First historical genome of a crop bacterial pathogen from herbarium specimen: Insights into citrus canker emergence.

Over the past decade, ancient genomics has been used in the study of various pathogens. In this context, herbarium specimens provide a precious source of dated and preserved DNA material, enabling a better understanding of plant disease emergences and pathogen evolutionary history. We report here the first historical genome of a crop bacterial pathogen, Xanthomonas citri pv. citri (Xci), obtained from an infected herbarium specimen dating back to 1937. Comparing the 1937 genome within a large set of modern genomes, we reconstructed their phylogenetic relationships and estimated evolutionary parameters using Bayesian tip-calibration inferences. The arrival of Xci in the South West Indian Ocean islands was dated to the 19th century, probably linked to human migrations following slavery abolishment. We also assessed the metagenomic community of the herbarium specimen, showed its authenticity using DNA damage patterns, and investigated its genomic features including functional SNPs and gene content, with a focus on virulence factors.

Days spent on non-invasive ventilation support: can it determine when to initiate VV- ECMO? Observational study in a cohort of Covid-19 patients.

BACKGROUND: The study evaluates the impact of the time between commencing non-invasive ventilation (NIV) support and initiation of venovenous extracorporeal membrane oxygenation (VV-ECMO) in a cohort of critically ill patients with coronavirus disease 2019 (COVID-19) associated acute respiratory distress syndrome (ARDS). METHODS: Prospective observational study design in an intensive Care Unit (ICU) of a tertiary hospital in Barcelona (Spain). All patients requiring VV-ECMO support due to COVID-19 associated ARDS between March 2020 and January 2022 were analysed. Survival outcome was determined at 90 days after VV-ECMO initiation. Demographic data, comorbidities at ICU admission, RESP (respiratory ECMO survival prediction) score, antiviral and immunomodulatory treatments received, inflammatory biomarkers, the need for vasopressors, the thromboprophylaxis regimen received, and respiratory parameters including the length of intubation previous to ECMO and the length of each NIV support (high-flow nasal cannula, continuous positive airway pressure and bi-level positive airway pressure), were also collated in order to assess risk factors for day-90 mortality. The effect of the time lapse between NIV support and VV-ECMO on survival was evaluated using logistic regression and adjusting the association with all factors that were significant in the univariate analysis. RESULTS: Seventy-two patients finally received VV-ECMO support. At 90 days after commencing VV-ECMO 35 patients (48%) had died and 37 patients (52%) were alive. Multivariable analysis showed that at VV-ECMO initiation, age (p = 0.02), lactate (p = 0.001), and days from initiation of NIV support to starting VV-ECMO (p = 0.04) were all associated with day-90 mortality. CONCLUSIONS: In our small cohort of VV-ECMO patients with COVID-19 associated ARDS, the time spent between initiation of NIV support and VV-ECMO (together with age and lactate) appeared to be a better predictor of mortality than the time between intubation and VV-ECMO.

Longitudinal Analysis of Urinary Cytokines and Biomarkers in COVID-19 Patients with Subclinical Acute Kidney Injury.

In hospitalized COVID-19 patients, disease progression leading to acute kidney injury (AKI) may be driven by immune dysregulation. We explored the role of urinary cytokines and their relationship with kidney stress biomarkers in COVID-19 patients before and after the development of AKI. Of 51 patients, 54.9% developed AKI. The principal component analysis indicated that in subclinical AKI, epidermal growth factor (EGF) and interferon (IFN)-α were associated with a lower risk of AKI, while interleukin-12 (IL-12) and macrophage inflammatory protein (MIP)-1ß were associated with a higher risk of AKI. After the manifestation of AKI, EGF and IFN-α remained associated with a lower risk of AKI, while IL-1 receptor (IL-1R), granulocyte-colony stimulating factor (G-CSF), interferon-gamma-inducible protein 10 (IP-10) and IL-5 were associated with a higher risk of AKI. EGF had an inverse correlation with kidney stress biomarkers. Subclinical AKI was characterized by a significant up-regulation of kidney stress biomarkers and proinflammatory cytokines. The lack of EGF regenerative effects and IFN-α antiviral activity seemed crucial for renal disease progression. AKI involved a proinflammatory urinary cytokine storm.

Development and comparative validation of genomic-driven PCR-based assays to detect Xanthomonas citri pv. citri in citrus plants.

BACKGROUND: Asiatic Citrus Canker, caused by Xanthomonas citri pv. citri, severely impacts citrus production worldwide and hampers international trade. Considerable regulatory procedures have been implemented to prevent the introduction and establishment of X. citri pv. citri into areas where it is not present. The effectiveness of this surveillance largely relies on the availability of specific and sensitive detection protocols. Although several PCR- or real-time PCR-based methods are available, most of them showed analytical specificity issues. Therefore, we developed new conventional and real-time quantitative PCR assays, which target a region identified by comparative genomic analyses, and compared them to existing protocols. RESULTS: Our assays target the X. citri pv. citri XAC1051 gene that encodes for a putative transmembrane protein. The real-time PCR assay includes an internal plant control (5.8S rDNA) for validating the assay in the absence of target amplification. A receiver-operating characteristic approach was used in order to determine a reliable cycle cut-off for providing accurate qualitative results. Repeatability, reproducibility and transferability between real-time devices were demonstrated for this duplex qPCR assay (XAC1051-2qPCR). When challenged with an extensive collection of target and non-target strains, both assays displayed a high analytical sensitivity and specificity performance: LOD95% = 754 CFU ml- 1 (15 cells per reaction), 100% inclusivity, 97.2% exclusivity for XAC1051-2qPCR; LOD95% = 5234 CFU ml- 1 (105 cells per reaction), 100% exclusivity and inclusivity for the conventional PCR. Both assays can detect the target from naturally infected citrus fruit. Interestingly, XAC1051-2qPCR detected X. citri pv. citri from herbarium citrus samples. The new PCR-based assays displayed enhanced analytical sensitivity and specificity when compared with previously published PCR and real-time qPCR assays. CONCLUSIONS: We developed new valuable detection assays useful for routine diagnostics and surveillance of X. citri pv. citri in citrus material. Their reliability was evidenced through numerous trials on a wide range of bacterial strains and plant samples. Successful detection of the pathogen was achieved from both artificially and naturally infected plants, as well as from citrus herbarium samples, suggesting that these assays will have positive impact both for future applied and academic research on this bacterium.

Intimate Partner Violence Against Low-Income Women in Mexico City and Associations with Child School Attendance: A Latent Class Analysis Using Cross-sectional Data.

INTRODUCTION: Few studies have investigated how intimate partner violence (IPV), and patterns of IPV experiences, may impact children's school attendance in low- and middle-income countries. METHODS: Using baseline data from a sub-sample of 659 women in Mexico City enrolled in a randomized controlled trial who reported having a child under age 18 and in school, multilevel latent class analysis (LCA) was used to classify women based on their reported IPV experiences. Multilevel risk regression analyses examined associations between latent class membership and IPV-related disruptions in children's schooling. Latent classes were identified in a prior study. RESULTS: Overall, 23.3% of women reported their child's school attendance was disrupted due to IPV. LCA identified four distinct classes of IPV experiences: Low Physical and Sexual Violence (39.1%); Low Physical and High Sexual Violence class (14.8%), High Physical and Low Sexual Violence and Injuries (36.5%); and High Physical and Sexual Violence and Injuries (9.6%). Compared with women in the Low Physical and Sexual Violence class, women in the High Physical and Sexual Violence and Injuries class and women in the High Physical and Low Sexual Violence and Injuries class were at greater risk of IPV disrupting children's school attendance (ARR 3.39, 95% CI 2.34, 4.92; ARR 2.22, 95% CI 1.54, 3.19, respectively). No other statistically significant associations emerged. DISCUSSION: High disruptions in children's school attendance due to IPV were reported and were differentially related to patterns of IPV experiences. Findings underscore the need to understand underlying mechanisms. Future work integrating both violence against women and violence against children is needed.

A nurse-delivered, clinic-based intervention to address intimate partner violence among low-income women in Mexico City: findings from a cluster randomized controlled trial.

BACKGROUND: Rigorous evaluations of health sector interventions addressing intimate partner violence (IPV) in low- and middle-income countries are lacking. We aimed to assess whether an enhanced nurse-delivered intervention would reduce IPV and improve levels of safety planning behaviors, use of community resources, reproductive coercion, and mental quality of life. METHODS: We randomized 42 public health clinics in Mexico City to treatment or control arms. In treatment clinics, women received the nurse-delivered session (IPV screening, supportive referrals, health/safety risk assessments) at baseline (T1), and a booster counselling session after 3 months (T2). In control clinics, women received screening and a referral card from nurses. Surveys were conducted at T1, T2, and T3 (15 months from baseline). Our main outcome was past-year physical and sexual IPV. Intent-to-treat analyses were conducted via three-level random intercepts models to evaluate the interaction term for treatment status by time. RESULTS: Between April and October 2013, 950 women (480 in control clinics, 470 in treatment clinics) with recent IPV experiences enrolled in the study. While reductions in IPV were observed for both women enrolled in treatment (OR, 0.40; 95% CI, 0.28-0.55; P < 0.01) and control (OR, 0.51; 95% CI, 0.36-0.72; P < 0.01) clinics at T3 (July to December 2014), no significant treatment effects were observed (OR, 0.78; 95% CI, 0.49-1.24; P = 0.30). At T2 (July to December 2013), women in treatment clinics reported significant improvements, compared to women in control clinics, in mental quality of life (ß, 1.45; 95% CI, 0.14-2.75; P = 0.03) and safety planning behaviors (ß, 0.41; 95% CI, 0.02-0.79; P = 0.04). CONCLUSION: While reductions in IPV levels were seen among women in both treatment and control clinics, the enhanced nurse intervention was no more effective in reducing IPV. The enhanced nursing intervention may offer short-term improvements in addressing safety planning and mental quality of life. Nurses can play a supportive role in assisting women with IPV experiences. TRIAL REGISTRATION: Clinicaltrials.gov ( NCT01661504 ). Registration Date: August 2, 2012.

No impact of surviving sepsis campaign care bundles in reducing sepsis-associated acute kidney injury
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BACKGROUND: The impact of Surviving Sepsis Campaign (SSC) care bundles in reducing sepsis-associated acute kidney injury (SA-AKI) was evaluated. METHODS: We conducted an observational single-center cohort study. Accomplishment of SSC care bundles was registered in all patients with severe sepsis admitted to the critical care department of a university hospital during three different periods. The main outcome measured was SA-AKI incidence defined as any worsening of AKI stage within the first 7 days from onset of sepsis. RESULTS: Among 260 patients with severe sepsis or septic shock finally meeting inclusion criteria, 82 (31.5%) patients developed SA-AKI. None of the SSC care tasks significantly decreased SA-AKI incidence, although a trend was observed with an initial better blood glucose control as well as with a more protective ventilation strategy. Hypotension requiring fluid challenge (hazard ratio (HR), 2.3; 95% confidence interval (CI), 1.2 - 4.2) and the presence of an abdominal sepsis etiology (HR, 1.8; 95% CI, 1.1 - 3.1) were independently associated with SA-AKI. Patients who developed SA-AKI had a higher 90-day mortality rate (62.2 vs. 40.4%). CONCLUSION: In a cohort of septic patients, none of the SSC care tasks significantly decreased SA-AKI incidence within the first week after onset of sepsis.
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[Experiences of street harassment and associations with perceptions of social cohesion among women in Mexico City]. / Acoso en la calle y su asociación con percepciones de cohesión social entre mujeres en la Ciudad de México.

OBJECTIVE:: To document the frequency and forms of street harassment and examine the association between street harassment experiences and perceptions of social cohesion. MATERIALS AND METHODS:: Baseline survey data collected among women seeking care in public health clinics in Mexico City were used for analysis. RESULTS:: Nearly two-thirds (62.8%) of women reported experiencing some form of street harassment in the prior month; women with street harassment experiences reported significantly lower perceived social cohesion (b=-0.46; 95%CI: -0.69,-0.22). CONCLUSIONS:: Findings indicate reducing street harassment may have important implications for improving women's perceived social cohesion and their safety in Mexico City.

Multidrug Resistance Related to Biofilm Formation in Acinetobacter baumannii and Klebsiella pneumoniae Clinical Strains from Different Pulsotypes.

The emergence of Acinetobacter baumannii and Klebsiella pneumoniae strains in the hospital environment has been associated with the presence of multiple genetic elements, virulence factors and the ability to form biofilms. This study evaluated the biofilm formation ability of clinical and environmental A. baumannii and K. pneumoniae strains, isolated from various sources and presenting different molecular characteristics, resistance profiles and pulsed-field gel electrophoresis patterns. Fifty-three isolates were recovered from 2009 to 2014 in a Brazilian university hospital. Investigation of biofilm formation was performed for 10 strains of each species assessed by an initial adhesion assay, biofilm cell concentration and biofilm biomass, evaluated by quantitative assays in replicates, in three independent experiments. All strains of A. baumannii were able to attach to polystyrene plates, although two strains adhered to a lesser degree than the control. K. pneumoniae strains showed opposite behaviour, where only three strains adhered significantly when compared to the control. Quantitative evaluation revealed that in five A. baumannii and four K. pneumoniae isolates the biomass production could be characterised as moderate. None of the isolates were strong biofilm producers. Our results demonstrate: (1) biofilm formation is a heterogeneous property amongst A. baumannii and K. pneumoniae clinical strains and it was not associated with certain clonal types; (2) no relationship between multidrug resistance and biofilm production was observed; (3) more virulent K. pneumoniae strains tended to present higher production of biofilm.

Measurement of meropenem concentration in different human biological fluids by ultra-performance liquid chromatography-tandem mass spectrometry.

Meropenem is a broad-spectrum antibiotic, often used for the empirical treatment of infections in critically ill patients with acute kidney injury. Meropenem has clinically insignificant protein binding and, as a carbapenem antibiotic, shows time-dependent bacterial killing, meaning that the unbound or free antibiotic concentration in blood should be maintained above the minimal inhibitory concentration of the pathogen for at least 40 % of the dosing interval. We developed and validated simple chromatographic methods by ultra-performance liquid chromatography-tandem mass spectrometry to measure plasma, filtrate-dialysate, and urine concentrations of meropenem. Chromatographic separation was achieved using an Acquity(®) UPLC(®) BEH(TM) (2.1 × 100 mm id, 1.7 µm) reverse-phase C(18) column, with a water/acetonitrile linear gradient containing 0.1 % formic acid at a 0.4-mL/min flow rate. Meropenem and its internal standard (ertapenem) were detected by electrospray ionization mass spectrometry in positive ion multiple reaction monitoring mode. The limits of quantification were 0.27, 0.24, and 1.22 mg/L, and linearity was observed between 0.27-150, 0.24-150, and 1.22-2,000 mg/L for plasma, filtrate-dialysate, and urine samples, respectively. Coefficients of variation and relative biases were less than 13.5 and 8.0 % for all biological fluids. Recovery values were greater than 68.3 %. Evaluation of the matrix effect showed ion suppression for meropenem and ertapenem. No carry-over was observed. The validated methods are useful for both therapeutic drug monitoring and pharmacokinetic studies. It could be applied to daily clinical laboratory practice to measure the concentration of meropenem in plasma, filtrate-dialysate, and urine.

A sustained endemic outbreak of vancomycin-resistant Enterococcus faecium: A 30-month surveillance study.

BACKGROUND: The assessment of risk factors for the nosocomial acquisition of colonization and infection by vancomycin-resistant Enterococcus faecium (VREfm) is often problematic due to scarce data on antibiotic use. A 30-month prospective cohort study was conducted to characterize VREfm strains isolated during an outbreak and endemic period, identifying the risk factors, antibiotic consumption, and prevalence of virulence determinants. METHODS: The study was conducted in a tertiary care hospital. A representative number (171 patients) of isolates that were classified as resistant to high-level vancomycin (minimum inhibitory concentration (MIC) ≥ 256 µg/ml) were investigated. RESULTS: Among 171 colonized patients, 22 (12.9%) developed VRE infection. All VREfm isolates harboured vanA genes. Genes codifying virulence factors such as enterococcal surface protein (esp), aggregation substance 1 (asa1), and gelatinase (gelE) were detected in the VREfm studied. All patients infected with VRE had previously been colonized and became infected on average 14 days after colonization. Only previous use of aminoglycosides was a risk factor independently associated with VRE infection; however, glycopeptide consumption in defined daily doses (DDD) per 1000 patient-days was associated with the presence of this microorganism. The monthly colonization pressure ranged from 0.004% to 1.32% during the 30-month study period. CONCLUSIONS: We found a high incidence of VRE in a tertiary care hospital, independently associated with the prior use of aminoglycosides and the administration of glycopeptides.

Evaluating a health care provider delivered intervention to reduce intimate partner violence and mitigate associated health risks: study protocol for a randomized controlled trial in Mexico City.

BACKGROUND: Intimate partner violence (IPV) victimization is a prevalent issue among women residing in Mexico City. Comprehensive and integrated health care provider (HCP) delivered programs in clinic-settings are needed, yet few have been evaluated in Latin America, including Mexico. In addition, there has been minimal attention to interventions among lower income women presenting at settings outside of antenatal care clinics. The current randomized controlled trial seeks to increase midlevel HCPs' capacity, specifically nurses, who are often the first point of contact in this setting, to identify women presenting at health clinics with experiences of IPV and to assist these women with health risk mitigation. Specific outcomes include changes in past-year IPV (physical and/or sexual), reproductive coercion, safety planning, use of community resources, and quality of life. METHODS/DESIGN: Forty-two public health clinics in Mexico City were randomized to treatment or control clinics. Nurses meeting eligibility criteria in treatment groups received an intensive training on screening for IPV, providing supportive referrals, and assessing for health and safety risks. Nurses meeting eligibility criteria at control clinics received the standard of care which included a one-day training focused on sensitizing staff to IPV as a health issue and referral cards to give to women. Women were screened for eligibility (currently experiencing abuse in a heterosexual relationship, 18-44 years of age, non-pregnant or in first trimester) by research assistants in private areas of waiting rooms in health clinics. Consenting women completed a baseline survey and received the study protocol for that clinic. In treatment clinics, women received the nurse delivered session at baseline and received a follow-up counseling session after three months. Surveys are conducted at baseline, three months, and fifteen months from baseline. DISCUSSION: This study will provide important insight into whether a nurse-delivered program can assist women currently experiencing abuse in a Latin American context. Findings can be used to inform IPV programs and policies in Mexico City's public health clinics. TRIAL REGISTRATION: NCT01661504.

Comparing research attitudes in Down syndrome and non-Down syndrome research decision-makers.

INTRODUCTION: Recruitment challenges in people with and without Down syndrome (DS) can delay research progress and risk sample bias. This study identified and quantified differences in research attitudes across populations of research enrollment decision-makers for individuals with and without DS. METHODS: We performed analyses using data from two registries: the University of California, Irvine Consent-to-Contact (C2C) Registry and DS-Connect. The former represented a sample of non-DS decision-makers (N = 4818), while for the latter, we excluded individuals with DS, leaving a population of DS family decision-makers (N = 976). We assessed scores on the Research Attitudes Questionnaire (RAQ) between DS and non-DS decision-makers. We compared total RAQ scores using linear regression and assessed item-level RAQ differences using proportional odds regression. RESULTS: Mean total RAQ scores were not statistically different between decision-makers in the two registries, after adjusting for age, sex, race and ethnicity, education, and the coronavirus disease 2019 (COVID-19) time frame (Est. Diff = 0.11, 95% confidence interval [CI]: -0.22, 0.43; p = 0.531). However, in a pre-specified analysis, we did find evidence of differential attitudes on item-level RAQ scores. Specifically, decision-makers for participants with DS had increased odds of a more favorable response to the question of responsibility to help others (DS vs. non-DS: odds ratio [OR] = 1.26, 95% CI: 1.08, 1.48) and decreased odds of a more favorable response to the question regarding the belief that medical research would find cures for major diseases during their lifetime (DS vs. non-DS: OR = 0.77, 95% CI: 0.66, 0.90). DISCUSSION: Our findings provide insights for researchers to develop strategies for recruiting individuals with and without DS into clinical research. The observed item-level differences warrant further investigation to instruct precise recruitment strategies. Highlights: Research attitudes between decision-makers for individuals with Down syndrome (DS) and decision-makers without DS were observed to be similar on average.Item-level differences in research attitudes were observed to differ for DS and non-DS decision-makers.These results can help facilitate precise recruitment strategies for populations with DS.

Appraising epidemiology data and antimicrobial resistance of urinary tract infections in critically ill adult patients: a 7-year retrospective study in a referral Brazilian hospital.

BACKGROUND: Urinary tract infections (UTI) are highly preventable and have significant clinical and financial impact on the patient and the health care system. OBJECTIVE: To investigate UTIs in critically ill adult patients and the relationship of antimicrobial consumption and multidrug-resistant isolate. DESIGN AND SETTING: A cohort study performed in a Brazilian tertiary-care university hospital in the city of Uberlandia (MG), located at the Federal University of Uberlandia, southeast region of the country. METHODS: We analyzed a cohort of 363 patients with first episode of UTIs from the adult intensive care unit (ICU), from January 2012 to December 2018. The daily doses of antimicrobial administered were calculated. RESULTS: The incidence rate of UTI was 7.2/1000 patient days, with 3.5/1000 patient-days of bacteriuria, and 2.1/1000 patient-days of candiduria. Of 373 microorganisms identified, 69 (18.4%) were Gram-positive cocci, 190 (50.9%) Gram-negative bacilli, and 114 yeasts (30.7%). Escherichia coli and Candida spp. were the most common. Patients with candiduria had higher comorbidity score (Charlson Comorbidity Index ≥ 3), longer length of stay (P = 0.0066), higher mortality (P = < 0.0001) severe sepsis, septic shock, and were immunocompromised when compared with patients with bacteriuria. We observed correlation between antibiotics consumption and multidrug-resistant (MDR) microorganisms. CONCLUSION: The UTIs incidence was high and was mainly caused by Gram-negative bacteria that were resistant to common antibiotics. We observed increase in the consumption of broad-spectrum antibiotics in ICU correlating with MDR microorganisms. In general, ICU-acquired candiduria may be associated with critical illness and poor prognosis.

Herbarium specimen sequencing allows precise dating of Xanthomonas citri pv. citri diversification history.

Herbarium collections are an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography can shed light on the emergence and evolutionary history of plant pathogens. Here, we reconstruct 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected Citrus herbarium specimens. Following authentication based on ancient DNA damage patterns, we compare them with a large set of modern genomes to estimate their phylogenetic relationships, pathogenicity-associated gene content and several evolutionary parameters. Our results indicate that Xci originated in Southern Asia ~11,500 years ago (perhaps in relation to Neolithic climate change and the development of agriculture) and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world (probably via human-driven expansion of citriculture through early East-West trade and colonization).

Role of Urinary Kidney Stress Biomarkers for Early Recognition of Subclinical Acute Kidney Injury in Critically Ill COVID-19 Patients.

A high proportion of critically ill patients with COVID-19 develop acute kidney injury (AKI) and die. The early recognition of subclinical AKI could contribute to AKI prevention. Therefore, this study was aimed at exploring the role of the urinary biomarkers NGAL and [TIMP-2] × [IGFBP7] for the early detection of AKI in this population. This prospective, longitudinal cohort study included critically ill COVID-19 patients without AKI at study entry. Urine samples were collected on admission to critical care areas for determination of NGAL and [TIMP-2] × [IGFBP7] concentrations. The demographic information, comorbidities, clinical, and laboratory data were recorded. The study outcomes were the development of AKI and mortality during hospitalization. Of the 51 individuals that were studied, 25 developed AKI during hospitalization (49%). Of those, 12 had persistent AKI (23.5%). The risk factors for AKI were male gender (HR = 7.57, 95% CI: 1.28-44.8; p = 0.026) and [TIMP-2] × [IGFBP7] ≥ 0.2 (ng/mL)2/1000 (HR = 7.23, 95% CI: 0.99-52.4; p = 0.050). Mortality during hospitalization was significantly higher in the group with AKI than in the group without AKI (p = 0.004). Persistent AKI was a risk factor for mortality (HR = 7.42, 95% CI: 1.04-53.04; p = 0.046). AKI was frequent in critically ill COVID-19 patients. The combination of [TIMP-2] × [IGFBP7] together with clinical information, were useful for the identification of subclinical AKI in critically ill COVID-19 patients. The role of additional biomarkers and their possible combinations for detection of AKI in ritically ill COVID-19 patients remains to be explored in large clinical trials.

Contribution of historical herbarium small RNAs to the reconstruction of a cassava mosaic geminivirus evolutionary history.

Emerging viral diseases of plants are recognised as a growing threat to global food security. However, little is known about the evolutionary processes and ecological factors underlying the emergence and success of viruses that have caused past epidemics. With technological advances in the field of ancient genomics, it is now possible to sequence historical genomes to provide a better understanding of viral plant disease emergence and pathogen evolutionary history. In this context, herbarium specimens represent a valuable source of dated and preserved material. We report here the first historical genome of a crop pathogen DNA virus, a 90-year-old African cassava mosaic virus (ACMV), reconstructed from small RNA sequences bearing hallmarks of small interfering RNAs. Relative to tip-calibrated dating inferences using only modern data, those performed with the historical genome yielded both molecular evolution rate estimates that were significantly lower, and lineage divergence times that were significantly older. Crucially, divergence times estimated without the historical genome appeared in discordance with both historical disease reports and the existence of the historical genome itself. In conclusion, our study reports an updated time-frame for the history and evolution of ACMV and illustrates how the study of crop viral diseases could benefit from natural history collections.

Genetic Alterations Associated with Polymyxin B Resistance in Nosocomial KPC-2-Producing Klebsiella pneumoniae from Brazil.

The rapid increased multidrug resistance in Klebsiella pneumoniae has led to a renewed interest in polymyxin antibiotics, such as colistin, as antibiotics of last resort, not least in low/middle income countries. We conducted a genomic survey of clinical polymyxin-resistant K. pneumoniae to investigate the genetic alterations in isolates harboring blaKPC-2. Whole-genome sequencing was performed using an Illumina NextSeq 500 paired-end reads. Mutations and insertion sequence detection were analyzed to seven isolates recovered from clinical specimens of patients hospitalized in Brazil, focusing on key genes associated with polymyxin resistance. Furthermore, the levels of mRNA expression of genes associated with resistance to polymyxin B and other antimicrobials were evaluated by quantitative real-time PCR. Eighty-five percent of the isolates were assigned to clonal complex 258, with a minimum inhibitory concentration range of 4 to >256 mg/L for polymyxin B. It was possible to observe the presence of one important insertion element, ISKpn13, in a strain recovered from the blood that have blaKPC-2. Deleterious mutations reported in PmrB (R256G), YciM (N212T), and AcrB (T598A) were common, and mobile colistin resistance (mcr) genes were absent in all the isolates. RT-qPCR analysis revealed an overexpression of the pmrC (1.160-fold), pmrD (2.258-fold), and kpnE (1.530-fold) genes in the polymyxin B-resistant isolates compared with the expression of the polymyxin B-susceptible K. pneumoniae isolate. Overall, these results demonstrate the diversity of genetic variations in polymyxin-resistant populations derived from the different clonal strains, but the same sequence types, and suggest that there are still unknown mechanisms of polymyxin resistance in K. pneumoniae.

Novel ST1465/CC216 Nosocomial Lineage of Carbapenem-Resistant Acinetobacter baumannii Harboring an Unusual Plasmid Carrying blaNDM-1 Gene.

This study used whole-genome sequencing to analyze the first case of NDM-1-producing Acinetobacter baumannii belonging to the novel sequence type 1465/CC216 recovered in Brazil. The study identified an unusual plasmid carrying blaNDM-1 gene, in which some genes of the Tn125 transposon were lost. Besides, on the chromosome, the strain reported here presented blaOXA-106 gene, a variant of blaOXA-51 gene, and blaADC-25 with ISAba1 upstream. The isolation of new STs of A. baumannii carrying blaNDM-1 genes elicits our concerns about the possible spread of these genes among clinically relevant bacteria.