Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study.

Antimicrobial resistance (AMR) poses a threat to public health. Clinical microbiology laboratories typically rely on culturing bacteria for antimicrobial-susceptibility testing (AST). As the implementation costs and technical barriers fall, whole-genome sequencing (WGS) has emerged as a 'one-stop' test for epidemiological and predictive AST results. Few published comparisons exist for the myriad analytical pipelines used for predicting AMR. To address this, we performed an inter-laboratory study providing sets of participating researchers with identical short-read WGS data from clinical isolates, allowing us to assess the reproducibility of the bioinformatic prediction of AMR between participants, and identify problem cases and factors that lead to discordant results. We produced ten WGS datasets of varying quality from cultured carbapenem-resistant organisms obtained from clinical samples sequenced on either an Illumina NextSeq or HiSeq instrument. Nine participating teams ('participants') were provided these sequence data without any other contextual information. Each participant used their choice of pipeline to determine the species, the presence of resistance-associated genes, and to predict susceptibility or resistance to amikacin, gentamicin, ciprofloxacin and cefotaxime. We found participants predicted different numbers of AMR-associated genes and different gene variants from the same clinical samples. The quality of the sequence data, choice of bioinformatic pipeline and interpretation of the results all contributed to discordance between participants. Although much of the inaccurate gene variant annotation did not affect genotypic resistance predictions, we observed low specificity when compared to phenotypic AST results, but this improved in samples with higher read depths. Had the results been used to predict AST and guide treatment, a different antibiotic would have been recommended for each isolate by at least one participant. These challenges, at the final analytical stage of using WGS to predict AMR, suggest the need for refinements when using this technology in clinical settings. Comprehensive public resistance sequence databases, full recommendations on sequence data quality and standardization in the comparisons between genotype and resistance phenotypes will all play a fundamental role in the successful implementation of AST prediction using WGS in clinical microbiology laboratories

Toward a Unified Genetic Map of Higher Plants, Transcending the Monocot-Dicot Divergence

Closely related (confamilial) genera often retain large chromosomal tracts in which gene order is colinear, punctuated by structural mutations such as inversions and translocations 1. To explore the possibility that conservation of gene order might extrapolate to more distantly related taxa, we first estimated an average structural mutation rate. Nine pairs of taxa, for which there exist both comparative genetic maps and plausible estimates of divergence time, showed an average of0.14 (±0.06) structural mutations per chromosome per million years of divergence (Myr; Table 1). This value is offered as a first approximation, acknowledging that refined comparative data and/or divergence estimates may impel revision

Consumer use of “Dr Google”: a survey on health information-seeking behaviors and navigational needs

BACKGROUND: The Internet provides a platform to access health information and support self-management by consumers with chronic health conditions. Despite recognized barriers to accessing Web-based health information, there is a lack of research quantitatively exploring whether consumers report difficulty finding desired health information on the Internet and whether these consumers would like assistance (ie, navigational needs). Understanding navigational needs can provide a basis for interventions guiding consumers to quality Web-based health resources. OBJECTIVE: We aimed to (1) estimate the proportion of consumers with navigational needs among seekers of Web-based health information with chronic health conditions, (2) describe Web-based health information-seeking behaviors, level of patient activation, and level of eHealth literacy among consumers with navigational needs, and (3) explore variables predicting navigational needs. METHODS: A questionnaire was developed based on findings from a qualitative study on Web-based health information-seeking behaviors and navigational needs. This questionnaire also incorporated the eHealth Literacy Scale (eHEALS; a measure of self-perceived eHealth literacy) and PAM-13 (a measure of patient activation). The target population was consumers of Web-based health information with chronic health conditions. We surveyed a sample of 400 Australian adults, with recruitment coordinated by Qualtrics. This sample size was required to estimate the proportion of consumers identified with navigational needs with a precision of 4.9% either side of the true population value, with 95% confidence. A subsample was invited to retake the survey after 2 weeks to assess the test-retest reliability of the eHEALS and PAM-13.RESULTS: Of 514 individuals who met our eligibility criteria, 400 (77.8%) completed the questionnaire and 43 participants completed the retest. Approximately half (51.3%; 95% CI 46.4-56.2) of the population was identified with navigational needs. Participants with navigational needs appeared to look for more types of health information on the Internet and from a greater variety of information sources compared to participants without navigational needs. However, participants with navigational needs were significantly less likely to have high levels of eHealth literacy (adjusted odds ratio=0.83, 95% CI 0.78-0.89, P<.001). Age was also a significant predictor (P=.02). CONCLUSIONS: Approximately half of the population of consumers of Web-based health information with chronic health conditions would benefit from support in finding health information on the Internet. Despite the popularity of the Internet as a source of health information, further work is recommended to maximize its potential as a tool to assist self-management in consumers with chronic health conditions

What happens to ART-eligible patients who do not start ART? Dropout between screening and ART initiation: a cohort study in Karonga, Malawi

BACKGROUND: Routine ART programme statistics generally only provide information about individuals who start treatment. We aimed to investigate the outcome of those who are eligible but do not start ART in the Malawi programme, factors associated with this dropout, and reasons for not starting treatment, in a prospective cohort study. METHODS: Individuals having a first screening visit at the ART clinic at Karonga District Hospital, northern Malawi, between September 2005 and July 2006 were interviewed. Study follow-up to identify treatment outcomes was conducted at the clinic and in the community. Logistic regression models were used to identify factors associated with dropout before ART initiation among participants identified as clinically eligible for ART. RESULTS: 88 participants eligible for ART at their first screening visit (out of 633, 13.9%) defaulted before starting ART. Participants with less education, difficulties in dressing, a more delayed ART initiation appointment, and mid-upper arm circumference (MUAC) < 22 cm were significantly less likely to have visited the clinic subsequently. Thirty-five (58%) of the 60 participants who defaulted and were tracked at home had died, 21 before their ART initiation appointment. CONCLUSIONS: MUAC and reported difficulties in dressing may provide useful screening indicators to identify sicker ART-eligible individuals at high risk of dropping out of the programme who might benefit from being brought back quickly or admitted to hospital for observation. Individuals with less education may need adapted health information at screening. Deaths of ART-eligible individuals occurring prior to ART initiation are not included in routine programme statistics. Considering all those who are eligible for ART as a denominator for programme indicators would help to highlight this vulnerable group, in order to identify new opportunities for further improving ART programmes

Population-Level Reduction in Adult Mortality after Extension of Free Anti-Retroviral Therapy Provision into Rural Areas in Northern Malawi

BACKGROUND: Four studies from sub-Saharan Africa have found a substantial population-level effect of ART provision on adult mortality. It is important to see if the impact changes with time since the start of treatment scale-up, and as treatment moves to smaller clinics. METHODS AND FINDINGS: During 2002-4 a demographic surveillance site (DSS) was established in Karonga district, northern Malawi. Information on births and deaths is collected monthly, with verbal autopsies conducted for all deaths; migrations are updated annually. We analysed mortality trends by comparing three time periods: pre-ART roll-out in the district (August 2002-June 2005), ART period 1 (July 2005-September 2006) when ART was available only in a town 70 km away, and ART period 2 (October 2006-September 2008), when ART was available at a clinic within the DSS area. HIV prevalence and ART uptake were estimated from a sero-survey conducted in 2007/2008. The all-cause mortality rate among 15-59 year olds was 10.2 per 1000 person-years in the pre-ART period (288 deaths/28285 person-years). It fell by 16% in ART period 1 and by 32% in ART period 2 (95% CI 18%-43%), compared with the pre-ART period. The AIDS mortality rate fell from 6.4 to 4.6 to 2.7 per 1000 person-years in the pre-ART period, period 1 and period 2 respectively (rate ratio for period 2 = 0.43, 95% CI 0.33-0.56). There was little change in non-AIDS mortality. Treatment coverage among individuals eligible to start ART was around 70% in 2008. CONCLUSIONS: ART can have a dramatic effect on mortality in a resource-constrained setting in Africa, at least in the early years of treatment provision. Our findings support the decentralised delivery of ART from peripheral health centres with unsophisticated facilities. Continued funding to maintain and further scale-up treatment provision will bring large benefits in terms of saving lives

Inheritance of isozyme and RFLP markers in Brassica campestris and comparison with B. oleracea

Using primarily cDNA restriction fragment length polymorphism markers (RFLPs) previously located to Brassica oleracea (cabbage, 2n=18) chromosomes, we initiated a comparative RFLP map in an F 2 population of B. campestris (turnip x mock pak-choi, 2n=20). As with B. oleracea , the genome of B. campestris showed extensive gene duplication, and the majority of detected duplicated loci were unlinked. Only 6 of the 49 identified loci were represented as a single copy, and 3 of these 6 were clustered on a single linkage group showing a distorted segregation ratio. Comparison with B. Oleracea indicates this synteny is conserved between species. Two other linkage groups also appeared syntenic between B. oleracea and B. campestris . One single copy locus appears to have changed synteny between B. oleracea and B. campestris . These observations suggest that B. oleracea and B. campestris share a common ancestor, but that chromosome repatterning has occurred during or after speciation. Within B. campestris , 5 loci appeared duplicated in one parent or the other, and 2 of these were linked. Differentiation through subspecies-specific duplication or deletion events is suggested as one mechansim for the evolution of numerous morphotypes within each of these species.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46007/1/122_2004_Article_BF00227309.pd

Tracheostomy in the COVID-19 era: global and multidisciplinary guidance

Global health care is experiencing an unprecedented surge in the number of critically ill patients who require mechanical ventilation due to the COVID-19 pandemic. The requirement for relatively long periods of ventilation in those who survive means that many are considered for tracheostomy to free patients from ventilatory support and maximise scarce resources. COVID-19 provides unique challenges for tracheostomy care: health-care workers need to safely undertake tracheostomy procedures and manage patients afterwards, minimising risks of nosocomial transmission and compromises in the quality of care. Conflicting recommendations exist about case selection, the timing and performance of tracheostomy, and the subsequent management of patients. In response, we convened an international working group of individuals with relevant expertise in tracheostomy. We did a literature and internet search for reports of research pertaining to tracheostomy during the COVID-19 pandemic, supplemented by sources comprising statements and guidance on tracheostomy care. By synthesising early experiences from countries that have managed a surge in patient numbers, emerging virological data, and international, multidisciplinary expert opinion, we aim to provide consensus guidelines and recommendations on the conduct and management of tracheostomy during the COVID-19 pandemic

Evaluation of volumetric modulated arc therapy (VMAT) with Oncentra MasterPlan® for the treatment of head and neck cancer

Background Several comparison studies have shown the capability of VMAT to achieve similar or better plan quality as IMRT, while reducing the treatment time. The experience of VMAT in a multi vendor environment is limited. We compared the plan quality and performance of VMAT to IMRT and we investigate the effects of varying various user-selectable parameters. Methods IMRT, single arc VMAT and dual arc VMAT were compared for four different head-and-neck tumors. For VMAT, the effect of varying gantry angle spacing and treatment time on the plan quality was investigated. A comparison of monitor units and treatment time was performed. Results IMRT and dual arc VMAT achieved a similar plan quality, while single arc could not provide an acceptable plan quality. Increasing the number of control points does not improve the plan quality. Dual arc VMAT delivery time is about 30% of IMRT delivery time. Conclusions Dual arc VMAT is a fast and accurate technique for the treatment of head and neck cancer. It applies similar number of MUs as IMRT, but the treatment time is strongly reduced, maintaining similar or better dose conformity to the PTV and OAR sparing

So Different, yet So Similar: Meta-Analysis and Policy Modeling of Willingness to Participate in Clinical Trials among Brazilians and Indians

BACKGROUND: With the global expansion of clinical trials and the expectations of the rise of the emerging economies known as BRICs (Brazil, Russia, India and China), the understanding of factors that affect the willingness to participate in clinical trials of patients from those countries assumes a central role in the future of health research. METHODS: We conducted a systematic review and meta-analysis (SRMA) of willingness to participate in clinical trials among Brazilian patients and then we compared it with Indian patients (with results of another SRMA previously conducted by our group) through a system dynamics model. RESULTS: Five studies were included in the SRMA of Brazilian patients. Our main findings are 1) the major motivation for Brazilian patients to participate in clinical trials is altruism, 2) monetary reimbursement is the least important factor motivating Brazilian patients, 3) the major barrier for Brazilian patients to not participate in clinical trials is the fear of side effects, and 4) Brazilian patients are more likely willing to participate in clinical trials than Indians. CONCLUSION: Our study provides important insights for investigators and sponsors for planning trials in Brazil (and India) in the future. Ignoring these results may lead to unnecessary fund/time spending. More studies are needed to validate our results and for better understanding of this poorly studied theme