community-acquired pneumonia. Infection can have high morbidity, with a high proportion of patients requiring ICU admission, and up to 10% mortality, which is exacerbated by the lack of efficacy of typical empirical antibiotic therapy against Legionella spp. The fastidious nature of the entire Legionellaceae family historically required inclusion of activated charcoal in the solid medium to remove growth inhibitors, which inherently interferes with accurate antimicrobial susceptibility determination, an acknowledged methodological shortfall, now rectified by a new solid medium that gives results comparable to those of microbroth dilution. Here, as an international Legionella community (with authors representing various international reference laboratories, countries and clinical stakeholders for diagnosis and treatment of legionellosis), we set out recommendations for the standardization of antimicrobial susceptibility testing methods, guidelines and reference strains to facilitate an improved era of antibiotic resistance determination. |
Use of Real-Time PCR for Chlamydia psittaci Detection in Human Specimens During an Outbreak of Psittacosis - Georgia and Virginia, 2018.
McGovern OL , Kobayashi M , Shaw KA , Szablewski C , Gabel J , Holsinger C , Drenzek C , Brennan S , Milucky J , Farrar JL , Wolff BJ , Benitez AJ , Thurman KA , Diaz MH , Winchell JM , Schrag S . MMWR Morb Mortal Wkly Rep 2021 70 (14) 505-509 Psittacosis is typically a mild febrile respiratory illness caused by infection with the bacterium Chlamydia psittaci and usually transmitted to humans by infected birds (1). On average, 11 psittacosis cases per year were reported in the United States during 2000-2017. During August-October 2018, the largest U.S. psittacosis outbreak in 30 years (82 cases identified*) occurred in two poultry slaughter plants, one each in Virginia and Georgia, that shared source farms (2). CDC used C. psittaci real-time polymerase chain reaction (PCR) to test 54 human specimens from this outbreak. This was the largest number of human specimens from a single outbreak ever tested for C. psittaci using real-time PCR, which is faster and more sensitive than commercially available serologic tests. This represented a rare opportunity to assess the utility of multiple specimen types for real-time PCR detection of C. psittaci. C. psittaci was detected more frequently in lower respiratory specimens (59% [10 of 17]) and stool (four of five) than in upper respiratory specimens (7% [two of 28]). Among six patients with sputum and nasopharyngeal swabs tested, C. psittaci was detected only in sputum in five patients. Cycle threshold (Ct) values suggested bacterial load was higher in lower respiratory specimens than in nasopharyngeal swabs. These findings support prioritizing lower respiratory specimens for real-time PCR detection of C. psittaci. Stool specimens might also have utility for diagnosis of psittacosis. |
Low but Increasing Prevalence of Reduced Beta-lactam Susceptibility Among Invasive Group B Streptococcal Isolates, US Population-Based Surveillance, 1998-2018.
Kobayashi M , McGee L , Chochua S , Apostol M , Alden NB , Farley MM , Harrison LH , Lynfield R , Vagnone PS , Smelser C , Muse A , Thomas AR , Deng L , Metcalf BJ , Beall BW , Schrag SJ . Open Forum Infect Dis 2021 8 (2) ofaa634 BACKGROUND: Invasive group B Streptococcus (iGBS) isolates with mutations in the pbp2x gene that encodes penicillin binding protein 2x can have reduced beta-lactam susceptibility (RBLS) when susceptible by Clinical and Laboratory Standards Institute (CLSI) criteria. We assessed the emergence and characteristics of RBLS strains in US iGBS isolates. METHODS: We analyzed iGBS isolates from 8 multistate population-based surveillance sites from 1998 to 2018. During 1998-2014, phenotypic antimicrobial susceptibility was determined by broth microdilution; criteria for 6 antibiotics were used to identify RBLS, followed by whole-genome sequencing (WGS). WGS for all isolates was added in 2015; we used phenotypic and genotypic results of >2000 isolates to validate phenotypic RBLS criteria and genotypic predictions. Since 2016, WGS has been used to screen for RBLS with broth microdilution confirmation of predicted RBLS isolates. RESULTS: Of 28 269 iGBS isolates, 28 (0.1%) were nonsusceptible by CLSI criteria; 137 (0.5%) met RBLS criteria. RBLS isolates were detected in all Active Bacterial Core surveillance sites. The RBLS proportion increased, especially since 2013 (odds ratio, 1.17; 95% CI, 1.03-1.32); the proportion that were nonsusceptible remained stable. CONCLUSIONS: The RBSL proportion was low but increasing among US iGBS isolates. Ongoing monitoring is needed to detect emerging threats to prevention and treatment of GBS infections. |
Early cases of SARS-CoV-2 infection in Uganda: epidemiology and lessons learned from risk-based testing approaches - March-April 2020.
Migisha R , Kwesiga B , Mirembe BB , Amanya G , Kabwama SN , Kadobera D , Bulage L , Nsereko G , Wadunde I , Tindyebwa T , Lubwama B , Kagirita AA , Kayiwa JT , Lutwama JJ , Boore AL , Harris JR , Bosa HK , Ario AR . Global Health 2020 16 (1) 114 BACKGROUND: On March 13, 2020, Uganda instituted COVID-19 symptom screening at its international airport, isolation and SARS-CoV-2 testing for symptomatic persons, and mandatory 14-day quarantine and testing of persons traveling through or from high-risk countries. On March 21, 2020, Uganda reported its first SARS-CoV-2 infection in a symptomatic traveler from Dubai. By April 12, 2020, 54 cases and 1257 contacts were identified. We describe the epidemiological, clinical, and transmission characteristics of these cases. METHODS: A confirmed case was laboratory-confirmed SARS-CoV-2 infection during March 21-April 12, 2020 in a resident of or traveler to Uganda. We reviewed case-person files and interviewed case-persons at isolation centers. We identified infected contacts from contact tracing records. RESULTS: Mean case-person age was 35 (±16) years; 34 (63%) were male. Forty-five (83%) had recently traveled internationally ('imported cases'), five (9.3%) were known contacts of travelers, and four (7.4%) were community cases. Of the 45 imported cases, only one (2.2%) was symptomatic at entry. Among all case-persons, 29 (54%) were symptomatic at testing and five (9.3%) were pre-symptomatic. Among the 34 (63%) case-persons who were ever symptomatic, all had mild disease: 16 (47%) had fever, 13 (38%) reported headache, and 10 (29%) reported cough. Fifteen (28%) case-persons had underlying conditions, including three persons with HIV. An average of 31 contacts (range, 4-130) were identified per case-person. Five (10%) case-persons, all symptomatic, infected one contact each. CONCLUSION: The first 54 case-persons with SARS-CoV-2 infection in Uganda primarily comprised incoming air travelers with asymptomatic or mild disease. Disease would likely not have been detected in these persons without the targeted testing interventions implemented in Uganda. Transmission was low among symptomatic persons and nonexistent from asymptomatic persons. Routine, systematic screening of travelers and at-risk persons, and thorough contact tracing will be needed for Uganda to maintain epidemic control. |
Invasive pneumococcal strain distributions and isolate clusters associated with persons experiencing homelessness during 2018.
Metcalf BJ , Chochua S , Walker H , Tran T , Li Z , Varghese J , Snippes Vagnone PM , Lynfield R , McGee L , Li Y , Pilishvili T , Beall B . Clin Infect Dis 2020 72 (12) e948-e956 OBJECTIVES: We aimed to characterize invasive pneumococcal disease (IPD) isolates collected from multistate surveillance in the USA during 2018 and examine within-serotype propensities of isolates to form related clusters. METHODS: We predicted strain features using whole genome sequence obtained from 2885 IPD isolates obtained through the Center for Disease Control and Prevention's Active Bacterial Core surveillance (ABCs) that has a surveillance population of approximately 34.5 million individuals distributed among 10 states. Phylogenetic analysis was provided for serotypes accounting for >27 isolates. RESULTS: Thirteen-valent conjugate vaccine (PCV13) serotypes together with 6C accounted for 23/105 (21.9%) of isolates from children aged <5 years and 820/2780 (29.5%) isolates from those aged >5 years. The most common serotypes from adult IPD isolates were serotypes 3 (413/2780, 14.9%), 22F (291/2780, 10.5%) and 9N (191/2780, 6.9%). Among children IPD isolates, serotypes 15BC (18/105, 17.1%), 3 (11/105, 10.5%) and 33F (10/105, 9.5%) were most common. Serotypes 4, 12F, 20, and 7F had the highest proportions of isolates that formed related clusters together with highest proportions of isolates from persons experiencing homelessness (PEH). Among 84 isolates from long-term care facilities, two instances of highly related isolate pairs from co-residents were identified. CONCLUSIONS: Non-PCV13 serotypes accounted for more than 70% of IPD in ABCs, however PCV13 serotype 3 is the most common IPD serotype overall. Serotypes most common among PEH were more often associated with temporally related clusters identified both among PEH and among persons not reportedly experiencing homelessness. |
Features of Streptococcus agalactiae strains recovered from pregnant women and newborns attending different hospitals in Ethiopia.
Ali MM , Woldeamanuel Y , Asrat D , Fenta DA , Beall B , Schrag S , McGee L . BMC Infect Dis 2020 20 (1) 848 BACKGROUND: Streptococcus agalactiae (Group B Streptococcus, GBS) serotypes, sequence types, and antimicrobial resistance profile vary across different geographic locations affecting disease patterns in newborns. These differences are important considerations for vaccine development efforts and data from large countries in Africa is limited. The aim of this study was to determine serotypes and genotypes of GBS isolates from pregnant women and their newborns in Ethiopia. METHODS: A hospital based cross-sectional study was conducted at three hospitals in Ethiopia from June 2014 to September 2015. Out of 225 GBS isolates, 121 GBS were recovered, confirmed and characterized at CDC's Streptococcus Laboratory using conventional microbiology methods and whole genome sequencing. RESULTS: Of the 121 isolates, 87 were from rectovaginal samples of pregnant women, 32 from different body parts of their newborns and 2 from blood of newborns with suspected sepsis. There were 25 mother-infant pairs and 24 pairs had concordant strains. The most prevalent serotypes among mothers and/or their babies were II, Ia and V (41.5, 20.6, 19.5 and 40.6%, 25 and 15.6%, respectively). Multilocus sequence typing (MLST) on 83 isolates showed ST10 (24; 28.9%) and ST2 (12; 14.5%) as most predominant sequence types. All GBS strains were susceptible to penicillin, cefotaxime and vancomycin, which correlated to the presence of wildtype PBP2x types and the lack of known vancomycin-resistance genes. Tetracycline resistance was high (73; 88%, associated primarily with tetM, but also tetO and tetL). Five isolates (6%) were resistant to erythromycin and clindamycin and 3 isolates were fluoroquinolone-resistant, containing associated mutations in gyrA and parC genes. All isolates were positive for one of four homologous Alpha/Rib family determinants and 1-2 of the three main pilus types. CONCLUSIONS: Predominant serotypes were II, Ia, and V. A limited number of clonal types were identified with two STs accounting for about half of the isolates. All strains collected in this study were susceptible to beta-lactam antibiotics and vancomycin. Typical of most GBS, these isolates were positive for single alpha-like family protein, serine-rich repeat gene, as well as 1-2 pilus determinants. |
The epidemiology and estimated etiology of pathogens detected from the upper respiratory tract of adults with severe acute respiratory infections in multiple countries, 2014-2015.
Milucky J , Pondo T , Gregory CJ , Iuliano D , Chaves SS , McCracken J , Mansour A , Zhang Y , Aleem MA , Wolff B , Whitaker B , Whistler T , Onyango C , Lopez MR , Liu N , Rahman MZ , Shang N , Winchell J , Chittaganpitch M , Fields B , Maldonado H , Xie Z , Lindstrom S , Sturm-Ramirez K , Montgomery J , Wu KH , Van Beneden CA . PLoS One 2020 15 (10) e0240309 INTRODUCTION: Etiology studies of severe acute respiratory infections (SARI) in adults are limited. We studied potential etiologies of SARI among adults in six countries using multi-pathogen diagnostics. METHODS: We enrolled both adults with SARI (acute respiratory illness onset with fever and cough requiring hospitalization) and asymptomatic adults (adults hospitalized with non-infectious illnesses, non-household members accompanying SARI patients, adults enrolled from outpatient departments, and community members) in each country. Demographics, clinical data, and nasopharyngeal and oropharyngeal specimens were collected from both SARI patients and asymptomatic adults. Specimens were tested for presence of 29 pathogens utilizing the Taqman® Array Card platform. We applied a non-parametric Bayesian regression extension of a partially latent class model approach to estimate proportions of SARI caused by specific pathogens. RESULTS: We enrolled 2,388 SARI patients and 1,135 asymptomatic adults from October 2013 through October 2015. We detected ≥1 pathogen in 76% of SARI patients and 67% of asymptomatic adults. Haemophilus influenzae and Streptococcus pneumoniae were most commonly detected (≥23% of SARI patients and asymptomatic adults). Through modeling, etiology was attributed to a pathogen in most SARI patients (range among countries: 57.3-93.2%); pathogens commonly attributed to SARI etiology included influenza A (14.4-54.4%), influenza B (1.9-19.1%), rhino/enterovirus (1.8-42.6%), and RSV (3.6-14.6%). CONCLUSIONS: Use of multi-pathogen diagnostics and modeling enabled attribution of etiology in most adult SARI patients, despite frequent detection of multiple pathogens in the upper respiratory tract. Seasonal flu vaccination and development of RSV vaccine would likely reduce the burden of SARI in these populations. |
Sequential quadriplex real-time PCR for identifying 20 common emm types of Group A Streptococcus .
Velusamy S , Jordak K , Kupor M , Chochua S , McGee L , Beall B . J Clin Microbiol 2020 59 (1) We developed a sequential quadriplex real-time PCR-based method for rapid identification of 20 emm types commonly found in invasive GAS (iGAS) strains recovered through the Centers for Disease Control and Prevention's Active Bacterial Core surveillance. Each emm real-time PCR assay shows high specificity and accurately identified the respective target emm type, including emm subtypes in the United States. Furthermore, this method is useful for rapid typing of GAS isolates and culture-negative specimens during outbreak investigations. |
Antibody Responses after Classroom Exposure to Teacher with Coronavirus Disease, March 2020.
Brown NE , Bryant-Genevier J , Bandy U , Browning CA , Berns AL , Dott M , Gosciminski M , Lester SN , Link-Gelles R , Quilliam DN , Sejvar J , Thornburg NJ , Wolff BJ , Watson J . Emerg Infect Dis 2020 26 (9) 2263-5 After returning from Europe to the United States, on March 1, 2020, a symptomatic teacher received positive test results for severe acute respiratory syndrome coronavirus 2. Of the 21 students exposed to the teacher in the classroom, serologic results suggested past infection for 2. Classroom contact may result in virus transmission. |
Upsurge of conjugate vaccine serotype 4 invasive pneumococcal disease clusters among adults experiencing homelessness in California, Colorado, and New Mexico.
Beall B , Walker H , Tran T , Li Z , Varghese J , McGee L , Li Y , Metcalf BJ , Gierke R , Mosites E , Chochua S , Pilishvili T . J Infect Dis 2020 223 (7) 1241-1249 After 7-valent pneumococcal conjugate vaccine introduction in the US in 2000, invasive pneumococcal disease (IPD) due to serotype 4 greatly decreased in children and adults. Starting in 2013, serotype 4 IPD incidence increased among adults >18 years old within three of ten Active Bacterial Core surveillance sites. Of 325 serotype 4 cases among adults in 2010-2018, 36% were from persons experiencing homelessness (PEH); incidence of serotype 4 IPD among PEH was 100-300 times higher than in the general population within these 3 areas. Genome sequencing for isolates recovered during 2015-2018 (n=246), revealed that increases in serotype 4 IPD were driven by lineages, ST10172, ST244, and ST695. Within each lineage, clusters of near-identical isolates indicated close temporal relatedness. Increases in serotype 4 IPD were limited to Colorado, California, and New Mexico, with highest increases observed among PEH, who were at increased risk for exposure to and infections caused by these strains. |
Estimating neonatal herpes simplex virus incidence and mortality using capture-recapture, Florida
Matthias J , du Bernard S , Schillinger JA , Hong J , Pearson V , Peterman TA . Clin Infect Dis 2020 73 (3) 506-512 BACKGROUND: Neonatal herpes simplex virus infection (nHSV) leads to severe morbidity and mortality, but national incidence is uncertain. Florida regulations require that healthcare providers report cases, and clinical laboratories report test results when herpes simplex virus (HSV) is detected. We estimated nHSV incidence using laboratory-confirmed provider-reported cases and electronic laboratory reports (ELR) stored separately from provider-reported cases. Mortality was estimated using provider-reported cases, ELR, and vital statistics death records. METHODS: For 2011-2017, we reviewed: provider-reported cases (infants <60 days of age with HSV infection confirmed by culture or polymerase chain reaction (PCR)), ELR of HSV-positive culture or PCR results in the same age group, and death certificates containing International Classification of Disease, Tenth Revision, codes for herpes infection: P35.2, B00.0-B00.9, and A60.0-A60.9. Provider-reported cases were matched against ELR reports. Death certificates were matched with provider and ELR reports. Chapman's capture-recapture method was used to estimate nHSV incidence and mortality. Mortality from all three sources was estimated using log-linear modelling. RESULTS: Providers reported 114 nHSV cases and ELR identified 197 nHSV cases. Forty-six cases were common to both datasets, leaving 265 unique nHSV reports. Chapman's estimate suggests 483 (95% C.I. 383-634) nHSV cases occurred (31.5 infections per 100,000 live births). nHSV deaths were reported by providers (n=9), ELR (n=18), and vital statistics (n=31), totaling 34 unique reports. Log-linear modeling estimates 35.8 fatal cases occurred (95% CI 34-40). CONCLUSIONS: Chapman's estimates using data collected over 7 years in Florida, conclude nHSV infections occurred at a rate of 1 per 3000 live births. |
Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates.
Gladstone RA , Lo SW , Goater R , Yeats C , Taylor B , Hadfield J , Lees JA , Croucher NJ , van Tonder AJ , Bentley LJ , Quah FX , Blaschke AJ , Pershing NL , Byington CL , Balaji V , Hryniewicz W , Sigauque B , Ravikumar KL , Almeida SCG , Ochoa TJ , Ho PL , du Plessis M , Ndlangisa KM , Cornick JE , Kwambana-Adams B , Benisty R , Nzenze SA , Madhi SA , Hawkins PA , Pollard AJ , Everett DB , Antonio M , Dagan R , Klugman KP , von Gottberg A , Metcalf BJ , Li Y , Beall BW , McGee L , Breiman RF , Aanensen DM , Bentley SD . Microb Genom 2020 6 (5) Knowledge of pneumococcal lineages, their geographic distribution and antibiotic resistance patterns, can give insights into global pneumococcal disease. We provide interactive bioinformatic outputs to explore such topics, aiming to increase dissemination of genomic insights to the wider community, without the need for specialist training. We prepared 12 country-specific phylogenetic snapshots, and international phylogenetic snapshots of 73 common Global Pneumococcal Sequence Clusters (GPSCs) previously defined using PopPUNK, and present them in Microreact. Gene presence and absence defined using Roary, and recombination profiles derived from Gubbins are presented in Phandango for each GPSC. Temporal phylogenetic signal was assessed for each GPSC using BactDating. We provide examples of how such resources can be used. In our example use of a country-specific phylogenetic snapshot we determined that serotype 14 was observed in nine unrelated genetic backgrounds in South Africa. The international phylogenetic snapshot of GPSC9, in which most serotype 14 isolates from South Africa were observed, highlights that there were three independent sub-clusters represented by South African serotype 14 isolates. We estimated from the GPSC9-dated tree that the sub-clusters were each established in South Africa during the 1980s. We show how recombination plots allowed the identification of a 20 kb recombination spanning the capsular polysaccharide locus within GPSC97. This was consistent with a switch from serotype 6A to 19A estimated to have occured in the 1990s from the GPSC97-dated tree. Plots of gene presence/absence of resistance genes (tet, erm, cat) across the GPSC23 phylogeny were consistent with acquisition of a composite transposon. We estimated from the GPSC23-dated tree that the acquisition occurred between 1953 and 1975. Finally, we demonstrate the assignment of GPSC31 to 17 externally generated pneumococcal serotype 1 assemblies from Utah via Pathogenwatch. Most of the Utah isolates clustered within GPSC31 in a USA-specific clade with the most recent common ancestor estimated between 1958 and 1981. The resources we have provided can be used to explore to data, test hypothesis and generate new hypotheses. The accessible assignment of GPSCs allows others to contextualize their own collections beyond the data presented here. |
Evaluation of Commercial Molecular Diagnostic Methods for the Detection and Determination of Macrolide Resistance in Mycoplasma pneumoniae .
Leal SMJr , Totten AH , Xiao L , Crabb DM , Ratliff A , Duffy LB , Fowler KB , Mixon E , Winchell JM , Diaz MH , Benitez AJ , Wolff BJ , Qin X , Tang YW , Gonzalez M , Selvarangan R , Hong T , Brooks E , Dallas S , Atkinson TP , Zheng X , Dien Bard J , Waites KB . J Clin Microbiol 2020 58 (6) We evaluated six commercial molecular tests targeting M. pneumoniae: the BioFire FilmArray Respiratory Panel (RP), the Meridian Alethia Mycoplasma Direct, the GenMark ePlex Respiratory Pathogen Panel (RPP), the Luminex NxTAG RPP, the ELITech ELITe InGenius Mycoplasma MGB Research Use Only Polymerase Chain Reaction (PCR), and the SpeeDx Resistance Plus MP. Laboratory-developed PCR assays at the University of Alabama at Birmingham and the Centers for Disease Control and Prevention were used as reference standards. Among 428 specimens, 212 were designated confirmed-positives for M. pneumoniae The highest clinical sensitivities were found with the InGenius (99.5%) and the FilmArray RP (98.1%). The Resistance Plus MP identified 93.3% of the confirmed-positive specimens, whereas 83.6%, 64.6%, and 55.7% were identified by the ePlex RPP, NxTAG RPP, and Mycoplasma Direct assays, respectively. There was no significant difference between the sensitivity of the reference methods and that of the FilmArray RP and InGenius assays, but the remaining four assays detected significantly fewer positive specimens (p < 0.05). Specificities of all assays were 99.5 - 100%. The Resistance Plus MP detected macrolide resistance in 27/33 specimens resulting in a sensitivity of 81.8%. This study provides the first large scale comparison of commercial molecular assays for detection of M. pneumoniae in the United States and identified clear differences among their performance. Additional studies are necessary to explore the impact of variable test performance on patient outcome. |
Entamoeba histolytica infections in wild and semi-wild orangutans in Sumatra and Kalimantan
Stuart P , Yalcindag E , Ali IKM , Peckova R , Nurcahyo W , Morrogh-Bernard H , Foitova I . Am J Primatol 2020 82 (5) e23124 Key to the success of orangutan conservation management practices is the prevention of the introduction of infectious diseases to the remaining populations. Previous reports of Entamoeba spp. positive orangutans are of concern as Entamoeba spp. infection has been linked to morbidity and mortality in primates. It remains to be determined if the Entamoeba species infecting orangutans is the pathogenic Entamoeba histolytica. Orangutan fecal samples have been collected from orangutans from sites in Sumatra (Bukit Lawang, Ketambe, and Suaq, 241 samples from 64 individuals), and two sites in Kalimantan (Sebangau and Tuanan, 129 samples from 39 individuals). All samples were from wild orangutans except for a proportion from Sumatra which were from semi-wild (108 samples, 10 individuals). E. histolytica-specific nested PCR assays were carried out on the fecal samples. A total of 36 samples from 17 individuals tested positive for E. histolytica. When compared with published sequences using NCBI BLAST the E. histolytica positive samples showed a 98-99% concordance. The majority (76%, n = 36) of the positive isolates came from semi-wild orangutans in Bukit Lawang. This study supports the growing body of evidence that contact with humans is an important risk factor for infection of wild primates with E. histolytica. |
Multistate, population-based distributions of candidate vaccine targets, clonal complexes, and resistance features of invasive Group B Streptococci within the US: 2015-2017.
McGee L , Chochua S , Li Z , Mathis S , Rivers J , Metcalf B , Ryan A , Alden N , Farley MM , Harrison LH , Snippes Vagnone P , Lynfield R , Smelser C , Muse A , Thomas AR , Schrag S , Beall BW . Clin Infect Dis 2020 72 (6) 1004-1013 BACKGROUND: Group B Streptococcus (GBS) is a leading cause of neonatal sepsis and meningitis and an important cause of invasive infections in pregnant and nonpregnant adults. Vaccines targeting capsule polysaccharides and common proteins are under development. METHODS: Using whole genome sequencing (WGS), a validated bioinformatics pipeline, and targeted antimicrobial susceptibility testing, we characterized 6,340 invasive GBS recovered during 2015-2017 through population-based Active Bacterial Core surveillance (ABCs) in eight states. RESULTS: Six serotypes accounted for 98.4% of isolates (21.8% Ia, 17.6% V, 17.1% II, 15.6% III, 14.5% Ib, 11.8% IV). Most (94.2%) isolates were in eleven clonal complexes (CCs) comprised of multilocus sequence types (MLSTs) identical or closely related to STs 1, 8, 12, 17, 19, 22, 23, 28, 88, 452 and 459. Fifty-four isolates (0.87%) had point mutations within pbp2x associated with non-susceptibility to one or more beta-lactam antibiotics. Genes conferring resistance to macrolides and/or lincosamides were found in 56% of isolates; 85.2% of isolates had tetracycline resistance genes. Two isolates carrying vanG were vancomycin-nonsusceptible (MIC 2microg/ml). Nearly all isolates possessed capsule genes, 1-2 of the three main pilus gene clusters, and one of four homologous Alpha/Rib family determinants. Presence of hvgA virulence gene was primarily restricted to serotype III/CC17 isolates (465 isolates), but 8 exceptions (7 IV/CC452 and 1 IV/CC17) were observed. CONCLUSIONS: This first comprehensive, population-based quantitation of strain features in the United States suggests current vaccine candidates should have good coverage. Beta-lactams remain appropriate for first line treatment and prophylaxis, but emergence of nonsusceptibility warrants ongoing monitoring. |
A replicable approach to promoting best practices: Translating cardiovascular disease prevention research
Hawkins NA , Bhuiya AR , Shantharam S , Chapel JM , Taylor LN , Thigpen S , Decker A , Moeti R , Bernard S , Jones CD , Schooley M . J Public Health Manag Pract 2020 27 (2) 109-116 OBJECTIVE: Significant delays in translating health care-related research into public health programs and medical practice mean that people may not get the best care when they need it. Regarding cardiovascular disease, translation delays can mean lives may be unnecessarily lost each year. To facilitate the translation of knowledge to action, we created a Best Practices Guide for Cardiovascular Disease Prevention Programs. DESIGN: Using the Rapid Synthesis Translation Process and the Best Practices Framework as guiding frameworks, we collected and rated research evidence for hypertension control and cholesterol management strategies. After identifying best practices, we gathered information about programs that were implementing the practices and about resources useful for implementation. Research evidence and supplementary information were consolidated in an informational resource and published online. Web metrics were collected and analyzed to measure use and reach of the guide. RESULTS: The Best Practices Guide was released in January 2018 and included background information and resources on 8 best practice strategies. It was published as an online resource, publicly accessible from the Centers for Disease Control and Prevention Web site in 2 different formats. Web metrics show that in the first year after publication, there were 25 589 Web page views and 2467 downloads. A query of partner use of the guide indicated that it was often shared in partners' own resources, newsletters, and online material. CONCLUSION: In following a systematic approach to creating the Best Practices Guide and documenting the steps taken in its development, we offer a replicable approach for translating research on health care practices into a resource to facilitate implementation. The success of this approach is attributed to 3 key factors: using a prescribed and documented approach to evidence translation, working closely with stakeholders throughout the process, and prioritizing the content design and accessibility of the final product. |
Mapping and analysis of US state and urban local sodium reduction laws
Sloan AA , Keane T , Pettie JR , Bhuiya AR , Taylor LN , Bates M , Bernard S , Akinleye F , Gilchrist S . J Public Health Manag Pract 2020 26 Suppl 2 S62-s70 CONTEXT: Excessive sodium consumption contributes to high blood pressure, which is a risk factor for cardiovascular disease. OBJECTIVES: To (1) identify state and urban local laws addressing adult or general population sodium consumption in foods and beverages and (2) align findings to a previously published evidence classification review, the Centers for Disease Control and Prevention Sodium Quality and Impact of Component (QuIC) evidence assessment. DESIGN: Systematic collection of sodium reduction laws from all 50 states, the 20 most populous counties in the United States, and the 20 most populous cities in the United States, including Washington, District of Columbia, effective on January 1, 2019. Relevant laws were assigned to 1 or more of 6 interventions: (1) provision of sodium information in restaurants or at point of purchase; (2) consumer incentives to purchase lower sodium foods; and provision of lower sodium offerings in (3) workplaces, (4) vending machines, (5) institutional meal services, and (6) grocery, corner, and convenience stores. The researchers used Westlaw, local policy databases or city Web sites, and general nutrition policy databases to identify relevant laws. RESULTS: Thirty-nine sodium reduction laws and 10 state laws preempting localities from enacting sodium reduction laws were identified. Sodium reduction laws were more common in local jurisdictions and in the Western United States. Sodium reduction laws addressing meal services (n = 17), workplaces (n = 12), labeling (n = 13), and vending machines (n = 11) were more common, while those addressing grocery stores (n = 2) or consumer incentives (n = 6) were less common. Laws with high QuIC evidence classifications were generally more common than laws with low QuIC evidence classifications. CONCLUSIONS: The distribution of sodium laws in the US differed by region, QuIC classification, and jurisdiction type, indicating influence from public health and nonpublic health factors. Ongoing research is warranted to determine how the strength of public health evidence evolves over time and how those changes correlate with uptake of sodium reduction law. |
Analysis of Global Collection of Group A Streptococcus Genomes Reveals that the Majority Encode a Trio of M and M-Like Proteins.
Frost HR , Davies MR , Delforge V , Lakhloufi D , Sanderson-Smith M , Srinivasan V , Steer AC , Walker MJ , Beall B , Botteaux A , Smeesters PR . mSphere 2020 5 (1) The core Mga (multiple gene activator) regulon of group A Streptococcus (GAS) contains genes encoding proteins involved in adhesion and immune evasion. While all GAS genomes contain genes for Mga and C5a peptidase, the intervening genes encoding M and M-like proteins vary between strains. The genetic make-up of the Mga regulon of GAS was characterized by utilizing a collection of 1,688 GAS genomes that are representative of the global GAS population. Sequence variations were examined with multiple alignments, and the expression of all core Mga regulon genes was examined by quantitative reverse transcription-PCR in a representative strain collection. In 85.2% of the sampled genomes, the Mga locus contained genes encoding Mga, Mrp, M, Enn, and C5a peptidase proteins. These isolates account for 53% of global infections. Only 9.1% of genomes did not contain either an mrp or an enn gene. The pairwise identity within Enn (68.6%) and Mrp (83.2%) protein sequences was higher than within M proteins (44.7%). Gene expression varied between strains tested, but high expression was recorded for all genes in at least one strain. Previous nomenclature issues were clarified with molecular gene definitions. Our findings support a shift in focus in the GAS research field to further consider the role of Mrp and Enn in virulence and vaccine development.IMPORTANCE While the GAS M protein has been the leading vaccine target for decades, the bacteria encode many other virulence factors of interest for vaccine development. In this work, we show that emm-like genes are encoded in a remarkable majority of GAS genomes and expressed at a level similar to that for the emm gene. In collaboration with the U.S. Centers for Disease Control, we developed molecular definitions of the different emm and emm-like gene families. This clarification should abrogate mistyping of strains, especially in the area of whole-genome typing. We have also updated the emm-typing collection by removing emm-like gene sequences and provided in-depth analysis of Mrp and Enn protein sequence structure and diversity. |
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