Early-life tobacco exposure is causally implicated in aberrant RAG-mediated recombination in childhood acute lymphoblastic leukemia.

Acute lymphoblastic leukemia (ALL) is the most common cancer in children, yet few environmental risk factors have been identified. We previously found an association between early-life tobacco smoke exposure and frequency of somatic deletions of 8 leukemia driver genes among childhood ALL patients in the California Childhood Leukemia Study. To expand analysis genome-wide and examine potential mechanisms, we conducted tumor whole-genome sequencing in 35 ALL patients, including 18 with high prenatal tobacco exposure and 17 with low exposure as determined by established epigenetic biomarkers. High tobacco exposure patients had significantly more structural variants (P < .001) and deletions (P = .001) genome-wide than low exposure patients. Investigation of off-target RAG recombination revealed that 41% of deletions in the high tobacco exposure patients were putatively RAG-mediated (full RAG motif identified at one or both breakpoints) compared with only 21% in the low exposure group (P = .001). In a multilevel model, deletions in high tobacco exposure patients were 2.44-fold (95% CI:1.13-5.38) more likely to be putatively RAG-mediated than deletions in low exposure patients. No point mutational signatures were associated with prenatal tobacco exposure. Our findings suggest that early-life tobacco smoke exposure may promote leukemogenesis by driving development of somatic deletions in pre-leukemic lymphocytes via off-target RAG recombination.

Antimicrobial resistance and antimicrobial stewardship in South Africa: a survey of healthcare workers in academic and nonacademic hospitals.

Objective: Antimicrobial stewardship programmes (ASPs) facilitate appropriate antimicrobial use and require contextualization for optimal functioning. We aimed to investigate perceptions of and antimicrobial resistance (AMR) and ASPs among healthcare workers in academic and nonacademic hospitals. Design: Cross-sectional survey. Setting: Three academic (Charlotte Maxeke Johannesburg Academic, Inkosi Albert Luthuli, Tygerberg) and three nonacademic hospitals (Leratong, Prince Mshiyeni Memorial, and Paarl) in South Africa from January to June 2022. Participants: Doctors, nurses, and pharmacists. Methods: Voluntary questionnaire using Google Forms, encompassing AMR, ASPs, and selected discipline-specific components. Results: Participants comprised 79 doctors (50 academic), 178 nurses (169 academic), and 21 pharmacists (18 academic) and were female predominant. AMR was a problem in academic hospitals (74.7% vs 51.2%, p 0.004); 73.5% overall reported inappropriate antimicrobial use as a major contributor. Adequate education on antimicrobials occurred in only 36.4% overall. Microbiological testing guided therapy more often in nonacademic settings (80.0% vs 50.2%, p <0.001). In both settings, antimicrobial availability drove selection in 48.2%. Overall, ASPs improved patient care (89.8%) and reduced antimicrobial use (86.9%), although felt to override prescriber autonomy in academic settings (29.4% vs 7.5%, p 0.007), mainly among nurses. Only 50.2% reported successful local ASPs. A minority of pharmacists (20.0%) reported sufficient hospital support for ASPs. Education, involvement of infection control staff, and inclusion of nurses in ASPs were most impactful on AMR. Conclusion: Selected healthcare worker perspectives differ by category and setting and can be targeted to improve ASPs. Further studies should target a higher number of clinical staff in both settings.

Epigenomic signature of major congenital heart defects in newborns with Down syndrome.

BACKGROUND: Congenital heart defects (CHDs) affect approximately half of individuals with Down syndrome (DS), but the molecular reasons for incomplete penetrance are unknown. Previous studies have largely focused on identifying genetic risk factors associated with CHDs in individuals with DS, but comprehensive studies of the contribution of epigenetic marks are lacking. We aimed to identify and characterize DNA methylation differences from newborn dried blood spots (NDBS) of DS individuals with major CHDs compared to DS individuals without CHDs. METHODS: We used the Illumina EPIC array and whole-genome bisulfite sequencing (WGBS) to quantitate DNA methylation for 86 NDBS samples from the California Biobank Program: (1) 45 DS-CHD (27 female, 18 male) and (2) 41 DS non-CHD (27 female, 14 male). We analyzed global CpG methylation and identified differentially methylated regions (DMRs) in DS-CHD versus DS non-CHD comparisons (both sex-combined and sex-stratified) corrected for sex, age of blood collection, and cell-type proportions. CHD DMRs were analyzed for enrichment in CpG and genic contexts, chromatin states, and histone modifications by genomic coordinates and for gene ontology enrichment by gene mapping. DMRs were also tested in a replication dataset and compared to methylation levels in DS versus typical development (TD) WGBS NDBS samples. RESULTS: We found global CpG hypomethylation in DS-CHD males compared to DS non-CHD males, which was attributable to elevated levels of nucleated red blood cells and not seen in females. At a regional level, we identified 58, 341, and 3938 CHD-associated DMRs in the Sex Combined, Females Only, and Males Only groups, respectively, and used machine learning algorithms to select 19 Males Only loci that could distinguish CHD from non-CHD. DMRs in all comparisons were enriched for gene exons, CpG islands, and bivalent chromatin and mapped to genes enriched for terms related to cardiac and immune functions. Lastly, a greater percentage of CHD-associated DMRs than background regions were differentially methylated in DS versus TD samples. CONCLUSIONS: A sex-specific signature of DNA methylation was detected in NDBS of DS-CHD compared to DS non-CHD individuals. This supports the hypothesis that epigenetics can reflect the variability of phenotypes in DS, particularly CHDs.

Microbiological analysis and predictors of gallbladder infection with antimicrobial susceptibility patterns in an HIV setting.

Background South Africa has a high prevalence of people living with human immunodeficiency virus (HIV; PLWH) who have shown to affect the prevalence and severity of infection and sepsis particularly gallbladder disease.  Empirical Antimicrobial (EA) therapy for acute cholecystitis (AC) is based largely on bacteria colonisation of bile (bacteriobilia) and antimicrobial susceptibility patterns (antibiograms) obtained from the developed world where the prevalence of PLWH is very low. In an ever-emerging era of increasing antimicrobial resistance, monitoring and updating local antibiograms is underscored.  Objective Due to the paucity of data available locally to guide treatment we found it pertinent to examine gallbladder bile for bacteriobilia and antibiograms in a setting with a high prevalence of PLWH to determine if this may demand a review of our local antimicrobial policies for gallbladder infections for both EA and pre-operative antimicrobial prophylaxis (PAP) for laparoscopic cholecystectomies (LC). Methodology A retrospective observational descriptive study was undertaken at King Edward VIII Hospital, Durban, KwaZulu-Natal, South Africa. Hospital records were reviewed for all patients undergoing cholecystectomy over a 3-year period. Gallbladder bacteriobilia and antibiograms were assessed and compared between PLWH and HIV uninfected (HIV-U). Pre-operative age, ERCP, PCT, CRP and NLR were used as predictors for bacteriobilia. Statistical analyses were performed using R Project and p values of less than 0.05 were considered as statistically significant. Results There were no differences in bacteriobilia or antibiograms between PLWH and HIV-U. There was >30% resistance to amoxicillin/clavulanate and cephalosporins. Aminoglycoside-based therapy, had good susceptibility patterns whilst carbapenem-based therapy demonstrated the lowest resistance levels. ERCP and age were predictors of bacteriobilia (p<0.001 and 0.002 respectively). PCT, CRP and NLR were not. Conclusion PLWH should follow the same PAP and EA recommendations as HIV-U. For EA, we recommend, a combination of amoxicillin/clavulanate with aminoglycoside-based therapy (amikacin or gentamycin) or piperacillin/tazobactam as monotherapy. Carbapenem-based therapy should be reserved for drug resistant species. For PAP, we recommend the routine use in older patients and patients with history of ERCP undergoing LC.

Epigenomic signature of major congenital heart defects in newborns with Down syndrome.

Background: Congenital heart defects (CHDs) affect approximately half of individuals with Down syndrome (DS) but the molecular reasons for incomplete penetrance are unknown. Previous studies have largely focused on identifying genetic risk factors associated with CHDs in individuals with DS, but comprehensive studies of the contribution of epigenetic marks are lacking. We aimed to identify and characterize DNA methylation differences from newborn dried blood spots (NDBS) of DS individuals with major CHDs compared to DS individuals without CHDs. Methods: We used the Illumina EPIC array and whole-genome bisulfite sequencing (WGBS) to quantitate DNA methylation for 86 NDBS samples from the California Biobank Program: 1) 45 DS-CHD (27 female, 18 male) and 2) 41 DS non-CHD (27 female, 14 male). We analyzed global CpG methylation and identified differentially methylated regions (DMRs) in DS-CHD vs DS non-CHD comparisons (both sex-combined and sex-stratified) corrected for sex, age of blood collection, and cell type proportions. CHD DMRs were analyzed for enrichment in CpG and genic contexts, chromatin states, and histone modifications by genomic coordinates and for gene ontology enrichment by gene mapping. DMRs were also tested in a replication dataset and compared to methylation levels in DS vs typical development (TD) WGBS NDBS samples. Results: We found global CpG hypomethylation in DS-CHD males compared to DS non-CHD males, which was attributable to elevated levels of nucleated red blood cells and not seen in females. At a regional level, we identified 58, 341, and 3,938 CHD-associated DMRs in the Sex Combined, Females Only, and Males Only groups, respectively, and used machine learning algorithms to select 19 Males Only loci that could distinguish CHD from non-CHD. DMRs in all comparisons were enriched for gene exons, CpG islands, and bivalent chromatin and mapped to genes enriched for terms related to cardiac and immune functions. Lastly, a greater percentage of CHD-associated DMRs than background regions were differentially methylated in DS vs TD samples. Conclusions: A sex-specific signature of DNA methylation was detected in NDBS of DS-CHD compared to DS non-CHD individuals. This supports the hypothesis that epigenetics can reflect the variability of phenotypes in DS, particularly CHDs.

Diagnostic yield of urine lipoarabinomannan and sputum tuberculosis tests in people living with HIV: a systematic review and meta-analysis of individual participant data.

BACKGROUND: Sputum is the most widely used sample to diagnose active tuberculosis, but many people living with HIV are unable to produce sputum. Urine, in contrast, is readily available. We hypothesised that sample availability influences the diagnostic yield of various tuberculosis tests. METHODS: In this systematic review and meta-analysis of individual participant data, we compared the diagnostic yield of point-of-care urine-based lipoarabinomannan tests with that of sputum-based nucleic acid amplification tests (NAATs) and sputum smear microscopy (SSM). We used microbiologically confirmed tuberculosis based on positive culture or NAAT from any body site as the denominator and accounted for sample provision. We searched PubMed, Web of Science, Embase, African Journals Online, and clinicaltrials.gov from database inception to Feb 24, 2022 for randomised controlled trials, cross-sectional studies, and cohort studies that assessed urine lipoarabinomannan point-of-care tests and sputum NAATs for active tuberculosis detection in participants irrespective of tuberculosis symptoms, HIV status, CD4 cell count, or study setting. We excluded studies in which recruitment was not consecutive, systematic, or random; provision of sputum or urine was an inclusion criterion; less than 30 participants were diagnosed with tuberculosis; early research assays without clearly defined cutoffs were tested; and humans were not studied. We extracted study-level data, and authors of eligible studies were invited to contribute deidentified individual participant data. The main outcomes were the tuberculosis diagnostic yields of urine lipoarabinomannan tests, sputum NAATs, and SSM. Diagnostic yields were predicted using Bayesian random-effects and mixed-effects meta-analyses. This study is registered with PROSPERO, CRD42021230337. FINDINGS: We identified 844 records, from which 20 datasets and 10 202 participants (4561 [45%] male participants and 5641 [55%] female participants) were included in the meta-analysis. All studies assessed sputum Xpert (MTB/RIF or Ultra, Cepheid, Sunnyvale, CA, USA) and urine Alere Determine TB LAM (AlereLAM, Abbott, Chicago, IL, USA) in people living with HIV aged 15 years or older. Nearly all (9957 [98%] of 10 202) participants provided urine, and 82% (8360 of 10 202) provided sputum within 2 days. In studies that enrolled unselected inpatients irrespective of tuberculosis symptoms, only 54% (1084 of 1993) of participants provided sputum, whereas 99% (1966 of 1993) provided urine. Diagnostic yield was 41% (95% credible interval [CrI] 15-66) for AlereLAM, 61% (95% Crl 25-88) for Xpert, and 32% (95% Crl 10-55) for SSM. Heterogeneity existed across studies in the diagnostic yield, influenced by CD4 cell count, tuberculosis symptoms, and clinical setting. In predefined subgroup analyses, all tests had higher yields in symptomatic participants, and AlereLAM yield was higher in those with low CD4 counts and inpatients. AlereLAM and Xpert yields were similar among inpatients in studies enrolling unselected participants who were not assessed for tuberculosis symptoms (51% vs 47%). AlereLAM and Xpert together had a yield of 71% in unselected inpatients, supporting the implementation of combined testing strategies. INTERPRETATION: AlereLAM, with its rapid turnaround time and simplicity, should be prioritised to inform tuberculosis therapy among inpatients who are HIV-positive, regardless of symptoms or CD4 cell count. The yield of sputum-based tuberculosis tests is undermined by people living with HIV who cannot produce sputum, whereas nearly all participants are able to provide urine. The strengths of this meta-analysis are its large size, the carefully harmonised denominator, and the use of Bayesian random-effects and mixed-effects models to predict yields; however, data were geographically restricted, clinically diagnosed tuberculosis was not considered in the denominator, and little information exists on strategies for obtaining sputum samples. FUNDING: FIND, the Global Alliance for Diagnostics.

Evaluating systematic targeted universal testing for tuberculosis in primary care clinics of South Africa: A cluster-randomized trial (The TUTT Trial).

BACKGROUND: The World Health Organization (WHO) recommends systematic symptom screening for tuberculosis (TB). However, TB prevalence surveys suggest that this strategy does not identify millions of TB patients, globally. Undiagnosed or delayed diagnosis of TB contribute to TB transmission and exacerbate morbidity and mortality. We conducted a cluster-randomized trial of large urban and rural primary healthcare clinics in 3 provinces of South Africa to evaluate whether a novel intervention of targeted universal testing for TB (TUTT) in high-risk groups diagnosed more patients with TB per month compared to current standard of care (SoC) symptom-directed TB testing. METHODS AND FINDINGS: Sixty-two clinics were randomized; with initiation of the intervention clinics over 6 months from March 2019. The study was prematurely stopped in March 2020 due to clinics restricting access to patients, and then a week later due to the Coronavirus Disease 2019 (COVID-19) national lockdown; by then, we had accrued a similar number of TB diagnoses to that of the power estimates and permanently stopped the trial. In intervention clinics, attendees living with HIV, those self-reporting a recent close contact with TB, or a prior episode of TB were all offered a sputum test for TB, irrespective of whether they reported symptoms of TB. We analyzed data abstracted from the national public sector laboratory database using Poisson regression models and compared the mean number of TB patients diagnosed per clinic per month between the study arms. Intervention clinics diagnosed 6,777 patients with TB, 20.7 patients with TB per clinic month (95% CI 16.7, 24.8) versus 6,750, 18.8 patients with TB per clinic month (95% CI 15.3, 22.2) in control clinics during study months. A direct comparison, adjusting for province and clinic TB case volume strata, did not show a significant difference in the number of TB cases between the 2 arms, incidence rate ratio (IRR) 1.14 (95% CI 0.94, 1.38, p = 0.46). However, prespecified difference-in-differences analyses showed that while the rate of TB diagnoses in control clinics decreased over time, intervention clinics had a 17% relative increase in TB patients diagnosed per month compared to the prior year, interaction IRR 1.17 (95% CI 1.14, 1.19, p < 0.001). Trial limitations were the premature stop due to COVID-19 lockdowns and the absence of between-arm comparisons of initiation and outcomes of TB treatment in those diagnosed with TB. CONCLUSIONS: Our trial suggests that the implementation of TUTT in these 3 groups at extreme risk of TB identified more TB patients than SoC and could assist in reducing undiagnosed TB patients in settings of high TB prevalence. TRIAL REGISTRATION: South African National Clinical Trials Registry DOH-27-092021-4901.

Postpasteurization Testing of Human Milk Sterility at Human Milk Banks in Resource-Limited Settings: An Alternative to Standard Microbiological Quality Testing.

Introduction: Pasteurized donor human milk provides nutrition and bioactive factors for infant growth and health when a mother's own milk is not available. Bacteriological testing is recommended for each pasteurized batch of donor milk before distribution to ensure that the milk is safe for use. Charm Peel Plates (CPPs) are a simplified, easy-to-use culture method for detecting microorganisms in milk and milk products. This study investigates the feasibility of using CPPs as an alternative test for current standard postpasteurization screening by human milk banks (HMBs), particularly those in resource-limited settings. Aim: The aim of this study was to evaluate the feasibility of using the CPP versus the 5% horse blood agar (HBA) plate (standard South African National Health Laboratory Service method) for detecting bacterial growth in pasteurized human milk samples. Methods: For each of the 50 pasteurized donor milk samples, 100-µL aliquots were cultured on routine HBA and 1 mL on CPPs for the total bacterial colony count. Any positive growth was identified using VITEK® 2 (bioMérieux). To demonstrate the ability of CPPs to support bacterial growth, four spiked samples were tested. Results: Concurrent negative test results were reported for 49/50 (98%) samples with only one positive test with HBA. Conclusions and Recommendations: The CPP is equivalent to HBA for detection of bacterial growth. Additional advantages of CPPs are ease of use and cost-effectiveness. The CPP is therefore recommended as a point-of-care, bacteriological screening method for donor human milk by HMBs, particularly those in resource-limited settings.

DNA methylation at birth in monozygotic twins discordant for pediatric acute lymphoblastic leukemia.

Aberrant DNA methylation constitutes a key feature of pediatric acute lymphoblastic leukemia at diagnosis, however its role as a predisposing or early contributor to leukemia development remains unknown. Here, we evaluate DNA methylation at birth in 41 leukemia-discordant monozygotic twin pairs using the Illumina EPIC array on archived neonatal blood spots to identify epigenetic variation associated with development of pediatric acute lymphoblastic leukemia, independent of genetic influence. Through conditional logistic regression we identify 240 significant probes and 10 regions associated with the discordant onset of leukemia. We identify a significant negative coefficient bias, indicating DNA hypomethylation in cases, across the array and enhanced in open sea, shelf/shore, and gene body regions compared to promoter and CpG island regions. Here, we show an association between global DNA hypomethylation and future development of pediatric acute lymphoblastic leukemia across disease-discordant genetically identical twins, implying DNA hypomethylation may contribute more generally to leukemia risk.

Low prevalence of macrolide resistance in Mycoplasma genitalium infections in a cohort of pregnant women living with human immunodeficiency virus.

OBJECTIVE: Macrolide resistance in Mycoplasma genitalium (M. genitalium) is increasing as a result of the widespread use of azithromycin in the treatment of sexually transmitted infections (STIs). To date, there are few published studies on macrolide resistance patterns in South African pregnant women. This study now contributes to the growing body of knowledge. METHODS: This study included 385 pregnant women living with HIV. Vaginal swabs were collected from consenting pregnant women and used for the detection of M. genitalium using the TaqMan assay. Macrolide resistance-associated mutations in the 23S rRNA gene were determined for all samples that tested positive for M. genitalium using the AllplexTM MG & AziR assay (Seegene) which allows for the simultaneous detection and identification of M. genitalium and six mutations (A2058C, A2058G, A2058T, A2059C, A2059G and A2059T) responsible for azithromycin resistance. The correlation between the TaqMan assay and AllplexTM MG & AziR assay (Seegene) for the detection of M. genitalium was also performed in a subset of 121 samples. RESULTS: Of the 385 samples tested in this study, 14 samples were positive for M. genitalium estimating a prevalence of 3.6%. The same 14 samples also tested positive on the AllplexTM assay indicating a good correlation between the TaqMan Assay and the AllplexTM. Of the 14 positive samples, one sample carried a mutation at position A2059G denoting macrolide resistance in this pathogen. Mutations in the other regions of the 23S rRNA were not detected. All assay controls used in the mutation scanning produced the desired results showing the validity of the assay. CONCLUSION: In this study, macrolide resistance in M. genitalium was detected. Despite the low prevalence of resistance determinants ongoing antimicrobial resistance surveillance is vital considering that azithromycin is used in the syndromic management for the treatment of vaginal discharge syndrome.

Assessment of Antibiotic Resistance and Efflux Pump Gene Expression in Neisseria Gonorrhoeae Isolates from South Africa by Quantitative Real-Time PCR and Regression Analysis.

Introduction: Treatment of gonorrhoea infection is limited by the increasing prevalence of multidrug-resistant strains. Cost-effective molecular diagnostic tests can guide effective antimicrobial stewardship. The aim of this study was to correlate mRNA expression levels in Neisseria gonorrhoeae antibiotic target genes and efflux pump genes to antibiotic resistance in our population. Methods: This study investigated the expression profile of antibiotic resistance-associated genes (penA, ponA, pilQ, mtrR, mtrA, mtrF, gyrA, parC, parE, rpsJ, 16S rRNA, and 23S rRNA) and efflux pump genes (macAB, norM, and mtrCDE), by quantitative real-time PCR, in clinical isolates from KwaZulu-Natal, South Africa. Whole-genome sequencing was used to determine the presence or absence of mutations. Results: N. gonorrhoeae isolates, from female and male patients presenting for care at clinics in KwaZulu-Natal, South Africa, were analysed. As determined by binomial regression and ROC analysis, the most significant (p ≤ 0.05) markers for resistance prediction in this population, and their cutoff values, were determined to be mtrC (p = 0.024; cutoff <0.089), gyrA (p = 0.027; cutoff <0.0518), parE (p = 0.036; cutoff <0.0033), rpsJ (p = 0.047; cutoff <0.0012), and 23S rRNA (p = 0.042; cutoff >7.754). Conclusion: Antimicrobial stewardship includes exploring options to conserve currently available drugs for gonorrhoea treatment. There is the potential to predict an isolate as either susceptible or nonsusceptible based on the mRNA expression level of specific candidate markers, to inform patient management. This real-time qPCR approach, with few targets, can be further investigated for use as a potentially cost-effective diagnostic tool to detect resistance.

Radiotherapy improves the outcomes of immunotherapy with Sintilimab in non-small-cell lung cancer: A real-world analysis.

Introduction: Radiotherapy may augment systemic antitumor responses to immunotherapy. We did a retrospective study to infer whether radiotherapy improves outcomes to immunotherapy in patients with stage III and IV non-small-cell lung cancer (NSCLC). Methods: This retrospective study conducted at Enze Medical Center enrolled 259 patients with histopathology confirmed NSCLC from December 2018 to December 31, 2021. All were treated with Sintilimab, some patients received radiotherapy at an appropriate time point. Radiation type includes conventional radiotherapy and stereotactic body radiotherapy. The progression-free survival (PFS), and overall survival (OS) were the primary endpoint. Results: A retrospective analysis was performed on 259 patients, of whom 140 had been treated with immunotherapy lonely and 119 had been remedied with immunotherapy plus radiotherapy. Baseline variables were well balanced between the two groups, including gender, age, smoking status, TNM staging, number of metastases, ECOG score, pathological type and lines of previous systemic therapy. The median PFS in the immunotherapy alone group was 5.00 months (95%CI 4.38-5.62) versus immunotherapy plus radiotherapy was 9.00 months (5.95-12.05; p<0.001). The median OS in the immunotherapy alone group was 16.00 months (12.59-19.42) versus immunotherapy plus radiotherapy was 30.00 months (20.75-39.25; p=0.027). PFS was finer in the radiotherapy plus immunotherapy group than the immunotherapy group alone in both stage III(P=0.0069) and Stage IV(P=0.006) patients. In the univariate analysis, radiotherapy, male, ECOG=0 and <2 lines of previous systemic therapy were connected with an observably better PFS (P<0.001; P=0.03; P=0.002;P=0.021). In a multivariate analysis, radiotherapy, ECOG=0 and <2 lines of previous systemic therapy were independent prognostic factors with a markedly better PFS (P<0.001; P=0.006;P=0.009). An univariate analysis, radiotherapy, male, stage III, non-metastasis, ECOG=0 and squamous carcinoma were associated with a significantly better OS (P=0.032, P=0.036,P=0.002,P<0.001,P=0.002,P=0.025). A multivariate analysis, non-metastasis was a standalone prognostic indicator with a significantly better OS (P=0.006). However, radiotherapy was a tendency indicator with a better OS (HR0.70 95% CI 0.47-1.06). There were also no obvious increases in adverse events in the combination group. Conclusions: Radiotherapy with addition of immunotherapy was observably linked to a better outcome in patients with III and IV staging NSCLC.

Localized variation in ancestral admixture identifies pilocytic astrocytoma risk loci among Latino children.

BACKGROUND: Pilocytic astrocytoma (PA) is the most common pediatric brain tumor. PA has at least a 50% higher incidence in populations of European ancestry compared to other ancestral groups, which may be due in part to genetic differences. METHODS: We first compared the global proportions of European, African, and Amerindian ancestries in 301 PA cases and 1185 controls of self-identified Latino ethnicity from the California Biobank. We then conducted admixture mapping analysis to assess PA risk with local ancestry. RESULTS: We found PA cases had a significantly higher proportion of global European ancestry than controls (case median = 0.55, control median = 0.51, P value = 3.5x10-3). Admixture mapping identified 13 SNPs in the 6q14.3 region (SNX14) contributing to risk, as well as three other peaks approaching significance on chromosomes 7, 10 and 13. Downstream fine mapping in these regions revealed several SNPs potentially contributing to childhood PA risk. CONCLUSIONS: There is a significant difference in genomic ancestry associated with Latino PA risk and several genomic loci potentially mediating this risk.

Pyrazinamide resistance in rifampicin discordant tuberculosis.

INTRODUCTION: Mycobacterium tuberculosis strains with phenotypically susceptible rpoB mutations (rifampicin discordant) have emerged following implementation of rapid molecular drug resistance testing for tuberculosis. Whilst rifampicin resistance is known to be associated with resistance to other rifamycins (rifapentine and rifabutin) as well as isoniazid and pyrazinamide, rifampicin discordant strains have shown high rates of susceptibility to isoniazid and rifabutin. However, pyrazinamide susceptibly testing results have not been reported. MATERIALS AND METHODS: We evaluated pyrazinamide resistance in 80 rifampicin discordant and 25 rifampicin and isoniazid susceptible isolates from KwaZulu-Natal in South Africa using Mycobacteria Growth Indicator Tube method and sequencing of the pncA. We also compared susceptibility of pyrazinamide with that of isoniazid. RESULTS: Pyrazinamide resistance was found in 6/80 (7.5%) rifampicin discordant isolates. All pyrazinamide resistant isolates were also resistant to isoniazid and pyrazinamide resistance was found to be associated with isoniazid resistance. No pyrazinamide resistance was found among the isoniazid susceptible isolates. CONCLUSION: Given the low prevalence of pyrazinamide resistance in rifampicin discordant TB, this anti-TB drug still has a significant role in the treatment of these patients. Performing pyrazinamide susceptibility testing remains a challenge, our findings show that isoniazid susceptible isolates are unlikely to be resistant to pyrazinamide among the discordant TB isolates.

Acinetobacter baumannii complex, national laboratory-based surveillance in South Africa, 2017 to 2019.

OBJECTIVE: We aimed to provide an analysis of A. baumannii complex (ABC) isolated from blood cultures in South Africa. MATERIALS AND METHODS: ABC surveillance was conducted from 1 April 2017 to 30 September 2019 at 19 hospital sites from blood cultures of any age and sex. Organism identification was performed using the MALDI-TOF MS and antimicrobial susceptibility testing (AST), MicroScan Walkaway System. We confirmed colistin resistance with Sensititre, FRCOL panel, and selected for whole-genome sequencing. RESULTS: During the study period, we identified 4822 cases of ABC, of which 2152 cases were from 19 enhanced surveillance sites were reported during the enhanced surveillance period (1 August 2018 to 30 September 2019). Males accounted for 54% (2611/4822). Of the cases with known age, 41% (1968/4822) were infants (< 1-year-old). Seventy-eight percent (1688/2152) of cases had a known hospital outcome, of which 36% (602/1688) died. HIV status was known for 69% (1168/1688) of cases, and 14% (238/1688) were positive. Eighty-two percent (1389/1688) received antimicrobial treatment in admission. Three percent (35/1389) of cases received single colistin. Four percent (75/2033) were resistant to colistin. At least 75% of the isolates (1530/2033) can be classified as extensively drug-resistant (XDR), with resistance to most antibiotics except for colistin. The majority, 83% (20/24), of the colistin-resistant isolates were of the sequence type (ST) 1. Resistance genes, both plasmid- and chromosomal- mediated were not observed. Although all isolates had, nine efflux pump genes related to antimicrobial resistance. CONCLUSION: Our surveillance data contributed to a better understanding of the natural course of A. baumannii disease, the patient characteristics among infants, and the level of resistance. At least two-thirds of the isolates were extensively drug-resistant, and four percent of isolates were resistant to colistin.

Impending Doom: A Rare Case of Metastatic Myoepithelial Carcinoma.

Myoepithelial carcinoma is a rare malignant tumor arising from myoepithelial cells. The usual sites of occurrence are the oral cavity and pharynx with the majority of tumors arising from the salivary gland. However, there have been reported cases of myoepithelial carcinoma seen in the superficial soft tissue, upper respiratory tract, breast, skin, and GI tract. Deep soft tissue myoepithelial carcinoma is relatively uncommon.  Due to the rarity of this malignancy, consensus on appropriate therapy remains sparse. However, complete resection and/or adjuvant chemotherapy and radiotherapy have been advocated for non-metastatic localized diseases. Sadly, the reported outcome in patients with metastatic disease remains dismal. In this case, we report a 79-year-old male incidentally found to have a deep soft tissue mass in the sacral area with a coexistent left axillary lymphadenopathy with biopsy and immunohistochemistry confirmation of metastatic myoepithelial carcinoma. He had a rapid clinical deterioration with subsequent fatality.

Wandering Cancer Cells: Metastatic Renal Cell Carcinoma Without Evidence of a Primary Tumor.

Renal cell carcinoma (RCC) usually presents clinically in the advanced stage including bone metastasis. However metastatic RCC without evidence of a primary tumor in the kidney is extremely rare. We herein report a case of a 70-year-old male initially evaluated for bone lesion and diagnosed with biopsy-proven metastatic clear cell RCC without a renal primary. Given the rare nature of the disease, there is no standardized course of treatment that has yet been established. We believe that our case will add to the body of knowledge about uncommon oncologic instances and consolidate the information that has already been published.

Accelerated epigenetic aging in newborns with Down syndrome.

Accelerated aging is a hallmark of Down syndrome (DS), with adults experiencing early-onset Alzheimer's disease and premature aging of the skin, hair, and immune and endocrine systems. Accelerated epigenetic aging has been found in the blood and brain tissue of adults with DS but when premature aging in DS begins remains unknown. We investigated whether accelerated aging in DS is already detectable in blood at birth. We assessed the association between age acceleration and DS using five epigenetic clocks in 346 newborns with DS and 567 newborns without DS using Illumina MethylationEPIC DNA methylation array data. We compared two epigenetic aging clocks (DNAmSkinBloodClock and pan-tissue DNAmAge) and three epigenetic gestational age clocks (Haftorn, Knight, and Bohlin) between DS and non-DS newborns using linear regression adjusting for observed age, sex, batch, deconvoluted blood cell proportions, and genetic ancestry. Targeted sequencing of GATA1 was performed in a subset of 184 newborns with DS to identify somatic mutations associated with transient abnormal myelopoiesis. DS was significantly associated with increased DNAmSkinBloodClock (effect estimate = 0.2442, p < 0.0001), with an epigenetic age acceleration of 244 days in newborns with DS after adjusting for potential confounding factors (95% confidence interval: 196-292 days). We also found evidence of epigenetic age acceleration associated with somatic GATA1 mutations among newborns with DS (p = 0.015). DS was not associated with epigenetic gestational age acceleration. We demonstrate that accelerated epigenetic aging in the blood of DS patients begins prenatally, with implications for the pathophysiology of immunosenescence and other aging-related traits in DS.

Detection of metronidazole resistance in Trichomonas vaginalis using uncultured vaginal swabs.

Trichomonas vaginalis (T. vaginalis) is the most prevalent sexually transmitted infection (STI) globally. Metronidazole is the drug of choice for treating T. vaginalis infections although metronidazole-resistant T. vaginalis has been reported in clinical isolates. The purpose of this study was to determine the presence of mutations in nitroreductase genes associated with metronidazole resistance in vaginal swabs testing positive for T. vaginalis. This study included 385 human immunodeficiency virus (HIV)-positive pregnant women. Vaginal swabs were collected from consenting pregnant women and used for the detection of T. vaginalis using the TaqMan assay. From the vaginal swabs, nitroreductase genes ntr4 and ntr6 containing mutations associated with metronidazole resistance were amplified using a quantitative polymerase chain reaction (PCR) assay. To validate the PCR assay, T. vaginalis cultured isolates with known metronidazole resistance profiles were used as controls in the mutation detection assays. The prevalence of T. vaginalis in the study population was 12.2% (47/385). Mutations associated with resistance to metronidazole were detected in more than 40% of the samples tested, i.e. 21/47 (45%) and 24/47 (51%) for ntr4 and ntr6, respectively. A total of 19 samples (40%) carried mutations for both ntr4 and ntr6 genes associated with metronidazole resistance. The validation assays showed a positive correlation between phenotypic and genotypic resistance profiles. This study found a high prevalence of mutations associated with metronidazole resistance. This is concerning since metronidazole is currently used in the syndromic management of STIs in South Africa. Molecular-based assays for monitoring metronidazole resistance profiles using nitroreductase genes may serve as a feasible method for antimicrobial surveillance studies for T. vaginalis.

The Tale of a Rubbery White Clot: Poorly Differentiated Spindle Cell Sarcoma Presenting As Superior Vena Cava Syndrome.

Sarcoma is an uncommon neoplasm of mesenchymal origin (1). The presentation is usually vague. It may present as a mass in the thigh or retroperitoneum, with resultant pain or paresthesia of the affected area. The diagnosis is very challenging due to its indistinct presentation. The prognosis remains poor due to delays in diagnosis and few available therapeutic options. We herein report the first case of superior vena cava (SVC) syndrome caused by spindle cell sarcoma.