Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement.

Multidrug-resistant organism (MDRO) colonization is a fundamental challenge in antimicrobial resistance. Limited studies have shown that fecal microbiota transplantation (FMT) can reduce MDRO colonization, but its mechanisms are poorly understood. We conducted a randomized, controlled trial of FMT for MDRO decolonization in renal transplant recipients called PREMIX (NCT02922816). Eleven participants were enrolled and randomized 1:1 to FMT or an observation period followed by delayed FMT if stool cultures were MDRO positive at day 36. Participants who were MDRO positive after one FMT were treated with a second FMT. At last visit, eight of nine patients who completed all treatments were MDRO culture negative. FMT-treated participants had longer time to recurrent MDRO infection versus PREMIX-eligible controls who were not treated with FMT. Key taxa (Akkermansia muciniphila, Alistipes putredinis, Phocaeicola dorei, Phascolarctobacterium faecium, Alistipes species, Mesosutterella massiliensis, Barnesiella intestinihominis, and Faecalibacterium prausnitzii) from the single feces donor used in the study that engrafted in recipients and metabolites such as short-chain fatty acids and bile acids in FMT-responding participants uncovered leads for rational microbiome therapeutic and diagnostic development. Metagenomic analyses revealed a previously unobserved mechanism of MDRO eradication by conspecific strain competition in an FMT-treated subset. Susceptible Enterobacterales strains that replaced baseline extended-spectrum ß-lactamase-producing strains were not detectable in donor microbiota manufactured as FMT doses but in one case were detectable in the recipient before FMT. These data suggest that FMT may provide a path to exploit strain competition to reduce MDRO colonization.

Longitudinal analysis of risk factors associated with severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection among hemodialysis patients and healthcare personnel in outpatient hemodialysis centers.

In this prospective, longitudinal study, we examined the risk factors for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection among a cohort of chronic hemodialysis (HD) patients and healthcare personnel (HCPs) over a 6-month period. The risk of SARS-CoV-2 infection among HD patients and HCPs was consistently associated with a household member having SARS-CoV-2 infection.

Predictors of humoral response to SARS-CoV-2 mRNA vaccine BNT162b2 in patients receiving maintenance dialysis.

Objective: Patients on dialysis are at high risk for severe COVID-19 and associated morbidity and mortality. We examined the humoral response to SARS-CoV-2 mRNA vaccine BNT162b2 in a maintenance dialysis population. Design: Single-center cohort study. Setting and participants: Adult maintenance dialysis patients at 3 outpatient dialysis units of a large academic center. Methods: Participants were vaccinated with 2 doses of BNT162b2, 3 weeks apart. We assessed anti-SARS-CoV-2 spike antibodies (anti-S) ∼4-7 weeks after the second dose and evaluated risk factors associated with insufficient response. Definitions of antibody response are as follows: nonresponse (anti-S level, <50 AU/mL), low response (anti-S level, 50-839 AU/mL), and sufficient response (anti-S level, ≥840 AU/mL). Results: Among the 173 participants who received 2 vaccine doses, the median age was 60 years (range, 28-88), 53.2% were men, 85% were of Black race, 86% were on in-center hemodialysis and 14% were on peritoneal dialysis. Also, 7 participants (4%) had no response, 27 (15.6%) had a low response, and 139 (80.3%) had a sufficient antibody response. In multivariable analysis, factors significantly associated with insufficient antibody response included end-stage renal disease comorbidity index score ≥5 and absence of prior hepatitis B vaccination response. Conclusions: Although most of our study participants seroconverted after 2 doses of BNT162b2, 20% of our cohort did not achieve sufficient humoral response. Our findings demonstrate the urgent need for a more effective vaccine strategy in this high-risk patient population and highlight the importance of ongoing preventative measures until protective immunity is achieved.

Concordance of SARS-CoV-2 Results in Self-collected Nasal Swabs vs Swabs Collected by Health Care Workers in Children and Adolescents.

Importance: Despite the expansion of SARS-CoV-2 testing, available tests have not received Emergency Use Authorization for performance with self-collected anterior nares (nasal) swabs from children younger than 14 years because the effect of pediatric self-swabbing on SARS-CoV-2 test sensitivity is unknown. Objective: To characterize the ability of school-aged children to self-collect nasal swabs for SARS-CoV-2 testing compared with collection by health care workers. Design, Setting, and Participants: Cross-sectional study of 197 symptomatic children and adolescents aged 4 to 14 years old. Individuals were recruited based on results of testing in the Children's Healthcare of Atlanta system from July to August 2021. Exposures: Children and adolescents were given instructional material consisting of a short instructional video and a handout with written and visual steps for self-swab collection. Participants first provided a self-collected nasal swab. Health care workers then collected a second specimen. Main Outcomes and Measures: The primary outcome was SARS-CoV-2 detection and relative quantitation by cycle threshold (Ct) in self- vs health care worker-collected nasal swabs when tested with a real-time reverse transcriptase-polymerase chain reaction test with Emergency Use Authorization. Results: Among the study participants, 108 of 194 (55.7%) were male and the median age was 9 years (IQR, 6-11). Of the 196 participants, 87 (44.4%) tested positive for SARS-CoV-2 and 105 (53.6%) tested negative by both self- and health care worker-collected swabs. Two children tested positive by self- or health care worker-collected swab alone; 1 child had an invalid health care worker swab. Compared with health care worker-collected swabs, self-collected swabs had 97.8% (95% CI, 94.7%-100.0%) and 98.1% (95% CI, 95.6%-100.0%) positive and negative percent agreement, respectively, and SARS-CoV-2 Ct values did not differ significantly between groups (mean [SD] Ct, self-swab: 26.7 [5.4] vs health care worker swab: 26.3 [6.0]; P = .65). Conclusions and Relevance: After hearing and seeing simple instructional materials, children and adolescents aged 4 to 14 years self-collected nasal swabs that closely agreed on SARS-CoV-2 detection with swabs collected by health care workers.

Isolation of SARS-CoV-2 in Viral Cell Culture in Immunocompromised Patients With Persistently Positive RT-PCR Results.

Immunocompromised adults can have prolonged acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive RT-PCR results, long after the initial diagnosis of coronavirus disease 2019 (COVID-19). This study aimed to determine if SARS-CoV-2 virus can be recovered in viral cell culture from immunocompromised adults with persistently positive SARS-CoV-2 RT-PCR tests. We obtained 20 remnant SARS-CoV-2 PCR positive nasopharyngeal swabs from 20 immunocompromised adults with a positive RT-PCR test ≥14 days after the initial positive test. The patients' 2nd test samples underwent SARS-CoV-2 antigen testing, and culture with Vero-hACE2-TMPRSS2 cells. Viral RNA and cultivable virus were recovered from the cultured cells after qRT-PCR and plaque assays. Of 20 patients, 10 (50%) had a solid organ transplant and 5 (25%) had a hematologic malignancy. For most patients, RT-PCR Ct values increased over time. There were 2 patients with positive viral cell cultures; one patient had chronic lymphocytic leukemia treated with venetoclax and obinutuzumab who had a low viral titer of 27 PFU/mL. The second patient had marginal zone lymphoma treated with bendamustine and rituximab who had a high viral titer of 2 x 106 PFU/mL. Most samples collected ≥7 days after an initial positive SARS-CoV-2 RT-PCR had negative viral cell cultures. The 2 patients with positive viral cell cultures had hematologic malignancies treated with chemotherapy and B cell depleting therapy. One patient had a high concentration titer of cultivable virus. Further data are needed to determine risk factors for persistent viral shedding and methods to prevent SARS-CoV-2 transmission from immunocompromised hosts.

Sampling for SARS-CoV-2 Aerosols in Hospital Patient Rooms.

Evidence varies as to how far aerosols spread from individuals infected with SARS-CoV-2 in hospital rooms. We investigated the presence of aerosols containing SARS-CoV-2 inside of dedicated COVID-19 patient rooms. Three National Institute for Occupational Safety and Health BC 251 two-stage cyclone samplers were set up in each patient room for a six-hour sampling period. Samplers were place on tripods, which each held two samplers at various heights above the floor. Extracted samples underwent reverse transcription polymerase chain reaction for selected gene regions of the SARS-CoV-2 virus nucleocapsid. Patient medical data were compared between participants in rooms where virus-containing aerosols were detected and those where they were not. Of 576 aerosols samples collected from 19 different rooms across 32 participants, 3% (19) were positive for SARS-CoV-2, the majority from near the head and foot of the bed. Seven of the positive samples were collected inside a single patient room. No significant differences in participant clinical characteristics were found between patients in rooms with positive and negative aerosol samples. SARS-CoV-2 viral aerosols were detected from the patient rooms of nine participants (28%). These findings provide reassurance that personal protective equipment that was recommended for this virus is appropriate given its spread in hospital rooms.

SARS-CoV-2 Infection Risk Factors among Maintenance Hemodialysis Patients and Health Care Personnel In Outpatient Hemodialysis Centers.

Increased risk of SARS-CoV-2 infection was associated with community prevalence.Increased risk of SARS-CoV-2 infection was associated with exposure to infected family members and personal infection prevention measures.

Impact of preoperative chlorhexidine gluconate (CHG) application methods on preoperative CHG skin concentration.

Elective surgical patients routinely bathe with chlorhexidine gluconate (CHG) at home days prior to their procedures. However, the impact of home CHG bathing on surgical site CHG concentration is unclear. We examined 3 different methods of applying CHG and hypothesized that different application methods would impact resulting CHG skin concentration.

Postdocs' lab engagement predicts trajectories of PhD students' skill development.

The doctoral advisor-typically the principal investigator (PI)-is often characterized as a singular or primary mentor who guides students using a cognitive apprenticeship model. Alternatively, the "cascading mentorship" model describes the members of laboratories or research groups receiving mentorship from more senior laboratory members and providing it to more junior members (i.e., PIs mentor postdocs, postdocs mentor senior graduate students, senior students mentor junior students, etc.). Here we show that PIs' laboratory and mentoring activities do not significantly predict students' skill development trajectories, but the engagement of postdocs and senior graduate students in laboratory interactions do. We found that the cascading mentorship model accounts best for doctoral student skill development in a longitudinal study of 336 PhD students in the United States. Specifically, when postdocs and senior doctoral students actively participate in laboratory discussions, junior PhD students are over 4 times as likely to have positive skill development trajectories. Thus, postdocs disproportionately enhance the doctoral training enterprise, despite typically having no formal mentorship role. These findings also illustrate both the importance and the feasibility of identifying evidence-based practices in graduate education.

Pool water quality and prevalence of microbes in filter backwash from metro-Atlanta swimming pools.

During the 2012 summer swim season, aquatic venue data and filter backwash samples were collected from 127 metro-Atlanta pools. Last-recorded water chemistry measures indicated 98% (157/161) of samples were from pools with ≥1 mg/L residual chlorine without stabilized chlorine or ≥2 mg/L with stabilized chlorine and 89% (144/161) had pH readings 7.2-7.8. These water quality parameters are consistent with the 2016 Model Aquatic Health Code (2nd edition) recommendations. We used previously validated real-time polymerase chain reaction assays for detection of seven enteric microbes, including Escherichia coli, and Pseudomonas aeruginosa. E. coli was detected in 58% (93/161) of samples, signifying that swimmers likely introduced fecal material into pool water. P. aeruginosa was detected in 59% (95/161) of samples, indicating contamination from swimmers or biofilm growth on surfaces. Cryptosporidium spp. and Giardia duodenalis were each detected in approximately 1% of samples. These findings indicate the need for aquatics staff, state and local environmental health practitioners, and swimmers to each take steps to minimize the risk of transmission of infectious pathogens.

Interlaboratory validation of an improved method for detection of Cyclospora cayetanensis in produce using a real-time PCR assay.

A collaborative validation study was performed to evaluate the performance of a new U.S. Food and Drug Administration method developed for detection of the protozoan parasite, Cyclospora cayetanensis, on cilantro and raspberries. The method includes a sample preparation step in which oocysts are recovered from produce using an enhanced produce washing solution containing 0.1% Alconox and a commercially available method to disrupt the C. cayetanensis oocysts and extract DNA. A real-time PCR assay targeting the C. cayetanensis 18S rDNA gene with an internal amplification control to monitor PCR inhibition provides species-specific identification. Five laboratories blindly analyzed a total of 319 samples consisting of 25 g of cilantro or 50 g of raspberries which were either uninoculated or artificially contaminated with C. cayetanensis oocysts. Detection rates for cilantro inoculated with 200, 10, and 5 oocysts, were 100%, 80%, and 31%, respectively. For raspberries, the detection rates for samples inoculated with 200, 10, and 5 oocysts were 100%, 90% and 50%, respectively. All uninoculated samples, DNA blank extracts, and no-template PCR controls were negative. Reproducibility between laboratories and analysts was high and the method was shown to be an effective analytical tool for detection of C. cayetanensis in produce.

Evaluation of the compartment bag test for the detection of Escherichia coli in water.

AIMS: Annually, more than 2 million diarrheal disease deaths can be attributed to the lack of access to water, sanitation and hygiene. These deaths occur mostly in developing countries where water quality testing resources are limited. Several tests are currently used to detect and quantify Escherichia coli and other fecal bacteria in drinking water; however they can be expensive, complex, and technically demanding. There is a need for a simple, reliable, low-cost water quality test that can be used in resource limited settings. Therefore, the purpose of this research was to perform a rigorous evaluation of the recently developed compartment bag test for detection and quantification of E. coli against the standard method of membrane filtration. METHODS AND RESULTS: A total of 270 water samples were collected from forty-five various naturally contaminated water sources around metro-Atlanta from August 2011 through April 2012. Samples were processed using the compartment bag test and membrane filtration with mI agar. Concentrations of E. coli were significantly correlated with a correlation coefficient of 0.904 (95% CI 0.859-0.950). Sensitivity and specificity were 94.9% and 96.6%, respectively. CONCLUSIONS: These results suggest that the compartment bag test produces results consistent with those produced by membrane filtration on mI agar. Based upon its performance, the compartment bag test has the potential to be used as a reliable, affordable drinking water quality test where other microbial water quality testing resources are not readily available.

Perceptions of per diems in the health sector: evidence and implications.

Per diems are used to pay work-related expenses and motivate employees, yet they also can distort incentives and may be abused. This study was designed to explore perceptions of per diems among 41 high-, mid- and low-level government officers and non-governmental organization (NGO) officials in Malawi and Uganda. Interviews explored attitudes about per diems, benefits and problems for organizations and individuals, and risks and patterns of abuse. The study found that per diems provide benefits such as encouraging training, increasing staff motivation and supplementing salary. Despite these advantages, respondents voiced many discontents about per diems, stating that they create conflict, contribute to a negative organizational culture where people expect to be paid for all activities, and lead to negative changes in work time allocation. Work practices are also manipulated in order to maximize financial gain by slowing work, scheduling unnecessary trainings, or exaggerating time needed for tasks. Officials may appropriate per diems meant for others or engage in various forms of fraud for personal financial gain. Abuse seemed more common in the government sector due to low pay and weaker controls. A striking finding was the distrust that lower-level workers felt toward their superiors: allowances were perceived to provide unfair financial advantages to already better-off and well-connected staff. To curb abuse of per diems, initiatives must reduce pressures and incentives to abuse, while controlling discretion and increasing transparency in policy implementation. Donors can play a role in reform by supporting development of policy analysis tools, design of control mechanisms and evaluation of reform strategies.

PEPFAR's support for orphans and vulnerable children: some beneficial effects, but too little data, and programs spread thin.

Sixteen million children in developing and middle-income countries have been orphaned by HIV/AIDS, and at least another million children per year are rendered vulnerable by parental HIV/AIDS-related illness. Since 2003 the US government has provided approximately $1.6 billion to give four million of these children care and support through the President's Emergency Plan for AIDS Relief (PEPFAR). We conducted five studies to evaluate the effectiveness of PEPFAR's interventions for such children in East Africa and southern Africa. We found evidence of beneficial changes in school enrollment rates and on the psychosocial well-being of children. However, we could not demonstrate empirically the impact of most of the PEPFAR initiatives that we examined, primarily because of a lack of baseline data and clear outcome and impact indicators. We also found that many programs were spread so thin across a vulnerable population that little in the way of services actually reached beneficiaries, which raises questions about whether PEPFAR funds are sufficient, or if the program is attempting to do much with too few resources. We offer several recommendations, including better measuring the effect of programs for orphans and vulnerable children by collecting baseline data and conducting well-designed, rigorous outcome and impact evaluations.

Measuring vulnerability among orphans and vulnerable children in rural Malawi: validation study of the Child Status Index tool.

OBJECTIVES: To validate the Child Status Index (CSI) as an instrument that can meaningfully measure the vulnerabilities of orphaned and vulnerable children, including those infected and affected by HIV/AIDS. METHODS: Two age-specific instruments, comprised of previously validated tools and indicators commonly considered best practice, were administered to 102 children aged 5-10 years and 100 children aged 11-17 years in Mchinji, Malawi. Respondents were randomly sampled from a roster of children recently scored with the CSI. For each of the CSI's 12 subdomains, we assessed construct validity using Spearman Rank correlation coefficients. We also calculated cross tabulations to explain the resulting correlation coefficients. Analyses were conducted separately for the 2 age groups. RESULTS: No relationships exceeded the standard for high construct validity (≥0.7). Only 2 were moderate (0.3-0.7), both for the younger age group: food security (0.4) and wellness (0.36). All other relationships were weak or negative. In most subcategories, a substantial proportion of surveyed children indicated distress that was not evident from CSI scores. In the abuse and exploitation subdomain, all children were rated as "good" or "fair" by the CSI, but among surveyed children aged 11-17, 20% or more reported being beaten, kicked, locked out of the house, threatened with abandonment, cursed, and made to feel ashamed. CONCLUSIONS: In this rural Malawi population, we were not able to validate the CSI as a tool for assessing the vulnerabilities of orphaned and vulnerable children. We recommend caution in interpreting CSI scores and revisions to the tool before global scale-up in its use.

Why are antiretroviral treatment patients lost to follow-up? A qualitative study from South Africa.

OBJECTIVES: To better understand the reasons why patients default from antiretroviral treatment (ART) programmes to help design interventions that improve treatment retention and ultimately, patient outcomes. METHODS: Prospective cohort study at two treatment sites in South Africa followed by qualitative interviews with patients that had defaulted. RESULTS: Respondents overwhelmingly reported that ART improved their health status and quality of life. Nevertheless, despite improved health from taking ART and worse health when treatment is stopped, serious barriers to treatment remained: transport costs, time needed for treatment, and logistical challenges were barriers to treatment, whereas stigma around HIV/AIDS, and side effects associated with ART were less influential. CONCLUSION: With a better understanding of the reasons for defaulting, interventions can be designed that improve treatment retention and ultimately, patient outcomes. This study argues for realistic interventions and policy changes designed to reduce the financial and time burden of ART and to reduce logistical barriers, such as simplifying the referral and transfer process, employing patient advocates, and adopting extended and weekend clinic hours.

Risk factors for surgical recurrence after ileocolic resection of Crohn's disease.

PURPOSE: We evaluated the effect of potential clinical factors on surgical recurrence of ileal Crohn's disease after initial ileocolic resection. METHODS: One hundred seventy-six patients with ileal Crohn's disease who underwent an ileocolic resection with anastomosis were identified from our database. The outcome of interest was time from first to second ileocolic resection. Survival analysis was used to assess the significance of the Montreal phenotype classification, smoking habit, a family history of inflammatory bowel disease and other clinical variables. RESULTS: In our final Cox model, a family history of inflammatory bowel disease (hazard ratio 2.24, 95 percent confidence interval 1.16-4.30, P = 0.016), smoking at time of initial ileocolic resection (hazard ratio 2.08, 95 percent confidence interval 1.11-3.91, P = 0.023) was associated with an increased risk of a second ileocolic resection while postoperative prescription of immunomodulators (hazard ratio 0.40, 95 percent confidence interval 0.18-0.88, P = 0.022) was associated with a decreased risk of a second ileocolic resection. CONCLUSIONS: Both a family history of inflammatory bowel disease and smoking at the time of the initial ileocolic resection are associated with an increased risk of a second ileocolic resection. Postoperative prescription of immunomodulators is associated with a reduced risk of surgical recurrence. This study supports the concept that both genetic and environmental factors influence the risk of surgical recurrence of ileal Crohn's disease.

Emerging health disparities in Botswana: examining the situation of orphans during the AIDS epidemic.

Botswana has the second highest HIV prevalence rate and highest rate of orphanhood in the world. Although child mortality rates have doubled in 15 years, the extent to which health disparities are connected to orphan status remains unclear. We conducted an analysis of the 2000 Botswana Multiple Indicator Cluster Survey to examine whether orphan-based health disparities exist. We measured health inequalities using anthropometric data among 2723 under-five year olds, nested in 1854 households, and 208 communities. We calculated multilevel logistic regression models to estimate the child, household, and regional determinants of growth failure. We found that orphaned children aged 0-4 are 49% more likely to be underweight than nonorphans (p<0.05) controlling for household poverty and other factors; and orphans disproportionately live in the poorest households. Throughout sub-Saharan Africa (SSA), Botswana is a leader in responding to the AIDS epidemic, in particular as one of the first countries to offer universal antiretroviral treatment. However, orphan-based health disparities confirm that the orphan response is still insufficient. Better data are needed to fully understand the mechanisms that lead to these disparities, and the public sector needs an increased capacity to fully implement the policies and programs designed to meet the needs of orphans. Findings from this study have important implications for countries throughout SSA, and Southern Africa in particular, where the number of orphans has doubled to tripled over the past 15 years.

Orphan care in Botswana's working households: growing responsibilities in the absence of adequate support.

OBJECTIVES: Botswana has one of the world's highest HIV-prevalence rates and the world's highest percentages of orphaned children among its population. We assessed the ability of income-earning households in Botswana to adequately care for orphans. METHODS: We used data from the Botswana Family Health Needs Study (2002), a sample of 1033 working adults with caregiving responsibilities who used public services, to assess whether households with orphan-care responsibilities encountered financial and other difficulties. Thirty-seven percent of respondents provided orphan care, usually to extended family members. We applied logistic regression models to determine the factors associated with experiencing problems related to orphan caregiving. RESULTS: Nearly half of working households with orphan-care responsibilities reported experiencing financial and other difficulties because of orphan care. Issues of concern included caring for multiple orphans, caring for sick adults and orphans simultaneously, receiving no assistance, and low income. CONCLUSIONS: The orphan crisis is impoverishing even working households, where caregivers lack sufficient resources to provide basic needs. Neither the public sector nor communities provide adequate safety nets. International assistance is critical to build capacity within the social welfare infrastructure and to fund community-level activities that support households. Lessons from Botswana's orphan crisis can provide valuable insights to policymakers throughout sub-Saharan Africa.