Last data update: Apr 16, 2024. (Total: 46543 publications since 2009)
Records 1-30 (of 213 Records) |
Query Trace: Lines C [original query] |
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Sequence introgression from exogenous lineages underlies genomic and biological differences among Cryptosporidium parvum IOWA lines
Huang W . Water Res 2024 254 121333 The IOWA strain of Cryptosporidium parvum is widely used in studies of the biology and detection of the waterborne pathogens Cryptosporidium spp. While several lines of the strain have been sequenced, IOWA-II, the only reference of the original subtype (IIaA15G2R1), exhibits significant assembly errors. Here we generated a fully assembled genome of IOWA-CDC of this subtype using PacBio and Illumina technologies. In comparative analyses of seven IOWA lines maintained in different laboratories (including two sequenced in this study) and 56 field isolates, IOWA lines (IIaA17G2R1) with less virulence had mixed genomes closely related to IOWA-CDC but with multiple sequence introgressions from IOWA-II and unknown lineages. In addition, the IOWA-IIaA17G2R1 lines showed unique nucleotide substitutions and loss of a gene associated with host infectivity, which were not observed in other isolates analyzed. These genomic differences among IOWA lines could be the genetic determinants of phenotypic traits in C. parvum. These data provide a new reference for comparative genomic analyses of Cryptosporidium spp. and rich targets for the development of advanced source tracking tools. |
Satellite data for environmental justice: a scoping review of the literature in the United States
Sayyed TK . Environ Res Lett 2024 19 (3) In support of the environmental justice (EJ) movement, researchers, activists, and policymakers often use environmental data to document evidence of the unequal distribution of environmental burdens and benefits along lines of race, class, and other socioeconomic characteristics. Numerous limitations, such as spatial or temporal discontinuities, exist with commonly used data measurement techniques, which include ground monitoring and federal screening tools. Satellite data is well poised to address these gaps in EJ measurement and monitoring; however, little is known about how satellite data has advanced findings in EJ or can help to promote EJ through interventions. Thus, this scoping review aims to (1) explore trends in study design, topics, geographic scope, and satellite datasets used to research EJ, (2) synthesize findings from studies that use satellite data to characterize disparities and inequities across socio-demographic groups for various environmental categories, and (3) capture how satellite data are relevant to policy and real-world impact. Following PRISMA extension guidelines for scoping reviews, we retrieved 81 articles that applied satellite data for EJ research in the United States from 2000 to 2022. The majority of the studies leveraged the technical advantages of satellite data to identify socio-demographic disparities in exposure to environmental risk factors, such as air pollution, and access to environmental benefits, such as green space, at wider coverage and with greater precision than previously possible. These disparities in exposure and access are associated with health outcomes such as increased cardiovascular and respiratory diseases, mental illness, and mortality. Research using satellite data to illuminate EJ concerns can contribute to efforts to mitigate environmental inequalities and reduce health disparities. Satellite data for EJ research can therefore support targeted interventions or influence planning and policy changes, but significant work remains to facilitate the application of satellite data for policy and community impact. © 2024 The Author(s). Published by IOP Publishing Ltd. |
Low-temperature culture enhances production of flavivirus virus-like particles in mammalian cells
Fan YC . Appl Microbiol Biotechnol 2024 108 (1) 242 Flavivirus virus-like particles (VLPs) exhibit a striking structural resemblance to viral particles, making them highly adaptable for various applications, including vaccines and diagnostics. Consequently, increasing VLPs production is important and can be achieved by optimizing expression plasmids and cell culture conditions. While attempting to express genotype III (GIII) Japanese encephalitis virus (JEV) VLPs containing the G104H mutation in the envelope (E) protein, we failed to generate VLPs in COS-1 cells. However, VLPs production was restored by cultivating plasmid-transfected cells at a lower temperature, specifically 28 °C. Furthermore, we observed that the enhancement in JEV VLPs production was independent of amino acid mutations in the E protein. The optimal condition for JEV VLPs production in plasmid-transfected COS-1 cells consisted of an initial culture at 37 °C for 6 h, followed by a shift to 28 °C (37/28 °C) for cultivation. Under 37/28 °C cultivation conditions, flavivirus VLPs production significantly increased in various mammalian cell lines regardless of whether its expression was transiently transfected or clonally selected cells. Remarkably, clonally selected cell lines expressing flavivirus VLPs consistently achieved yields exceeding 1 μg/ml. Binding affinity analyses using monoclonal antibodies revealed similar binding patterns for VLPs of genotype I (GI) JEV, GIII JEV, West Nile virus (WNV), and dengue virus serotype 2 (DENV-2) produced under both 37 °C or 37/28 °C cultivation conditions. In summary, our study demonstrated that the production of flavivirus VLPs can be significantly improved under 37/28 °C cultivation conditions without affecting the conformational structure of the E protein. KEYPOINTS: • Low-temperature culture (37/28 °C) enhances production of flavivirus VLPs. • Flavivirus VLPs consistently achieved yields exceeding 1 μg/ml. • 37/28 °C cultivation did not alter the structure of flavivirus VLPs. |
Metabolome dynamics during wheat domestication.
Ben-Abu Y , Itsko M . Sci Rep 2022 12 (1) 8532 One of the most important crops worldwide is wheat. Wheat domestication took place about 10,000 years ago. Not only that its wild progenitors have been discovered and phenotypically characterized, but their genomes were also sequenced and compared to modern wheat. While comparative genomics is essential to track genes that contribute to improvement in crop yield, comparative analyses of functional biological end-products, such as metabolites, are still lacking. With the advent of rigorous mass-spectrometry technologies, it is now possible to address that problem on a big-data scale. In attempt to reveal classes of metabolites, which are associated with wheat domestication, we analyzed the metabolomes of wheat kernel samples from various wheat lines. These wheat lines represented subspecies of tetraploid wheat along primary and secondary domestications, including wild emmer, domesticated emmer, landraces durum, and modern durum. We detected that the groups of plant metabolites such as plant-defense metabolites, antioxidants and plant hormones underwent significant changes during wheat domestication. Our data suggest that these metabolites may have contributed to the improvement in the agricultural fitness of wheat. Closer evaluation of specific metabolic pathways may result in the future in genetically-engineered high-yield crops. |
Building the vector in: construction practices and the invasion and persistence of Anopheles stephensi in Jigjiga, Ethiopia
Yared S , Gebresilassie A , Aklilu E , Abdulahi E , Kirstein OD , Gonzalez-Olvera G , Che-Mendoza A , Bibiano-Marin W , Waymire E , Lines J , Lenhart A , Kitron U , Carter T , Manrique-Saide P , Vazquez-Prokopec GM . Lancet Planet Health 2023 7 (12) e999-e1005 Anopheles stephensi is a major vector of malaria in Asia and the Arabian Peninsula, and its recent invasion into Africa poses a major threat to malaria control and elimination efforts on the continent. The mosquito is well adapted to urban environments, and its presence in Africa could potentially lead to an increase in malaria transmission in cities. Most of the knowledge about An stephensi ecology in Africa has been generated from studies conducted during the rainy season, when vectors are most abundant. Here, we provide evidence from the peak of the dry season in the city of Jigjiga in Ethiopia, and report An stephensi immature stages infesting predominantly in water reservoirs made to support construction operations (ie, in construction sites or associated with brick-manufacturing businesses). Political and economic changes in Ethiopia (particularly the Somali Region) have fuelled an unprecedented construction boom since 2018 that, in our opinion, has been instrumental in the establishment, persistence, and propagation of An stephensi via the year-round availability of perennial larval habitats associated with construction. We argue that larval source management during the dry season might provide a unique opportunity for focused control of An stephensi in Jigjiga and similar areas. |
Executive summary: A compendium of strategies to prevent healthcare-associated infections in acute-care hospitals: 2022 updates
Yokoe DS , Advani SD , Anderson DJ , Babcock HM , Bell M , Berenholtz SM , Bryant KA , Buetti N , Calderwood MS , Calfee DP , Dubberke ER , Ellingson KD , Fishman NO , Gerding DN , Glowicz J , Hayden MK , Kaye KS , Klompas M , Kociolek LK , Landon E , Larson EL , Malani AN , Marschall J , Meddings J , Mermel LA , Patel PK , Perl TM , Popovich KJ , Schaffzin JK , Septimus E , Trivedi KK , Weinstein RA , Maragakis LL . Infect Control Hosp Epidemiol 2023 44 (10) 1-15 Strategies to prevent catheter-associated urinary tract infections (CAUTIs) | Essential practices | Infrastructure and resources | 1 Perform a CAUTI risk assessment and implement an organization-wide program to identify and remove catheters that are no longer necessary using 1 or | more methods documented to be effective. (Quality of evidence: MODERATE) | 2 Provide appropriate infrastructure for preventing CAUTI. (Quality of evidence: LOW) | 3 Provide and implement evidence-based protocols to address multiple steps of the urinary catheter life cycle: catheter appropriateness (step 0), insertion | technique (step 1), maintenance care (step 2), and prompt removal (step 3) when no longer appropriate. (Quality of evidence: LOW) | 4 Ensure that only trained healthcare personnel (HCP) insert urinary catheters and that competency is assessed regularly. (Quality of evidence: LOW) | 5 Ensure that supplies necessary for aseptic technique for catheter insertion are available and conveniently located. (Quality of evidence: LOW) | 6 Implement a system for documenting the following in the patient record: physician order for catheter placement, indications for catheter insertion, date | and time of catheter insertion, name of individual who inserted catheter, nursing documentation of placement, daily presence of a catheter and | maintenance care tasks, and date and time of catheter removal. Record criteria for removal and justification for continued use. (Quality of evidence: | LOW) | 7 Ensure that sufficiently trained HCP and technology resources are available to support surveillance for catheter use and outcomes. (Quality of evidence: | LOW) | 8 Perform surveillance for CAUTI if indicated based on facility risk assessment or regulatory requirements. (Quality of evidence: LOW) | 9 Standardize urine culturing by adapting an institutional protocol for appropriate indications for urine cultures in patients with and without indwelling | catheters. Consider incorporating these indications into the electronic medical record, and review indications for ordering urine cultures in the CAUTI | risk assessment. (Quality of evidence: LOW) | Education and training | 1 Educate HCP involved in the insertion, care, and maintenance of urinary catheters about CAUTI prevention, including alternatives to indwelling | catheters, and procedures for catheter insertion, management, and removal. (Quality of evidence: LOW) | 2 Assess healthcare professional competency in catheter use, catheter care, and maintenance. (Quality of evidence: LOW) | 3 Educate HCP about the importance of urine-culture stewardship and provide indications for urine cultures. (Quality of evidence: LOW) | 4 Provide training on appropriate collection of urine. Specimens should be collected and should arrive at the microbiology laboratory as soon as possible, | preferably within an hour. If delay in transport to the laboratory is expected, samples should be refrigerated (no more than 24 hours) or collected in | preservative urine transport tubes. (Quality of evidence: LOW) | 5 Train clinicians to consider other methods for bladder management, such as intermittent catheterization or external male or female collection devices, | when appropriate, before placing an indwelling urethral catheter. (Quality of evidence: LOW) | 6 Share data in a timely fashion and report to appropriate stakeholders. (Quality of evidence: LOW) | Insertion of indwelling catheters | 1 Insert urinary catheters only when necessary for patient care and leave in place only as long as indications remain. (Quality of evidence: MODERATE) | 2 Consider other methods for bladder management such as intermittent catheterization, or external male or female collection devices, when appropriate. | (Quality of evidence: LOW) | 3 Use appropriate technique for catheter insertion. (Quality of evidence: MODERATE). | 4 Consider working in pairs to help perform patient positioning and monitor for potential contamination during placement. (Quality of evidence: LOW) | 5 Practice hand hygiene (based on CDC or WHO guidelines) immediately before insertion of the catheter and before and after any manipulation of the | catheter site or apparatus. (Quality of evidence: LOW) | 6 Insert catheters following aseptic technique and using sterile equipment. (Quality of evidence: LOW) | 7 Use sterile gloves, drape, and sponges, a sterile antiseptic solution for cleaning the urethral meatus, and a sterile single-use packet of lubricant jelly for | insertion. (Quality of evidence: LOW) | 8 Use a catheter with the smallest feasible diameter consistent with proper drainage to minimize urethral trauma but consider other catheter types and | sizes when warranted for patients with anticipated difficult catheterization to reduce the likelihood that a patient will experience multiple, sometimes | traumatic, catheterization attempts. (Quality of evidence: LOW) | Management of indwelling catheters | 1 Properly secure indwelling catheters after insertion to prevent movement and urethral traction. (Quality of evidence: LOW) | 2 Maintain a sterile, continuously closed drainage system. (Quality of evidence: LOW) | 3 Replace the catheter and the collecting system using aseptic technique when breaks in aseptic technique, disconnection, or leakage occur. (Quality of | evidence: LOW) | 4 For examination of fresh urine, collect a small sample by aspirating urine from the needleless sampling port with a sterile syringe/cannula adaptor after | cleansing the port with disinfectant. (Quality of evidence: LOW) | (Continued) | 2 Deborah S. Yokoe et al | https://doi.org/10.1017/ice.2023.138 Published online by Cambridge University Press | Strategies to prevent central-line–associated bloodstream infections (CLABSIs) | (Continued ) | 5 Facilitate timely transport of urine samples to laboratory. If timely transport is not feasible, consider refrigerating urine samples or using samplecollection cups with preservatives. Obtain larger volumes of urine for special analyses (eg, 24-hour urine) aseptically from the drainage bag. (Quality of | evidence: LOW) | 6 Maintain unobstructed urine flow. (Quality of evidence: LOW) | 7 Employ routine hygiene. Cleaning the meatal area with antiseptic solutions is an unresolved issue, though emerging literature supports chlorhexidine | use prior to catheter insertion. Alcohol-based products should be avoided given concerns about the alcohol causing drying of the mucosal tissues. | (Quality of evidence: LOW) | Additional approaches | 1 Develop a protocol for standardizing diagnosis and management of postoperative urinary retention, including nurse-directed use of intermittent | catheterization and use of bladder scanners when appropriate as alternatives to indwelling urethral catheterization. (Quality of evidence: MODERATE) | 2 Establish a system for analyzing and reporting data on catheter use and adverse events from catheter use. (Quality of evidence: LOW) | 3 Establish a system for defining, analyzing, and reporting data on non–catheter-associated UTIs, particularly UTIs associated with the use of devices | being used as alternatives to indwelling urethral catheters. (Quality of evidence: LOW) | Essential practices | Before insertion | 1 Provide easy access to an evidence-based list of indications for CVC use to minimize unnecessary CVC placement. (Quality of evidence: LOW) | 2 Require education and competency assessment of healthcare personnel (HCP) involved in insertion, care and maintenance of CVCs about CLABSI | prevention. (Quality of evidence: MODERATE) | 3 Bathe ICU patients aged >2 months with a chlorhexidine preparation on a daily basis. (Quality of evidence: HIGH) | At insertion | 1 In ICU and non-ICU settings, a facility should have a process in place, such as a checklist, to ensure adherence to infection prevention practices at the | time of CVC insertion. (Quality of evidence: MODERATE) | 2 Perform hand hygiene prior to catheter insertion or manipulation. (Quality of evidence: MODERATE) | 3 The subclavian site is preferred to reduce infectious complications when the catheter is placed in the ICU setting. (Quality of evidence: HIGH) | 4 Use an all-inclusive catheter cart or kit. (Quality of evidence: MODERATE) | 5 Use ultrasound guidance for catheter insertion. (Quality of evidence: HIGH) | 6 Use maximum sterile barrier precautions during CVC insertion. (Quality of evidence: MODERATE) | After insertion | 1 Ensure appropriate nurse-to-patient ratio and limit use of float nurses in ICUs. (Quality of evidence: HIGH) | 2 Use chlorhexidine-containing dressings for CVCs in patients aged >2 months. (Quality of evidence: HIGH) | 3 For nontunneled CVCs in adults and children, change transparent dressings and perform site care with a chlorhexidine-based antiseptic at least every 7 | days or immediately if the dressing is soiled, loose, or damp. Change gauze dressings every 2 days or earlier if the dressing is soiled, loose, or damp. | (Quality of evidence: MODERATE) | 4 Disinfect catheter hubs, needleless connectors, and injection ports before accessing the catheter. (Quality of evidence: MODERATE) | 5 Remove nonessential catheters. (Quality of evidence: MODERATE) | 6 Routine replacement of administration sets not used for blood, blood products, or lipid formulations can be performed at intervals up to 7 days. | (Quality of evidence: HIGH) | 7 Perform surveillance for CLABSI in ICU and non-ICU settings. (Quality of evidence: HIGH) | Additional approaches | 1 Use antiseptic or antimicrobial-impregnated CVCs. (Quality of evidence: HIGH in adult patients; MODERATE in pediatric patients) | 2 Use antimicrobial lock therapy for long-term CVCs. (Quality of evidence: HIGH) | 3 Use recombinant tissue plasminogen activating factor (rt-PA) once weekly after hemodialysis in patients undergoing hemodialysis through a CVC. | (Quality of evidence: HIGH) | 4 Utilize infusion or vascular access teams for reducing CLABSI rates. (Quality of evidence: LOW) | 5 Use antimicrobial ointments for hemodialysis catheter-insertion sites. (Quality of evidence: HIGH) | 6 Use an antiseptic-containing hub, connector cap, or port protector to cover connectors. (Quality of evidence: MODERATE) | Infection Control & Hospital Epidemiology 3 | https://doi.org/10.1017/ice.2023.138 Published online by Cambridge University Press | Strategies to prevent Clostridioides difficile infections (CDIs) | Strategies to prevent methicillin-resistant Staphylococcus aureus (MRSA) transmission and infection | Essential practices | 1 Encourage appropriate use of antimicrobials through implementation of an antimicrobial stewardship program. (Quality of evidence: MODERATE) | 2 Implement diagnostic stewardship practices for ensuring appropriate use and interpretation of C. difficile testing. (Quality of evidence: LOW) | 3 Use contact precautions for infected patients, single-patient room preferred. (Quality of evidence: LOW for hand hygiene; MODERATE for gloves; LOW | for gowns; LOW for single-patient room) | 4 Adequately clean and disinfect equipment and the environment of patients with CDI. (Quality of evidence: LOW for equipment; LOW for environment) | 5 Assess the adequacy of room cleaning. (Quality of evidence: LOW) | 6 Implement a laboratory-based alert system to provide immediate notification to infection preventionists and clinical personnel about newly diagnosed | patients with CDI. (Quality of evidence: LOW) | 7 Conduct CDI surveillance and analyze and report CDI data. (Quality of evidence: LOW) | 8 Educate healthcare personnel (HCP), environmental service personnel, and hospital administration about CDI. (Quality of evidence: LOW) | 9 Educate patients and their families about CDI as appropriate. (Quality of evidence: LOW) | 10 Measure compliance with CDC or WHO hand hygiene and contact precaution recommendations. (Quality of evidence: LOW) | Additional approaches | 1 Intensify the assessment of compliance with process measures. (Quality of evidence: LOW) | 2 Perform hand hygiene with soap and water as the preferred method following care of or interacting with the healthcare environment of a patient with | CDI. (Quality of evidence: LOW) | 3 Place patients with diarrhea on contact precautions while C. difficile testing is pending. (Quality of evidence: LOW) | 4 Prolong the duration of contact precautions after the patient becomes asymptomatic until hospital discharge. (Quality of evidence: LOW) | 5 Use an EPA-approved sporicidal disinfectant, such as diluted (1:10) sodium hypochlorite, for environmental cleaning and disinfection. Implement a | system to coordinate with environmental services if it is determined that sodium hypochlorite is needed for environmental disinfection. (Quality of | evidence: LOW) | Essential practices | 1 Implement an MRSA monitoring program. (Quality of evidence: LOW) | 2 Conduct an MRSA risk assessment. (Quality of evidence: LOW) | 3 Promote compliance with CDC or World Health Organization (WHO) hand hygiene recommendations. (Quality of evidence: MODERATE) | 4 Use contact precautions for MRSA-colonized and MRSA-infected patients. A facility that chooses or has already chosen to modify the use of contact | precautions for some or all of these patients should conduct an MRSA-specific risk assessment to evaluate the facility for transmission risks and to | assess the effectiveness of other MRSA risk mitigation strategies (eg, hand hygiene, cleaning and disinfection of the environment, single occupancy | patient rooms) and should establish a process for ongoing monitoring, oversight, and risk assessment. (Quality of evidence: MODERATE) | 5 Ensure cleaning and disinfection of equipment and the environment. (Quality of evidence: MODERATE) | 6 Implement a laboratory-based alert system that notifies healthcare personnel (HCP) of new MRSA-colonized or MRSA-infected patients in a timely | manner. (Quality of evidence: LOW) | 7 Implement an alert system that identifies readmitted or transferred MRSA-colonized or MRSA-infected patients. (Quality of evidence: LOW) | 8 Provide MRSA data and outcome measures to key stakeholders, including senior leadership, physicians, nursing staff, and others. (Quality of evidence: | LOW) | 9 Educate healthcare personnel about MRSA. (Quality of evidence: LOW) | 10 Educate patients and families about MRSA. (Quality of evidence: LOW) | 11 Implement an antimicrobial stewardship program. (Quality of evidence: LOW) | Additional approaches | Active surveillance testing (AST) | 1 Implement an MRSA AST program for select patient populations as part of a multifaceted strategy to control and prevent MRSA. (Quality of evidence: | MODERATE) Note: specific populations may have different evidence ratings. | 2 Active surveillance for MRSA in conjunction with decolonization can be performed in targeted populations prior to surgery to prevent postsurgical | MRSA infection. (Quality of evidence: MODERATE) | (Continued) | 4 Deborah S. Yokoe et al | https://doi.org/10.1017/ice.2023.138 Published online by Cambridge University Press | Strategies to prevent surgical-site infections (SSIs) | (Continued ) | 3 Active surveillance with contact precautions is inferior to universal decolonization for reduction of MRSA clinical isolates in adult ICUs. (Quality of | evidence: HIGH) | 4 Hospital-wide active surveillance for MRSA can be used in conjunction with contact precautions to reduce the incidence of MRSA infection. (Quality of | evidence: MODERATE) | 5 Active surveillance can be performed in the setting of an MRSA outbreak or evidence of ongoing transmission of MRSA within a unit as part of a | multifaceted strategy to halt transmission. (Quality of evidence: MODERATE) | Screen healthcare personnel for MRSA infection or colonization | 1 Screen HCP for MRSA infection or colonization if they are epidemiologically linked to a cluster of MRSA infections. (Quality of evidence: LOW) | MRSA decolonization therapy | 1 Use universal decolonization (ie, daily CHG bathing plus 5 days of nasal decolonization) for all patients in adult ICUs to reduce endemic MRSA clinical | cultures. (Quality of evidence: HIGH) | 2 Perform preoperative nares screening with targeted use of CHG and nasal decolonization in MRSA carriers to reduce MRSA SSI from surgical | procedures involving implantation of hardware. (Quality of evidence: MODERATE) | 3 Screen for MRSA and provide targeted decolonization with CHG bathing and nasal decolonization to MRSA carriers in surgical units to reduce | postoperative MRSA inpatient infections. (Quality of evidence: MODERATE) | 4 Provide CHG bathing plus nasal decolonization to known MRSA carriers outside the ICU with medical devices, specifically central lines, midline | catheters, and lumbar drains to reduce MRSA clinical cultures. (Quality of evidence: MODERATE) | 5 Consider postdischarge decolonization of MRSA carriers to reduce postdischarge MRSA infections and readmissions. (Quality of evidence: HIGH) | 6 Neonatal ICUs should consider targeted or universal decolonization during times of above-average MRSA infection rates or targeted decolonization for | patients at high risk of MRSA infection (eg, low birth weight, indwelling devices, or prior to high-risk surgeries). (Quality of evidence: MODERATE) | 7 Burn units should consider targeted or universal decolonization during times of above-average MRSA infection rates. (Quality of evidence: MODERATE) | 8 Consider targeted or universal decolonization of hemodialysis patients. (Quality of evidence: MODERATE) | 9 Decolonization should be strongly considered as part of a multimodal approach to control MRSA outbreaks. (Quality of evidence: MODERATE) | Universal use of gowns and gloves | 1 Use gowns and gloves when providing care to or entering the room of any adult ICU patient, regardless of MRSA colonization status. (Quality of | evidence: MODERATE) | Essential practices | 1 Administer antimicrobial prophylaxis according to evidence-based standards and guidelines. (Quality of evidence: HIGH) | 2 Use a combination of parenteral and oral antimicrobial prophylaxis prior to elective colorectal surgery to reduce the risk of SSI. (Quality of evidence: | HIGH) | 3 Decolonize surgical patients with an anti-staphylococcal agent in the preoperative setting for orthopedic and cardiothoracic procedures. (Quality of | evidence: HIGH) | Decolonize surgical patients in other procedures at high risk of staphylococcal SSI, such as those involving prosthetic material. (Quality of evidence: | LOW) | 4 Use antiseptic-containing preoperative vaginal preparation agents for patients undergoing cesarean delivery or hysterectomy. (Quality of evidence: | MODERATE) | 5 Do not remove hair at the operative site unless the presence of hair will interfere with the surgical procedure. (Quality of evidence: MODERATE) | 6 Use alcohol-containing preoperative skin preparatory agents in combination with an antiseptic. (Quality of evidence: HIGH) | 7 For procedures not requiring hypothermia, maintain normothermia (temperature >35.5 °C) during the perioperative period. (Quality of evidence: HIGH). | 8 Use impervious plastic wound protectors for gastrointestinal and biliary tract surgery. (Quality of evidence: HIGH) | 9 Perform intraoperative antiseptic wound lavage. (Quality of evidence: MODERATE) | 10 Control blood glucose level during the immediate postoperative period for all patients. (Quality of evidence: HIGH) | 11 Use a checklist and/or bundle to ensure compliance with best practices to improve surgical patient safety. (Quality of evidence: HIGH) | 12 Perform surveillance for SSI. (Quality of evidence: MODERATE) | 13 Increase the efficiency of surveillance by utilizing automated data. (Quality of evidence: MODERATE) | 14 Provide ongoing SSI rate feedback to surgical and perioperative personnel and leadership. (Quality of evidence: MODERATE) | 15 Measure and provide feedback to healthcare personnel (HCP) regarding rates of compliance with process measures. (Quality of evidence: LOW) | (Continued) | Infection Control & Hospital Epidemiology 5 | https://doi.org/10.1017/ice.2023.138 Published online by Cambridge University Press | Strategies to prevent ventilator-associated pneumonia (VAP) and ventilator-associated events (VAEs) | Adult patients | (Continued ) | 16 Educate surgeons and perioperative personnel about SSI prevention measures. (Quality of evidence: LOW) | 17 Educate patients and their families about SSI prevention as appropriate. (Quality of evidence: LOW) | 18 Implement policies and practices to reduce the risk of SSI for patients that align with applicable evidence-based standards, rules and regulations, and | medical device manufacturer instructions for use. (Quality of evidence: MODERATE) | 19 Observe and review operating room personnel and the environment of care in the operating room and in central sterile reprocessing. (Quality of | evidence: LOW) | Additional approaches | 1 Perform an SSI risk assessment. (Quality of evidence: LOW) | 2 Consider use of negative-pressure dressings in patients who may benefit. (Quality of evidence: MODERATE) | 3 Observe and review practices in the preoperative clinic, post-anesthesia care unit, surgical intensive care unit, and/or surgical ward. (Quality of | evidence: MODERATE) | 4 Use antiseptic-impregnated sutures as a strategy to prevent SSI. (Quality of evidence: MODERATE) | Essential practices | Interventions with little risk of harm and that are associated with decreases in duration of mechanical ventilation, length of stay, mortality, antibiotic utilization, | and/or costs | Avoid intubation and prevent reintubation if possible. | 1 Use high flow nasal oxygen or non-invasive positive pressure ventilation (NIPPV) as appropriate, whenever safe and feasible. (Quality of evidence: HIGH) | Minimize sedation. | 1 Minimize sedation of ventilated patients whenever possible. (Quality of evidence: HIGH) | 2 Preferentially use multimodal strategies and medications other than benzodiazepines to manage agitation. (Quality of evidence: HIGH) | 3 Utilize a protocol to minimize sedation. (Quality of evidence: HIGH) | 4 Implement a ventilator liberation protocol. (Quality of evidence: HIGH) | Maintain and improve physical conditioning. | 1 Provide early exercise and mobilization. (Quality of evidence: MODERATE) | Elevate the head of the bed to 30°–45°. (Quality of evidence: LOW) | Provide oral care with toothbrushing but without chlorhexidine. (Quality of evidence: MODERATE) | Provide early enteral rather than parenteral nutrition. (Quality of evidence: HIGH) | Maintain ventilator circuits. | 1 Change the ventilator circuit only if visibly soiled or malfunctioning (or per manufacturers’ instructions) (Quality of evidence: HIGH). | Additional approaches | May decrease duration of mechanical ventilation, length of stay, and/or mortality in some populations but not in others, and they may confer some risk of harm | in some populations. | 1 Consider using selective decontamination of the oropharynx and digestive tract to decrease microbial burden in ICUs with low prevalence of antibiotic | resistant organisms. Antimicrobial decontamination is not recommended in countries, regions, or ICUs with high prevalence of antibiotic-resistant | organisms. (Quality of evidence: HIGH) | Additional approaches | May lower VAP rates, but current data are insufficient to determine their impact on duration of mechanical ventilation, length of stay, and mortality. | 1 Consider using endotracheal tubes with subglottic secretion drainage ports to minimize pooling of secretions above the endotracheal cuff in patients | likely to require >48–72 hours of intubation. (Quality of evidence: MODERATE) | 2 Consider early tracheostomy. (Quality of evidence: MODERATE) | 3 Consider postpyloric feeding tube placement in patients with gastric feeding intolerance at high risk for aspiration. (Quality of evidence: MODERATE) | 6 Deborah S. Yokoe et al | https://doi.org/10.1017/ice.2023.138 Published online by Cambridge University Press | Preterm neonatal patients | Pediatric patients | Essential practices | Confer minimal risk of harm and may lower VAP and/or PedVAE rates. | Avoid intubation. (Quality of evidence: HIGH) | Minimize duration of mechanical ventilation. (Quality of evidence: HIGH) | 1 Manage patients without sedation whenever possible. (Quality of evidence: LOW) | 2 Use caffeine therapy for apnea of prematurity within 72 hours after birth to facilitate extubation. (Quality of evidence: HIGH) | 3 Assess readiness to extubate daily. (Quality of evidence: LOW) | 4 Take steps to minimize unplanned extubation and reintubation. (Quality of evidence: LOW) | 5 Provide regular oral care with sterile water (extrapolated from practice in infants and children, no data in preterm neonates). (Quality of evidence: | LOW) | 6 Change the ventilator circuit only if visibly soiled or malfunctioning or according to the manufacturer’s instructions for use (extrapolated from studies in | adults and children, no data in preterm neonates). (Quality of evidence: LOW) | Additional approaches | Minimal risks of harm, but impact on VAP and VAE rates is unknown. | 1 Lateral recumbent positioning. (Quality of evidence: LOW) | 2 Reverse Trendelenberg positioning. (Quality of evidence: LOW) | 3 Closed or in-line suctioning. (Quality of evidence: LOW) | 4 Oral care with maternal colostrum. (Quality of evidence: MODERATE) | Essential practices | Confer minimal risk of harm and some data suggest that they may lower VAP rates, PedVAE rates, and/or duration of mechanical ventilation. | Avoid intubation. | 1 Use noninvasive positive pressure ventilation (NIPPV) or high-flow oxygen by nasal cannula whenever safe and feasible. (Quality of evidence: | MODERATE) | Minimize duration of mechanical ventilation. | 1 Assess readiness to extubate daily using spontaneous breathing trials in patients without contraindications. (Quality of evidence: MODERATE) | 2 Take steps to minimize unplanned extubations and reintubations. (Quality of evidence: LOW) | 3 Avoid fluid overload. (Quality of evidence: MODERATE) | Provide regular oral care (ie, toothbrushing or gauze if no teeth). (Quality of evidence: LOW) | Elevate the head of the bed unless medically contraindicated. (Quality of evidence: LOW) | Maintain ventilator circuits. | 1 Change ventilator circuits only when visibly soiled or malfunctioning (or per manufacturer’s instructions). (Quality of evidence: MODERATE) | 2 Remove condensate from the ventilator circuit frequently and avoid draining the condensate toward the patient. (Quality of evidence: LOW) | Endotracheal tube selection and management | 1 Use cuffed endotracheal tubes. (Quality of evidence: LOW) | 2 Maintain cuff pressure and volume at the minimal occlusive settings to prevent clinically significant air leaks around the endotracheal tube, typically | 20-25cm H2O. This “minimal leak” approach is associated with lower rates of post-extubation stridor. (Quality of evidence: LOW) | 3 Suction oral secretions before each position change. (Quality of evidence: LOW) | Additional approaches | Minimal risks of harm and some evidence of benefit in adult patients but data in pediatric populations are limited. | 1 Minimize sedation. (Quality of evidence: MODERATE) | 2 Use endotracheal tubes with subglottic secretion drainage ports for patients ≥10 years of age. (Quality of evidence: LOW) | 3 Consider early tracheostomy. (Quality of evidence: LOW) | Infection Control & Hospital Epidemiology 7 | https://doi.org/10.1017/ice.2023.138 Published online by Cambridge University Press | Strategies to prevent nonventilator hospital-acquired pneumonia (NV-HAP) | Strategies to prevent healthcare-associated infections through hand hygiene | Essential practices | Promote the maintenance of healthy hand skin and nails. (Quality of evidence: HIGH) | 1 Promote the preferential use of alcohol-based hand sanitizer (ABHS) in most clinical situations. (Quality of evidence: HIGH) | 2 Perform hand hygiene as indicated by CDC or the WHO Five Moments. (Quality of evidence: HIGH) | 3 Include fingernail care in facility-specific policies related to hand hygiene. (Quality of evidence: HIGH) | a) Healthcare personnel (HCP) should maintain short, natural fingernails. | b) Nails should not extend past the fingertip. | c) HCP who provide direct or indirect care in high-risk areas | (eg, ICU or perioperative) should not wear artificial fingernail extenders. | d) Prohibitions against fingernail polish (standard or gel shellac) are at the discretion of the infection prevention program, except among scrubbed | individuals who interact with the sterile field during surgical procedures; these individuals should not wear fingernail polish or gel shellac. | 4 Engage all HCP in primary prevention of occupational irritant and allergic contact dermatitis. (Quality of evidence: HIGH) | 5 Provide cotton glove liners for HCP with hand irritation and educate these HCP on their use. (Quality of evidence: MODERATE) | Select appropriate products. | 1 For routine hand hygiene, choose liquid, gel, or foam ABHS with at least 60% alcohol. (Quality of evidence: HIGH) | 2 Involve HCP in selection of products. (Quality of evidence: HIGH) | 3 Obtain and consider manufacturers’ product-specific data if seeking ABHS with ingredients that may enhance efficacy against organisms anticipated to | be less susceptible to biocides. (Quality of evidence: MODERATE) | 4 Confirm that the volume of ABHS dispensed is consistent with the volume shown to be efficacious. (Quality of evidence: HIGH) | 5 Educate HCP about an appropriate volume of ABHS and the time required to obtain effectiveness. (Quality of evidence: HIGH) | 6 Provide facility-approved hand moisturizer that is compatible with antiseptics and gloves. (Quality of evidence: HIGH) | 7 For surgical antisepsis, use an FDA-approved surgical hand scrub or waterless surgical hand rub. (Quality of evidence: HIGH) | Ensure the accessibility of hand hygiene supplies. (Quality of evidence: HIGH) | 1 Ensure ABHS dispensers are unambiguous, visible, and accessible within the workflow of HCP. (Quality of evidence: HIGH) | 2 In private rooms, consider 2 ABHS dispensers the minimum threshold for adequate numbers of dispensers: 1 dispenser in the hallway, and 1 in the | patient room. (Quality of evidence: HIGH) | 3 In semiprivate rooms, suites, bays, and other multipatient bed configurations, consider 1 dispenser per 2 beds the minimum threshold for adequate | numbers of dispensers. Place ABHS dispensers in the workflow of HCP. (Quality of evidence: LOW) | 4 Ensure that the placement of hand hygiene supplies (eg, individual pocket-sized dispensers, bed mounted ABHS dispenser, single use pump bottles) is | easily accessible for HCP in all areas where patients receive care. (Quality of evidence: HIGH) | 5 Evaluate for the risk of intentional consumption. Utilize dispensers that mitigate this risk, such as wall-mounted dispensers that allow limited numbers | of activations within short periods (eg, 5 seconds). (Quality of evidence: LOW) | 6 Have surgical hand rub and scrub available in perioperative areas. (Quality of evidence: HIGH) | 7 Consider providing ABHS hand rubs or handwash with FDA-approved antiseptics for use in procedural areas and prior to high-risk bedside procedures | (eg, central-line insertion). (Quality of evidence: LOW) | (Continued) | Practices supported by interventional studies suggesting lower | NV-HAP rates | 1 Provide regular oral care. | 2 Diagnose and manage dysphagia. | 3 Provide early mobilization. | 4 Implement multimodal interventions to prevent viral infections. | 5 Use prevention bundles. | 8 Deborah S. Yokoe et al | https://doi.org/10.1017/ice.2023.138 Published online by Cambridge University Press | Implementing strategies to prevent healthcare-associated infections | Standard approach to implementation | Examples of implementation frameworks | (Continued ) | Ensure appropriate glove use to reduce hand and environmental contamination. (Quality of Evidence: HIGH) | 1 Use gloves for all contact with the patient and environment as indicated by standard and contact precautions during the care of individuals with | organisms confirmed to be less susceptible to biocides (e.g., C. difficile or norovirus) | 2 Educate HCP about the potential for self-contamination and environmental contamination when gloves are worn. (Quality of evidence: HIGH) | 3 Educate and confirm the ability of HCP to doff gloves in a manner that avoids contamination. (Quality of evidence: HIGH) | Take steps to reduce environmental contamination associated with sinks and sink drains. (Quality of evidence: HIGH) | Monitor adherence to hand hygiene. (Quality of evidence: HIGH) | Provide timely and meaningful feedback to enhance a culture of safety. (Quality of evidence: MODERATE) | Additional approaches during outbreaks | 1 Consider educating HCP using a structured approach (eg, WHO Steps) for handwashing or hand sanitizing. Evaluate HCP adherence to technique. | (Quality of evidence: LOW) | 2 For waterborne pathogens of premise plumbing, consider disinfection of sink drains using an EPA-registered disinfectant with claims against biofilms. | Consult with state or local public health for assistance in determining appropriate protocols for use and other actions needed to ensure safe supply. | (Quality of evidence: LOW) | 3 For C. difficile and norovirus, in addition to contact precautions, encourage hand washing with soap and water after the care of patients with known or | suspected infections. (Quality of evidence: LOW) | 1 Assess determinants of change and | classify as follows: | • Facilitators: promote practice or | change, or | • Barriers: hinder practice or change | Individual level: healthcare personnel, leaders, patients, and visitors’ preferences, needs, attitudes, and | knowledge. | Facility level: team composition, communication, culture, capacity, policies, resources. | Partners: degree of support and buy-in. | 2 Choose measures Measurement methods must be appropriate for the question(s) they seek to answer and adhere to the | methods’ data collection and analysis rules: | • Outcome measure: ultimate goal (eg, HAI reduction). | • Process measure: action reliability (eg, bundle adherence). | • Balancing measure: undesired outcome of change (eg, staff absences due to required vaccine side effects). | 3 Select framework(s) See below and “Implementing Strategies to Prevent Infections in Acute Care Settings” (Table 3) | 32 | Framework Published Experience Resources | 4Es Settings | • Healthcare facilities | • Large-scale projects including multiple | sites | Infection prevention and control | • HAI prevention (including mortality | reduction and cost savings) | • 4Es Framework11 | • HAI reduction12–14 | • Mortality reduction15 | • Cost savings16 | Behavior Change Wheel Settings | • Community-based practice | • Healthcare facilities | Healthy behaviors | • Smoking cessation | • Obesity prevention | • Increased physical activity | Infection prevention and control | • Hand hygiene adherence | • Antibiotic prescribing17 | • Behavior Change Wheel: A Guide to Designing Interventions18 | • Stand More at Work (SMArT Work)19 | (Continued) | Infection Control & Hospital Epidemiology 9 | https://doi.org/10.1017/ice.2023.138 Published online by Cambridge University Press | Acknowledgments. The Compendium Partners thank the authors for their | dedication to this work, including maintaining adherence to the rigorous | process for the development of the Compendium: 2022 Updates, involving but | not limited to screening of thousands of articles; achieving multilevel consensus; | and consideration of, response to, and incorporation of many organizations’ | feedback and comments. We acknowledge these efforts especially because they | occurred as the authors handled the demands of the COVID-19 pandemic. The | authors thank Valerie Deloney, MBA, for her organizational expertise in the | development of this manuscript and Janet Waters, MLS, BSN, RN, for her | expertise in developing the strategies used for the literature searches that | informed this manuscript. The authors thank the many individuals and | organizations who gave their time and expertise to review and provide | (Continued ) | Comprehensive Unit-based | Safety Program (CUSP) | Settings | • Intensive care units | • Ambulatory centers | Improvements | • Antibiotic prescribing | • CLABSI prevention | • CAUTI prevention | • CUSP Implementation Toolkit20 | • AHA/HRET: Eliminating CAUTI (Stop CAUTI)21 | • AHRQ Toolkit to Improve Safety in Ambulatory Surgery Centers22 | European Mixed Methods Settings | • European institutions of varied | healthcare systems and cultures | Improvements: | • CLABSI prevention | • Hand hygiene | • PROHIBIT: Description and Materials23 | Getting to Outcomes (GTO)® Settings | • Community programs and services | Improvements | • Sexual health promotion | • Dual-disorder treatment program in | veterans | • Community emergency preparedness | • RAND Guide for Emergency Preparedness24 (illustrated overview of GTO® methodology) | Model for Improvement Settings | • Healthcare (inpatient, perioperative, | ambulatory) | • Public health | Interventions | • PPE use | • HAI prevention | • Public health process evaluation | • Institute for Healthcare Improvement25 | • The Improvement Guide26 | • Deming’s System of Profound Knowledge27 | Reach, Effectiveness, Adoption, | Implementation, Maintenance | (RE-AIM) | Settings | • Healthcare | • Public health | • Community programs | • Sexual health | Evaluations | • Antimicrobial stewardship in the ICU | • Clinical practice guidelines for STIs | • Promotion of vaccination | • Implementation of contact tracing | • RE-AIM.org28 | • Understanding and applying the RE-AIM framework: Clarifications and | resources29 | Replicating Effective Practices | (REP) | Settings | • Healthcare | • Public health | • HIV prevention | Interventions that have produced | positive results are reframed for local | relevance | CDC Compendium of HIV Prevention Interventions with Evidence of | Effectiveness30 (see Section C, Intervention Checklist) | Theoretical Domains Settings | • Healthcare (inpatient, perioperative, | ambulatory) | • Community (individual and communitybased behaviors) | Health maintenance | • Diabetes management in primary care | • Pregnancy weight management | HCP practice | • ICU blood transfusion | • Selective GI tract decontamination | • Preoperative testing | • Spine imaging | • Hand hygiene |
MicroRNA-based discovery of biomarkers, therapeutic targets, and repositioning drugs for breast cancer
Ye Q , Raese RA , Luo D , Feng J , Xin W , Dong C , Qian Y , Guo NL . Cells 2023 12 (14) Breast cancer treatment can be improved with biomarkers for early detection and individualized therapy. A set of 86 microRNAs (miRNAs) were identified to separate breast cancer tumors from normal breast tissues (n = 52) with an overall accuracy of 90.4%. Six miRNAs had concordant expression in both tumors and breast cancer patient blood samples compared with the normal control samples. Twelve miRNAs showed concordant expression in tumors vs. normal breast tissues and patient survival (n = 1093), with seven as potential tumor suppressors and five as potential oncomiRs. From experimentally validated target genes of these 86 miRNAs, pan-sensitive and pan-resistant genes with concordant mRNA and protein expression associated with in-vitro drug response to 19 NCCN-recommended breast cancer drugs were selected. Combined with in-vitro proliferation assays using CRISPR-Cas9/RNAi and patient survival analysis, MEK inhibitors PD19830 and BRD-K12244279, pilocarpine, and tremorine were discovered as potential new drug options for treating breast cancer. Multi-omics biomarkers of response to the discovered drugs were identified using human breast cancer cell lines. This study presented an artificial intelligence pipeline of miRNA-based discovery of biomarkers, therapeutic targets, and repositioning drugs that can be applied to many cancer types. |
Cell culture systems for studying hepatitis B and hepatitis D virus infections
Lee GS , Purdy MA , Choi Y . Life (Basel) 2023 13 (7) The hepatitis B virus (HBV) and hepatitis D virus (HDV) infections cause liver disease, including hepatitis, cirrhosis, and hepatocellular carcinoma (HCC). HBV infection remains a major global health problem. In 2019, 296 million people were living with chronic hepatitis B and about 5% of them were co-infected with HDV. In vitro cell culture systems are instrumental in the development of therapeutic targets. Cell culture systems contribute to identifying molecular mechanisms for HBV and HDV propagation, finding drug targets for antiviral therapies, and testing antiviral agents. Current HBV therapeutics, such as nucleoside analogs, effectively suppress viral replication but are not curative. Additionally, no effective treatment for HDV infection is currently available. Therefore, there is an urgent need to develop therapies to treat both viral infections. A robust in vitro cell culture system supporting HBV and HDV infections (HBV/HDV) is a critical prerequisite to studying HBV/HDV pathogenesis, the complete life cycle of HBV/HDV infections, and consequently identifying new therapeutics. However, the lack of an efficient cell culture system hampers the development of novel antiviral strategies for HBV/HDV infections. In vitro cell culture models have evolved with significant improvements over several decades. Recently, the development of the HepG2-NTCP sec+ cell line, expressing the sodium taurocholate co-transporting polypeptide receptor (NTCP) and self-assembling co-cultured primary human hepatocytes (SACC-PHHs) has opened new perspectives for a better understanding of HBV and HDV lifecycles and the development of specific antiviral drug targets against HBV/HDV infections. We address various cell culture systems along with different cell lines and how these cell culture systems can be used to provide better tools for HBV and HDV studies. |
Measles virus transmission patterns and public health responses during Operation Allies Welcome: a descriptive epidemiological study
Masters NB , Beck AS , Mathis AD , Leung J , Raines K , Paul P , Stanley SE , Weg AL , Pieracci EG , Gearhart S , Jumabaeva M , Bankamp B , Rota PA , Sugerman DE , Gastañaduy PA . Lancet Public Health 2023 8 (8) e618-e628 BACKGROUND: On Aug 29, 2021, Operation Allies Welcome (OAW) was established to support the resettlement of more than 80 000 Afghan evacuees in the USA. After identification of measles among evacuees, incoming evacuee flights were temporarily paused, and mass measles vaccination of evacuees aged 6 months or older was introduced domestically and overseas, with a 21-day quarantine period after vaccination. We aimed to evaluate patterns of measles virus transmission during this outbreak and the impact of control measures. METHODS: We conducted a measles outbreak investigation among Afghan evacuees who were resettled in the USA as part of OAW. Patients with measles were defined as individuals with an acute febrile rash illness between Aug 29, 2021, and Nov 26, 2021, and either laboratory confirmation of infection or epidemiological link to a patient with measles with laboratory confirmation. We analysed the demographics and clinical characteristics of patients with measles and used epidemiological information and whole-genome sequencing to track transmission pathways. A transmission model was used to evaluate the effects of vaccination and other interventions. FINDINGS: 47 people with measles (attack rate: 0·65 per 1000 evacuees) were reported in six US locations housing evacuees in four states. The median age of patients was 1 year (range 0-26); 33 (70%) were younger than 5 years. The age distribution shifted during the outbreak towards infants younger than 12 months. 20 (43%) patients with wild-type measles virus had rash onset after vaccination. No fatalities or community spread were identified, nor further importations after flight resumption. In a non-intervention scenario, transmission models estimated that a median of 5506 cases (IQR 10-5626) could have occurred. Infection clusters based on epidemiological criteria could be delineated into smaller clusters using phylogenetic analyses; however, sequences with few substitution count differences did not always indicate single lines of transmission. INTERPRETATION: Implementation of control measures limited measles transmission during OAW. Our findings highlight the importance of integration between epidemiological and genetic information in discerning between individual lines of transmission in an elimination setting. FUNDING: US Centers for Disease Control and Prevention. |
Efficient rescue of a newly classified Ebinur lake orthobunyavirus with GFP reporter and its application in rapid antiviral screening (preprint)
Ren N , Wang F , Zhao L , Wang S , Zhang G , Li J , Zhang B , Bergeron E , Yuan Z , Xia H . bioRxiv 2022 2022.03.25.485793 Orthobunyaviruses have been reported to cause severe diseases in humans or animals, posing a threat to human health and social economy. Ebinur lake virus (EBIV) is a newly classified orthobunyavirus, which needs further intensive study and therapies to cope with its potential infection risk to human and animals. Here, through the reverse genetics system, the recombinant EBIV of wild type (rEBIV/WT) and NP-conjugated-eGFP (rEBIV/eGFP/S) were rescued for the application of the rapid antiviral drug screening. The eGFP fluorescence signal of the rEBIV/eGFP/S was stable in the process of successive passage in BHK-21 cells (over 10 passages) and this recombinant virus could replicate in various cell lines. Compared to the wild type EBIV, the rEBIV/eGFP/S caused the smaller plaques and its peak titers were lower, suggesting attenuation due to the eGFP insertion. Through the high-content screening (HCS) system, ribavirin showed an inhibitory effect on the rEBIV/eGFP/S with an EC50 of 21.91 μM, while favipiravir did not inhibit, even at high concentrations. In addition, five of ninety-six natural compounds had antiviral against EBIV. The robust reverse genetics system for EBIV will facilitate investigation into replication and assembly mechanisms and assist drug and vaccine development.Competing Interest StatementThe authors have declared no competing interest. |
SARS-CoV-2 susceptibility of cell lines and substrates commonly used in diagnosis and isolation of influenza and other viruses (preprint)
Wang L , Fan X , Bonenfant G , Cui D , Hossain J , Jiang N , Larson G , Currier M , Liddell J , Wilson M , Tamin A , Harcourt J , Ciomperlik-Patton J , Pang H , Dybdahl-Sissoko N , Campagnoli R , Shi PY , Barnes J , Thornburg NJ , Wentworth DE , Zhou B . bioRxiv 2021 2021.01.04.425336 Coinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other viruses is inevitable as the COVID-19 pandemic continues. This study aimed to evaluate cell lines commonly used in virus diagnosis and isolation for their susceptibility to SARS-CoV-2. While multiple kidney cell lines from monkeys were susceptible and permissive to SARS-CoV-2, many cell types derived from human, dog, mink, cat, mouse, or chicken were not. Analysis of MDCK cells, which are most commonly used for surveillance and study of influenza viruses, demonstrated that they were insusceptible to SARS-CoV-2 and that the cellular barrier to productive infection was due to low expression level of the angiotensin converting enzyme 2 (ACE2) receptor and lower receptor affinity to SARS-CoV-2 spike, which could be overcome by over-expression of canine ACE2 in trans. Moreover, SARS-CoV-2 cell tropism did not appear to be affected by a D614G mutation in the spike protein.Competing Interest StatementThe authors have declared no competing interest. |
Building the vector in? Construction practices contribute to the invasion and persistence of Anopheles stephensi in Jigjiga, Ethiopia (preprint)
Yared S , Gebresilassie A , Aklilu E , Abdulahi E , Kirstein OD , Gonzalez-Olvera G , Che-Mendoza A , Bibiano-Marin W , Waymire E , Lines J , Lenhart A , Kitron U , Carter T , Manrique-Saide P , Vazquez-Prokopec GM . bioRxiv 2023 24 Anopheles stephensi is a major vector of malaria in Asia and the Arabian Peninsula, and its recent invasion into Africa poses a significant threat to malaria control and elimination efforts on the continent. The mosquito is well-adapted to urban environments, and its presence in Africa could potentially lead to an increase in malaria transmission in cities. Most of the knowledge about An. stephensi ecology in Africa has been generated from studies conducted during the rainy season, when vectors are most abundant. Here, we provide evidence from the peak of the dry season in the city of Jigjiga, Ethiopia, and report the finding of An. stephensi immature stages infesting predominantly water reservoirs made to support construction operations (in construction sites or associated with brick manufacturing businesses). Political and economic changes in Ethiopia (and particularly the Somali Region) have fueled an unprecedented construction boom since 2018 that, in our opinion, has been instrumental in the establishment, persistence and propagation of An. stephensi via the year-round availability of perennial larval habitats associated with construction. We argue that larval source management during the dry season may provide a unique opportunity for focused control of An. stephensi in Jigjiga and similar areas. Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. |
Characterization of reference materials for CYP3A4 and CYP3A5: A genetic testing reference material coordination program collaborative project
Gaedigk A , Boone EC , Turner AJ , van Schaik RHN , Chernova D , Wang WY , Broeckel U , Granfield CA , Hodge JC , Ly RC , Lynnes TC , Mitchell MW , Moyer AM , Oliva J , Kalman LV . J Mol Diagn 2023 25 (9) 655-664 Pharmacogenetic testing for CYP3A4 is increasingly provided by clinical and research laboratories; however, only a limited number of quality control and reference materials are currently available for many of the CYP3A4 variants included in clinical tests. To address this need, the Division of Laboratory Systems, CDC-based Genetic Testing Reference Material Coordination Program, in collaboration with members of the pharmacogenetic testing and research communities and the Coriell Institute for Medical Research, has characterized 30 DNA samples derived from Coriell cell lines for CYP3A4. Samples were distributed to five volunteer laboratories for genotyping using a variety of commercially available and laboratory-developed tests. Sanger and next-generation sequencing were also utilized by some of the laboratories. Whole-genome sequencing data from the 1000 Genomes Projects were utilized to inform genotype. Twenty CYP3A4 alleles were identified in the 30 samples characterized for CYP3A4: CYP3A4∗4, CYP3A4∗5, CYP3A4∗6, CYP3A4∗7, CYP3A4∗8, CYP3A4∗9, CYP3A4∗10, CYP3A4∗11, CYP3A4∗12, CYP3A4∗15, CYP3A4∗16, CYP3A4∗18, CYP3A4∗19, CYP3A4∗20, CYP3A4∗21, CYP3A4∗22, CYP3A4∗23, CYP3A4∗24, CYP3A4∗35, and a novel allele, CYP3A4∗38. Nineteen additional samples with preexisting data for CYP3A4 or CYP3A5 were re-analyzed to generate comprehensive reference material panels for these genes. These publicly available and well-characterized materials can be used to support the quality assurance and quality control programs of clinical laboratories performing clinical pharmacogenetic testing. |
Cyclospora cayetanensis comprises at least three species that cause human cyclosporiasis
Barratt JLN , Shen J , Houghton K , Richins T , Sapp SGH , Cama V , Arrowood MJ , Straily A , Qvarnstrom Y . Parasitology 2023 150 (3) 269-285 The apicomplexan parasite Cyclospora cayetanensis causes seasonal foodborne outbreaks of the gastrointestinal illness cyclosporiasis. Prior to the coronavirus disease-2019 pandemic, annually reported cases were increasing in the USA, leading the US Centers for Disease Control and Prevention to develop a genotyping tool to complement cyclosporiasis outbreak investigations. Thousands of US isolates and 1 from China (strain CHN_HEN01) were genotyped by Illumina amplicon sequencing, revealing 2 lineages (A and B). The allelic composition of isolates was examined at each locus. Two nuclear loci (CDS3 and 360i2) distinguished lineages A and B. CDS3 had 2 major alleles: 1 almost exclusive to lineage A and the other to lineage B. Six 360i2 alleles were observed 2 exclusive to lineage A (alleles A1 and A2), 2 to lineage B (B1 and B2) and 1 (B4) was exclusive to CHN_HEN01 which shared allele B3 with lineage B. Examination of heterozygous genotypes revealed that mixtures of A- and B-type 360i2 alleles occurred rarely, suggesting a lack of gene flow between lineages. Phylogenetic analysis of loci from whole-genome shotgun sequences, mitochondrial and apicoplast genomes, revealed that CHN_HEN01 represents a distinct lineage (C). Retrospective examination of epidemiologic data revealed associations between lineage and the geographical distribution of US infections plus strong temporal associations. Given the multiple lines of evidence for speciation within human-infecting Cyclospora, we provide an updated taxonomic description of C. cayetanensis, and describe 2 novel species as aetiological agents of human cyclosporiasis: Cyclospora ashfordi sp. nov. and Cyclospora henanensis sp. nov. (Apicomplexa: Eimeriidae). |
Experiences of health departments on community engagement and implementation of a COVID-19 self-testing program
Lane-Barlow C , Thomas I , Horter L , Fleurence R , Green J , Juluru K , Byrkit R , Weitz A , Ricaldi JN , Valencia D . J Public Health Manag Pract 2023 29 (4) 539-546 CONTEXT: Health departments (HDs) work on the front lines to ensure the health of their communities, providing a unique perspective to public health response activities. Say Yes! COVID Test (SYCT) is a US federally funded program providing free COVID-19 self-tests to communities with high COVID-19 transmission, low vaccination rates, and high social vulnerability. The collaboration with 9 HDs was key for the program distribution of 5.8 million COVID-19 self-tests between March 31 and November 30, 2021. OBJECTIVE: The objective of this study was to gather qualitative in-depth information on the experiences of HDs with the SYCT program to better understand the successes and barriers to implementing community-focused self-testing programs. DESIGN: Key informant (KI) interviews. SETTING: Online interviews conducted between November and December 2021. PARTICIPANTS: Sixteen program leads representing 9 HDs were purposefully sampled as KIs. KIs completed 60-minute structured interviews conducted by one trained facilitator and recorded. MAIN OUTCOME MEASURES: Key themes and lessons learned were identified using grounded theory. RESULTS: Based on perceptions of KIs, HDs that maximized community partnerships for test distribution were more certain that populations at a higher risk for COVID-19 were reached. Where the HD relied predominantly on direct-to-consumer distribution, KIs were less certain that communities at higher risk were served. Privacy and anonymity in testing were themes linked to higher perceived community acceptance. KIs reported that self-test demand and distribution levels increased during higher COVID-19 transmission levels. CONCLUSION: HDs that build bridges and engage with community partners and trusted leaders are better prepared to identify and link high-risk populations with health services and resources. When collaborating with trusted community organizations, KIs perceived that the SYCT program overcame barriers such as mistrust of government intervention and desire for privacy and motivated community members to utilize this resource to protect themselves against COVID-19. |
Tuberculosis Infection in Children
Stewart RJ , Wortham J , Parvez F , Bamrah Morris S , Kirking HL , Hatzenbuehler Cameron L , Cruz AT . J Nurse Pract 2020 16 (9) 673-678 Globally, tuberculosis (TB) is the leading cause of infectious disease mortality; however, clinicians in the United States are increasingly unfamiliar with TB and the recommended tests and treatment for latent TB infection. Compared with adults, children who develop TB more often develop severe disease, and children < 2 years are particularly susceptible to developing TB disease after initial infection. Nurse practitioners who work in primary care are on the front lines of identifying children at high risk and obtaining testing and treatment. This article reviews the clinical course for identifying children at risk for TB and provides updated guidelines for testing and treatment. |
Effect of parental age, parity, and pairing approach on reproduction in strain 13/N guinea pigs (Cavia porcellus)
Genzer SC , Flietstra T , Coleman-McCray JD , Tansey C , Welch SR , Spengler JR . Animals 2023 13 (5) Guinea pigs are important animal models for human disease, and both outbred and inbred lines are utilized in biomedical research. The optimal maintenance of guinea pig colonies, commercially and in research settings, relies on robust informed breeding programs, however, breeding data on specialized inbred strains are limited. Here, we investigated the effects of parental age, parity, and pairing approaches on mean total fetus count, percentage of female pups in the litter, and pup survival rate after 10 days in strain 13/N guinea pigs. Our analysis of colony breeding data indicates that the average litter size is 3.3 pups, with a 25.2% stillbirth rate, a failure-to-thrive outcome in 5.1% of pups, and a 10 day survival rate of 69.7%. The only variable to significantly affect the reproductive outcomes examined was parental age (p < 0.05). In comparison to adults, both juvenile and geriatric sows had lower total fetus counts; juvenile boars had a higher percentage of females in litters, and geriatric boars had a lower 10 day survival rate of pups. These studies provide valuable information regarding the reproductive characteristics of strain 13/N guinea pigs, and support a variety of breeding approaches without significant effects on breeding success. |
Determining Gaps in Publicly Shared SARS-CoV-2 Genomic Surveillance Data by Analysis of Global Submissions.
Ohlsen EC , Hawksworth AW , Wong K , Guagliardo SAJ , Fuller JA , Sloan ML , O'Laughlin K . Emerg Infect Dis 2022 28 (13) S85-s92 Viral genomic surveillance has been a critical source of information during the COVID-19 pandemic, but publicly available data can be sparse, concentrated in wealthy countries, and often made public weeks or months after collection. We used publicly available viral genomic surveillance data submitted to GISAID and GenBank to examine sequencing coverage and lag time to submission during 2020-2021. We compared publicly submitted sequences by country with reported infection rates and population and also examined data based on country-level World Bank income status and World Health Organization region. We found that as global capacity for viral genomic surveillance increased, international disparities in sequencing capacity and timeliness persisted along economic lines. Our analysis suggests that increasing viral genomic surveillance coverage worldwide and decreasing turnaround times could improve timely availability of sequencing data to inform public health action. |
Habitat connectivity and host relatedness influence virus spread across an urbanising landscape in a fragmentation-sensitive carnivore.
Kozakiewicz CP , Burridge CP , Lee JS , Kraberger SJ , Fountain-Jones NM , Fisher RN , Lyren LM , Jennings MK , Riley SPD , Serieys LEK , Craft ME , Funk WC , Crooks KR , VandeWoude S , Carver S . Virus Evol 2023 9 (1) veac122 Spatially heterogeneous landscape factors such as urbanisation can have substantial effects on the severity and spread of wildlife diseases. However, research linking patterns of pathogen transmission to landscape features remains rare. Using a combination of phylogeographic and machine learning approaches, we tested the influence of landscape and host factors on feline immunodeficiency virus (FIV(Lru)) genetic variation and spread among bobcats (Lynx rufus) sampled from coastal southern California. We found evidence for increased rates of FIV(Lru) lineage spread through areas of higher vegetation density. Furthermore, single-nucleotide polymorphism (SNP) variation among FIV(Lru) sequences was associated with host genetic distances and geographic location, with FIV(Lru) genetic discontinuities precisely correlating with known urban barriers to host dispersal. An effect of forest land cover on FIV(Lru) SNP variation was likely attributable to host population structure and differences in forest land cover between different populations. Taken together, these results suggest that the spread of FIV(Lru) is constrained by large-scale urban barriers to host movement. Although urbanisation at fine spatial scales did not appear to directly influence virus transmission or spread, we found evidence that viruses transmit and spread more quickly through areas containing higher proportions of natural habitat. These multiple lines of evidence demonstrate how urbanisation can change patterns of contact-dependent pathogen transmission and provide insights into how continued urban development may influence the incidence and management of wildlife disease. |
Isolation and characterization of mammalian orthoreovirus from bats in the United States.
Wang L , Zheng B , Shen Z , Nath ND , Li Y , Walsh T , Li Y , Mitchell W , He D , Lee J , Moore S , Tong S , Zhang S , Ma W . J Med Virol 2023 95 (2) e28492 Mammalian orthoreovirus (MRV) infects many mammalian species including humans, bats, and domestic animals. To determine the prevalence of MRV in bats in the United States, we screened more than 900 bats of different species collected during 2015 to 2019 by a real-time RT-PCR assay; 4.4% bats tested MRV-positive and 13 MRVs were isolated. Sequence and phylogenetic analysis revealed that these isolates belonged to four different strains/genotypes of viruses in serotypes 1 or 2, which contain genes similar to those of MRVs detected in humans, bats, bovine, and deer. Further characterization showed that these four MRV strains replicated efficiently on human, canine, monkey, ferret and swine cell lines. The 40/Bat/USA/2018 strain belonging to the serotype 1 demonstrated the ability to infect and transmit in pigs without prior adaptation. Taken together, this is evidence for different genotypes and serotypes of MRVs circulating in U.S. bats, which can be a mixing vessel of MRVs that may spread to other species, including humans, resulting in cross-species infections. This article is protected by copyright. All rights reserved. |
Efficient rescue of a newly classified Ebinur lake orthobunyavirus with GFP reporter and its application in rapid antiviral screening.
Ren N , Wang F , Zhao L , Wang S , Zhang G , Li J , Zhang B , Wang J , Bergeron E , Yuan Z , Xia H . Antiviral Res 2022 207 105421 Orthobunyaviruses have been reported to cause severe diseases in humans or animals, posing a potential threat to human health and socio-economy. Ebinur lake virus (EBIV) is a newly classified orthobunyavirus, which can induce the histopathogenic change and even the high mortality of infected BALB/c mice. Therefore, it is needed to further study the viral replication and pathogenesis, and develop the therapies to cope with its potential infection to human or animals. Here, through the reverse genetics system, the recombinant EBIV of wild type (rEBIV/WT) and NP-conjugated-eGFP (rEBIV/eGFP/S) were rescued for the application of the high-content screening (HCS) of antiviral drug. The eGFP fluorescence signal of the rEBIV/eGFP/S was stable in the process of successive passage in BHK-21 cells (over 10 passages) and this recombinant virus could replicate in various cell lines. Compared to the wild type EBIV, the rEBIV/eGFP/S caused the smaller plaques (diameter around 1 mm on 3 dpi) and lower peak titers (10(5) PFU/mL), suggesting attenuation due to the eGFP insertion. Through the high-content screening (HCS) system, two antiviral compounds, ribavirin and favipiravir, which previously reported to have effect to some bunyavirus were tested firstly. Ribavirin showed an inhibitory effect on the rEBIV/eGFP/S (EC50 = 14.38 μM) as our expect, while favipiravir with no inhibitory effect even using high doses. Furthermore, Tyrphostin A9 (EC50 = 0.72 μM for rEBIV/eGFP/S, EC50 = 0.05 μM for EBIV-WT) and UNC0638 (EC50 = 1.26 μM for rEBIV/eGFP/S, EC50 = 1.10 μM for rEBIV/eGFP/S) were identified with strong antiviral effect against EBIV in vitro from 150 antiviral compounds. In addition, the time-of-addition assay indicated that Tyrphostin A9 worked in the stage of viral post-infection, and the UNC0638 in all pre-, co-, and post-infection stages. This robust reverse genetics system will facilitate the investigation into the studying of viral replication and assembly mechanisms, and the development of drug and vaccine for EBIV in the future. |
Cost-effectiveness of pharmacologic treatment options for women with endocrine-refractory or triple-negative metastatic breast cancer
Wheeler SB , Rotter J , Gogate A , Reeder-Hayes KE , Drier SW , Ekwueme DU , Fairley TL , Rocque GB , Trogdon JG . J Clin Oncol 2022 41 (1) Jco2102473 PURPOSE: Treatments for endocrine-refractory or triple-negative metastatic breast cancer (mBC) are modestly effective at prolonging life and improving quality of life but can be extremely expensive. Given these tradeoffs in quality of life and cost, the optimal choice of treatment sequencing is unclear. Cost-effectiveness analysis can explicitly quantify such tradeoffs, enabling more informed decision making. Our objective was to estimate the societal cost-effectiveness of different therapeutic alternatives in the first- to third-line sequences of single-agent chemotherapy regimens among patients with endocrine-refractory or triple-negative mBC. METHODS: Using three dynamic microsimulation models of 10,000 patients each, three cohorts were simulated, based upon prior chemotherapy exposure: (1) unexposed to either taxane or anthracycline, (2) taxane- and anthracycline-exposed, and (3) taxane-exposed/anthracycline-naive. We focused on the following single-agent chemotherapy regimens as reasonable and commonly used options in the first three lines of therapy for each cohort, based upon feedback from oncologists treating endocrine-refractory or triple-negative mBC: (1) for taxane- and anthracycline-unexposed patients, paclitaxel, capecitabine (CAPE), or pegylated liposomal doxorubicin; (2) for taxane- and anthracycline-exposed patients, Eribulin, CAPE, or carboplatin; and (3) for taxane-exposed/anthracycline-naive patients, pegylated liposomal doxorubicin, CAPE, or Eribulin. RESULTS: In each cohort, accumulated quality-adjusted life-years were similar between regimens, but total societal costs varied considerably. Sequences beginning first-line treatment with paclitaxel, carboplatin, and CAPE, respectively, for cohorts 1, 2, and 3, had lower costs and similar or slightly better outcomes compared with alternative options. CONCLUSION: In this setting where multiple single-agent chemotherapy options are recommended by clinical guidelines and share similar survival and adverse event trajectories, treatment sequencing approaches that minimize costs early may improve the value of care. |
Characterization of Reference Materials for TPMT and NUDT15 - A GeT-RM Collaborative Project.
Pratt VM , Wang WY , Boone EC , Broeckel U , Cody N , Edleman L , Gaedigk A , Lynnes TC , Medeiros E , Moyer AM , Mitchell MM , Scott SA , Starostik P , Turner A , Kalman LV . J Mol Diagn 2022 24 (10) 1079-1088 Pharmacogenetic testing is increasingly provided by clinical and research laboratories; however, only a limited number of quality control and reference materials (RMs) are currently available for many of the TPMT and NUDT15 variants included in clinical tests. To address this need, the Division of Laboratory Systems, Centers for Disease Control and Prevention (CDC) based Genetic Testing Reference Material Coordination Program (GeT-RM), in collaboration with members of the pharmacogenetic testing and research communities and the Coriell Institute for Medical Research, has characterized 19 DNA samples derived from Coriell cell lines. DNA samples were distributed to four volunteer testing laboratories for genotyping using a variety of commercially available and laboratory developed tests and/or Sanger sequencing. Of the 12 samples characterized for TPMT, newly identified variants include TPMT*2, *6, *12, *16, *21, *24, *32, *33, *40; for the 7 NUDT15 reference material samples, newly identified variants are NUDT15*2, *3, *4, *5, *6, and *9. In addition, a novel haplotype, TPMT*46, was identified in this study. Pre-existing data on an additional 11 Coriell samples, as well as some supplemental testing, was utilized to create comprehensive reference material panels for TPMT and NUDT15. These publicly available and well characterized materials can be used to support the quality assurance and quality control programs of clinical laboratories performing clinical pharmacogenetic testing. |
How I came to write papers for clinicians in the late 1980s about improving the quality of reviews
Thacker SB . J R Soc Med 2022 115 (7) 273-275 I arrived at my interest in systematic reviews and meta-analysis through a circuitous route. In 1976, I joined the Epidemic Intelligence Service (EIS) Programme at the Communicable Disease Center (now Centers for Disease Control and Prevention). The EIS was established in 1951 by Alexander D Langmuir in response to concerns about the threat of biological weapons at the time of the Korean conflict.1 The Service is modelled along the lines of a clinical residency, with the ‘resident’ learning on the job in a mentored experience in applied epidemiology. EIS officers are known as ‘the disease detectives’ because they investigate epidemics of disease, the health effects of disasters, and trends over time of infectious disease, environmental health, chronic disease, violence, and unintentional injuries, as well as maternal and child health.2 I was assigned to the health department in Washington, DC, but spent my first few weeks with a team investigating the epidemic of Legionnaires Disease in Pennsylvania. Subsequently, I led investigations of diverse problems in hospitals, schools, restaurants, nursing homes, an institution for the mentally disabled and communities, including a study of the effects of a severe drought in Haiti. However, it was an investigation of a small cluster of febrile morbidity in a Washington, DC, hospital for women that led to my first systematic review and meta-analysis, although I had heard of neither of those terms at the time. |
Propagation and Quantification of SARS-CoV-2.
Jureka AS , Basler CF . Methods Mol Biol 2022 2452 111-129 In late 2019, the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China. Since its emergence, SARS-CoV-2 has been responsible for a world-wide pandemic resulting in over 80 million infections and over 1.8 million deaths. The severity of the pandemic has prompted widespread research efforts to more fully understand SARS-CoV-2 and the disease it causes, COVID-19. Research into this novel virus will be facilitated by the availability of clearly described and effective protocols that enable the propagation and quantification of infectious virus. Here, we describe protocols for the propagation of SARS-CoV-2 in Vero E6 cells as well as two human cells lines, the intestinal epithelial Caco-2 cell line and the respiratory epithelial Calu-3 cell line. Additionally, we provide protocols for the quantification of SARS-CoV-2 by plaque assays and immunofocus forming assays in Vero E6 cells utilizing liquid overlays. These protocols provide a foundation for laboratories acquiring the ability to study SARS-CoV-2 to address this ongoing pandemic. |
Development of HEK-293 cell lines constitutively expressing flaviviral antigens for use in diagnostics
Powers JA , Skinner B , Davis BS , Biggerstaff BJ , Robb L , Gordon E , Calvert AE , Chang GJ . Microbiol Spectr 2022 10 (3) e0059222 Flaviviruses are important human pathogens worldwide. Diagnostic testing for these viruses is difficult because many of the pathogens require specialized biocontainment. To address this issue, we generated 39 virus-like particle (VLP)- and nonstructural protein 1 (NS1)-secreting stable cell lines in HEK-293 cells of 13 different flaviviruses, including dengue, yellow fever, Japanese encephalitis, West Nile, St. Louis encephalitis, Zika, Rocio, Ilheus, Usutu, and Powassan viruses. Antigen secretion was stable for at least 10 cell passages, as measured by enzyme-linked immunosorbent assays and immunofluorescence assays. Thirty-five cell lines (90%) had stable antigen expression over 10 passages, with three of these cell lines (7%) increasing in antigen expression and one cell line (3%) decreasing in antigen expression. Antigen secretion in the HEK-293 cell lines was higher than in previously developed COS-1 cell line counterparts. These antigens can replace current antigens derived from live or inactivated virus for safer use in diagnostic testing. IMPORTANCE Serological diagnostic testing for flaviviral infections is hindered by the need for specialized biocontainment for preparation of reagents and assay implementation. The use of previously developed COS-1 cell lines secreting noninfectious recombinant viral antigen is limited due to diminished antigen secretion over time. Here, we describe the generation of 39 flaviviral virus-like particle (VLP)- and nonstructural protein 1 (NS1)-secreting stable cell lines in HEK-293 cells representing 13 medically important flaviviruses. Antigen production was more stable and statistically higher in these newly developed cell lines than in their COS-1 cell line counterparts. The use of these cell lines for production of flaviviral antigens will expand serological diagnostic testing of flaviviruses worldwide. |
Association between growth rate and pathogenicity of spotted fever group Rickettsia
Bourchookarn A , Paddock CD , Macaluso KR , Bourchookarn W . J Pure Appl Microbiol 2022 16 (1) 374-383 Rickettsia parkeri and Rickettsia amblyommatis are spotted fever group Rickettsia (SFGR) associated with Amblyomma ticks. R. parkeri is a recognized human pathogen that causes an eschar-associated febrile illness, while R. amblyommatis has not been confirmed as a causative agent of human disease. We hypothesized that the rate of replication is one of the factors contributing to rickettsial pathogenicity. In this study, growth and infectivity of R. parkeri and R. amblyommatis in mammalian (Vero E6) and tick-derived (ISE6) cell lines were assessed and compared over a 96-hour time course of infection using quantitative real-time polymerase chain reaction and microscopy. The pathogenic R. parkeri displayed a significantly higher level of infection in both Vero E6 and ISE6 cells than R. amblyommatis at 72 hours post-inoculation (hpi). Distinct growth profiles between rickettsial species with known and uncertain pathogenicity were identified. R. parkeri burdens were significantly greater than those of R. amblyommatis from 24 to 96 hpi. The relative fold changes of load were significantly higher in the pathogenic agent than in R. amblyommatis from 48 hpi onward and reached the maximum fold increase of 2002- and 296-fold in Vero E6 cells and 1363- and 161-fold in ISE6 cells, respectively, at 96 hpi. The results from the present study demonstrate that growth rate is associated with the pathogenicity of rickettsiae. Understanding SFGR growth characteristics in mammalian and tick cells will provide insight into rickettsial biology and pathogenesis. The Author(s) 2022. |
Collateral consequences of agricultural fungicides on pathogenic yeasts: a One Health perspective to tackle azole resistance.
Castelo-Branco D , Lockhart SR , Chen YC , Santos DA , Hagen F , Hawkins NJ , Lavergne RA , Meis J , Le Pape P , Rocha MFG , Sidrim JJC , Arendrup M , Morio F . Mycoses 2021 65 (3) 303-311 Candida and Cryptococcus affect millions of people yearly, being responsible for a wide array of clinical presentations, including life-threatening diseases. Interestingly, most human pathogenic yeasts are not restricted to the clinical setting, as they are also ubiquitous in the environment. Recent studies raise concern regarding the potential impact of agricultural use of azoles on resistance to medical antifungals in yeasts, as previously outlined with Aspergillus fumigatus. Thus, we undertook a narrative review of the literature and provide lines of evidence suggesting that an alternative, environmental route of azole resistance, may develop in pathogenic yeasts, in addition to patient route. However, it warrants sound evidence to support that pathogenic yeasts cross border between plants, animals and humans and that environmental reservoirs may contribute to azole resistance in Candida or other yeasts for humans. As these possibilities could concern public health, we propose a road map for future studies under the One Health perspective. |
Public Health Strategies: A Pathway for Public Health Practice to Leverage Law in Advancing Equity.
Weber SB , Penn M . J Public Health Manag Pract 2022 28 S27-s37 This article outlines a pathway for public health departments and practitioners to incorporate law into their efforts to advance equity in health outcomes. We assert that examining and applying law can accelerate public health efforts to mitigate structural and systemic inequities, including racism. Recent events such as the COVID-19 pandemic and the community impacts of policing have brought into sharp relief the inequities faced by many populations. These stark and explosive examples arise out of long-standing, persistent, and sometimes hidden structural and systemic inequities that are difficult to trace because they are embedded in laws and accompanying policies and practices. We emphasize this point with a case study involving a small, majority Black community in semirural Appalachia that spent almost 50 years attempting to gain access to the local public water system, despite being surrounded by water lines. We suggest that public health practitioners have a role to play in addressing these kinds of public health problems, which are so clearly tied to the ways laws and policies are developed and executed. We further suggest that public health practitioners, invoking the 10 Essential Public Health Services, can employ law as a tool to increase their capacity to craft and implement evidence-based interventions. |
Development and Evaluation of a TaqMan Real-Time PCR Assay for the Rapid Detection of Cross-Contamination of RD (Human) and L20B (Mouse) Cell Lines Used in Poliovirus Surveillance.
Ahmad A , Lee JR , Metz JM , Tang X , Lin SC , Bagarozzi DAJr , Petway D , Herzegh O . J Virol Methods 2021 300 114354 BACKGROUND: The cross-contamination of cell lines in culture is a persistent problem. Genetically modified L20B (Mouse) and RD (Human Rhabdomyosarcoma) cell lines are commonly used in poliovirus research, surveillance, and diagnostics. Cross-contamination between these cell lines leads to unreproducible results and unreliable surveillance data, negatively affecting public health. The gold standard method for cell authentication is Short Tandem Repeats analysis, which is time-consuming and expensive. The disadvantage of STR is limited detection of interspecies contamination. METHODS: This assay targets the mitochondrial cytochrome c oxidase subunit I (MTCO1) gene, a highly conserved and emergent DNA barcode region for detection of cross-contamination in RD and L20B cell lines. The MagNA Pure Compact instrument and ABI 7500 Fast Dx Real-time PCR systems were used for DNA extraction and to perform real-time PCR respectively. RESULTS: The newly developed assay is very sensitive with a limit of detection of 100 RD cells/1 million L20B/mL. The amplification efficiency and R(2)-value were 102.26% and 0.9969 respectively. We evaluated specificity of the assay with five human and four mouse cell lines, as well as monkey and rat cell lines. The assay showed no cross-reactivity with genomic DNA from human, mouse, rat, or monkey cell lines. The analytical sensitivity was also evaluated by spiking varying amounts of RD cells (0.001% - 10%) into L20B cells. There was no difference in C(T) values when running single-plex or duplex PCR reactions with similar experimental conditions. CONCLUSIONS: We have developed and validated a TaqMan real-time PCR assay, a sensitive method for the detection of cross-contamination of RD and L20B cell lines. |
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