Emergence of Canonical and Noncanonical Genomic Variants following In Vitro Exposure of Clinical Mycobacterium tuberculosis Strains to Bedaquiline or Clofazimine

In Mycobacterium tuberculosis, bedaquiline and clofazimine resistance occurs primarily through Rv0678 variants, a gene encoding a repressor protein that regulates mmpS5/mmpL5 efflux pump gene expression. Despite the shared effect of both drugs on efflux, little else is known about other pathways affected. We hypothesized that in vitro generation of bedaquiline- or clofazimine-resistant mutants could provide insight into additional mechanisms of action. We performed whole-genome sequencing and determined phenotypic MICs for both drugs on progenitor and mutant progenies. Mutants were induced through serial passage on increasing concentrations of bedaquiline or clofazimine. Rv0678 variants were identified in both clofazimine- and bedaquiline-resistant mutants, with concurrent atpE SNPs occurring in the latter. Of concern was the acquisition of variants in the F420 biosynthesis pathway in clofazimine-resistant mutants obtained from either a fully susceptible (fbiD: del555GCT) or rifampicin mono-resistant (fbiA: 283delTG and T862C) progenitor. The acquisition of these variants possibly implicates a shared pathway between clofazimine and nitroimidazoles. Pathways associated with drug tolerance and persistence, F420 biosynthesis, glycerol uptake and metabolism, efflux, and NADH homeostasis appear to be affected following exposure to these drugs. Shared genes affected by both drugs include Rv0678, glpK, nuoG, and uvrD1. Genes with variants in the bedaquiline resistant mutants included atpE, fadE28, truA, mmpL5, glnH, and pks8, while clofazimine-resistant mutants displayed ppsD, fbiA, fbiD, mutT3, fadE18, Rv0988, and Rv2082 variants. These results show the importance of epistatic mechanisms as a means of responding to drug pressure and highlight the complexity of resistance acquisition in M. tuberculosis.

644 Improving VTE Prophylaxis in Spinal Patients – a Closed Loop Audit

Aim

Venous thromboembolism (VTE) prophylaxis is one of the key components of safe patient care and can be particularly challenging when it concerns spinal admissions to the orthopaedic trauma ward. The first cycle of our closed loop audit aimed to assess the safety of VTE prescribing in spinal admissions at a district general hospital. The current cycle aims to evaluate guideline compliance following our interventions.

Method

Quality of VTE prophylaxis prescribing was measured against NICE (NG89) recommendations as well as local guidelines. Patients were identified based on prospectively maintained admission lists. The initial audit cycle was presented locally, and the following measures were introduced in order to improve prescribing: staff teaching sessions, nomination of a VTE guardian, inclusion of VTE plans in op-notes, publication of a dedicated spinal guideline and addition of a spinal section into the trust principal VTE guideline. The current audit cycle identified 22 spinal admissions.

Results

Out of the 22 patients, only one (4%) received inadequate VTE prophylaxis which is a significant improvement compared to the initial data (8 cases - 18%). Minor prescribing concerns were noted in three cases (14%) versus 15 cases (34%) in the first cycle. Overall, the re-audit proved that following departmental interventions the majority of patients received appropriate VTE prophylaxis with no prescribing or documentation errors (82% in the current cycle vs 48% initially).

Conclusions

We have demonstrated that significant improvement in VTE prophylaxis prescribing can be achieved by the means of educating staff and introducing simple and cost-effective measures.

CD8 lymphocytes mitigate HIV-1 persistence in lymph node follicular helper T cells during hyperacute-treated infection

HIV persistence in tissue sites despite ART is a major barrier to HIV cure. Detailed studies of HIV-infected cells and immune responses in native lymph node tissue environment is critical for gaining insight into immune mechanisms impacting HIV persistence and clearance in tissue sanctuary sites. We compared HIV persistence and HIV-specific T cell responses in lymph node biopsies obtained from 14 individuals who initiated therapy in Fiebig stages I/II, 5 persons treated in Fiebig stages III-V and 17 late treated individuals who initiated ART in Fiebig VI and beyond. Using multicolor immunofluorescence staining and in situ hybridization, we detect HIV RNA and/or protein in 12 of 14 Fiebig I/II treated persons on suppressive therapy for 1 to 55 months, and in late treated persons with persistent antigens. CXCR3+ T follicular helper cells harbor the greatest amounts of gag mRNA transcripts. Notably, HIV-specific CD8+ T cells responses are associated with lower HIV antigen burden, suggesting that these responses may contribute to HIV suppression in lymph nodes during therapy. These results reveal HIV persistence despite the initiation of ART in hyperacute infection and highlight the contribution of virus-specific responses to HIV suppression in tissue sanctuaries during suppressive ART.

Evaluation of prognostic risk models for postoperative pulmonary complications in adult patients undergoing major abdominal surgery: a systematic review and international external validation cohort study

BACKGROUND

Stratifying risk of postoperative pulmonary complications after major abdominal surgery allows clinicians to modify risk through targeted interventions and enhanced monitoring. In this study, we aimed to identify and validate prognostic models against a new consensus definition of postoperative pulmonary complications.

METHODS

We did a systematic review and international external validation cohort study. The systematic review was done in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We searched MEDLINE and Embase on March 1, 2020, for articles published in English that reported on risk prediction models for postoperative pulmonary complications following abdominal surgery. External validation of existing models was done within a prospective international cohort study of adult patients (≥18 years) undergoing major abdominal surgery. Data were collected between Jan 1, 2019, and April 30, 2019, in the UK, Ireland, and Australia. Discriminative ability and prognostic accuracy summary statistics were compared between models for the 30-day postoperative pulmonary complication rate as defined by the Standardised Endpoints in Perioperative Medicine Core Outcome Measures in Perioperative and Anaesthetic Care (StEP-COMPAC). Model performance was compared using the area under the receiver operating characteristic curve (AUROCC).

FINDINGS

In total, we identified 2903 records from our literature search; of which, 2514 (86·6%) unique records were screened, 121 (4·8%) of 2514 full texts were assessed for eligibility, and 29 unique prognostic models were identified. Nine (31·0%) of 29 models had score development reported only, 19 (65·5%) had undergone internal validation, and only four (13·8%) had been externally validated. Data to validate six eligible models were collected in the international external validation cohort study. Data from 11 591 patients were available, with an overall postoperative pulmonary complication rate of 7·8% (n=903). None of the six models showed good discrimination (defined as AUROCC ≥0·70) for identifying postoperative pulmonary complications, with the Assess Respiratory Risk in Surgical Patients in Catalonia score showing the best discrimination (AUROCC 0·700 [95% CI 0·683-0·717]).

INTERPRETATION

In the pre-COVID-19 pandemic data, variability in the risk of pulmonary complications (StEP-COMPAC definition) following major abdominal surgery was poorly described by existing prognostication tools. To improve surgical safety during the COVID-19 pandemic recovery and beyond, novel risk stratification tools are required.

FUNDING

British Journal of Surgery Society.

Longitudinal Association between Sarcopenia and Cognitive Impairment among Older Adults in Rural Malaysia

Sarcopenia is a condition that is highly prevalent among older adults. This condition is linked to numerous adverse health outcomes, including cognitive impairment that impairs healthy ageing. While sarcopenia and cognitive impairment may share a common pathway, limited longitudinal studies exist to show the relationship between these two conditions. Therefore, this study aimed to examine the longitudinal association between sarcopenia and cognitive impairment. This is a cohort study among older adults residing in Kuala Pilah District, Negeri Sembilan, Malaysia. There were 2404 respondents at the baseline and 1946 respondents at one-year follow-up. Cognitive impairment was determined using Mini-mental State Examination scores. Sarcopenia was identified using the Asian Working Group for Sarcopenia 2019 criteria, gait speed was measured using a 4-meter gait test, handgrip strength was assessed using Jamar handheld dynamometer, and appendicular skeletal muscle mass was measured using bioelectrical impedance analysis. Generalized estimating equation (GEE) was used to determine the longitudinal association between sarcopenia and cognitive impairment, presented as relative risk (RR) and its 95% confidence interval. The prevalence of sarcopenia was 5.0% (95% CI 4.00–5.90), and severe sarcopenia was 3.60% (95% CI 2.84–4.31). Upon adjusting for covariates, older adults with sarcopenia have an 80 per cent increased risk of cognitive impairment compared to those without (RR 1.80; 95% CI 1.18–2.75). Similarly, severe sarcopenia was found to significantly increase the risk of cognitive impairment by 101 per cent in the adjusted model (RR 2.01; 95% CI 1.24–3.27). Our study showed that sarcopenia, severe sarcopenia, low physical activity, depressive symptoms, hearing impairment and chronic pain were associated with a higher risk of cognitive impairment among community-dwelling older adults. Therefore, early intervention to prevent sarcopenia, depressive symptoms, hearing impairment, chronic pain, and higher physical activity among older adults is recommended.

Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation

Vaginal microbiota composition affects many facets of reproductive health. Lactobacillus iners-dominated microbial communities are associated with poorer outcomes, including higher risk of bacterial vaginosis (BV), compared with vaginal microbiota rich in L. crispatus. Unfortunately, standard-of-care metronidazole therapy for BV typically results in dominance of L. iners, probably contributing to post-treatment relapse. Here we generate an L. iners isolate collection comprising 34 previously unreported isolates from 14 South African women with and without BV and 4 previously unreported isolates from 3 US women. We also report an associated genome catalogue comprising 1,218 vaginal Lactobacillus isolate genomes and metagenome-assembled genomes from >300 women across 4 continents. We show that, unlike L. crispatus, L. iners growth is dependent on L-cysteine in vitro and we trace this phenotype to the absence of canonical cysteine biosynthesis pathways and a restricted repertoire of cysteine-related transport mechanisms. We further show that cysteine concentrations in cervicovaginal lavage samples correlate with Lactobacillus abundance in vivo and that cystine uptake inhibitors selectively inhibit L. iners growth in vitro. Combining an inhibitor with metronidazole promotes L. crispatus dominance of defined BV-like communities in vitro by suppressing L. iners growth. Our findings enable a better understanding of L. iners biology and suggest candidate treatments to modulate the vaginal microbiota to improve reproductive health for women globally.

Antigen Presenting Cells Contribute to Persistent Immune Activation Despite Antiretroviral Therapy Initiation During Hyperacute HIV-1 Infection

Human immunodeficiency virus (HIV)-induced changes in immune cells during the acute phase of infection can cause irreversible immunological damage and predict the rate of disease progression. Antiretroviral therapy (ART) remains the most effective strategy for successful immune restoration in immunocompromised people living with HIV and the earlier ART is initiated after infection, the better the long-term clinical outcomes. Here we explored the effect of ART on peripheral antigen presenting cell (APC) phenotype and function in women with HIV-1 subtype C infection who initiated ART in the hyperacute phase (before peak viremia) or during chronic infection. Peripheral blood mononuclear cells obtained longitudinally from study participants were used for immunophenotyping and functional analysis of monocytes and dendritic cells (DCs) using multiparametric flow cytometry and matched plasma was used for measurement of inflammatory markers IL-6 and soluble CD14 (sCD14) by enzyme-linked immunosorbent assay. HIV infection was associated with expansion of monocyte and plasmacytoid DC (pDC) frequencies and perturbation of monocyte subsets compared to uninfected persons despite antiretroviral treatment during hyperacute infection. Expression of activation marker CD69 on monocytes and pDCs in early treated HIV was similar to uninfected individuals. However, despite early ART, HIV infection was associated with elevation of plasma IL-6 and sCD14 levels which correlated with monocyte activation. Furthermore, HIV infection with or without early ART was associated with downmodulation of the co-stimulatory molecule CD86. Notably, early ART was associated with preserved toll-like receptor (TLR)-induced IFN-α responses of pDCs. Overall, this data provides evidence of the beneficial impact of ART initiated in hyperacute infection in preservation of APC functional cytokine production activity; but also highlights persistent inflammation facilitated by monocyte activation even after prolonged viral suppression and suggests the need for therapeutic interventions that target residual immune activation.

Antigen Presenting Cells Link the Female Genital Tract Microbiome to Mucosal Inflammation, With Hormonal Contraception as an Additional Modulator of Inflammatory Signatures

The microbiome of the female genital tract (FGT) is closely linked to reproductive health outcomes. Diverse, anaerobe-dominated communities with low Lactobacillus abundance are associated with a number of adverse reproductive outcomes, such as preterm birth, cervical dysplasia, and sexually transmitted infections (STIs), including HIV. Vaginal dysbiosis is associated with local mucosal inflammation, which likely serves as a biological mediator of poor reproductive outcomes. Yet the precise mechanisms of this FGT inflammation remain unclear. Studies in humans have been complicated by confounding demographic, behavioral, and clinical variables. Specifically, hormonal contraception is associated both with changes in the vaginal microbiome and with mucosal inflammation. In this study, we examined the transcriptional landscape of cervical cell populations in a cohort of South African women with differing vaginal microbial community types. We also investigate effects of reproductive hormones on the transcriptional profiles of cervical cells, focusing on the contraceptive depot medroxyprogesterone acetate (DMPA), the most common form of contraception in sub-Saharan Africa. We found that antigen presenting cells (APCs) are key mediators of microbiome associated FGT inflammation. We also found that DMPA is associated with significant transcriptional changes across multiple cell lineages, with some shared and some distinct pathways compared to the inflammatory signature seen with dysbiosis. These results highlight the importance of an integrated, systems-level approach to understanding host-microbe interactions, with an appreciation for important variables, such as reproductive hormones, in the complex system of the FGT mucosa.

Antibacterial and Antifouling Properties of the Horseshoe Crab Carcinoscorpius rotundicauda

<b>Background and Objective:</b> Horseshoe crabs are widely used in both traditional and modern pharmaceutical applications. Most of the previous studies on horseshoe crabs focused on their blood which contains hemolymph and amoebocyte lysate. This study aimed to determine the potential antibacterial and antifouling properties of different extracts from the carapace and the book gills of <i>Carcinoscorpius rotundicauda</i>. <b>Materials and Methods:</b> The crude extracts were subjected to the bioactivity tests using the disc-diffusion and the inhibition of biofilm-formation measurement assays, for both the antibacterial and antifouling activities respectively. <b>Results:</b> The results obtained indicated that the carapace extracts had stronger antibacterial and antifouling effects compared to the book gills extracts. Extracts obtained from the male displayed more activity compared to the extracts from the female with a few exceptions. Methanol and acetone carapace crude extracts showed the best overall performance. A sterol compound was isolated from the carapace acetone extracts of the male of <i>C. rotundicauda</i>. However, the compound did not display strong activity compared to the crude extract. The compound might be contributing to the observed activity with other components through a synergistic effect. <b>Conclusion:</b> The presence of antibacterial and antifouling activities in the carapace and book gills extracts could be added to the complexity of the defence mechanisms of horseshoe crabs. The results of this study, therefore, may contribute to the knowledge of the defence mechanisms of <i>C. rotundicauda</i>. Further research is needed to determine the bioactivities of other parts of the animal and to explore their potential applications.

Modeling the temporal dynamics of cervicovaginal microbiota identifies targets that may promote reproductive health

BACKGROUND

Cervicovaginal bacterial communities composed of diverse anaerobes with low Lactobacillus abundance are associated with poor reproductive outcomes such as preterm birth, infertility, cervicitis, and risk of sexually transmitted infections (STIs), including human immunodeficiency virus (HIV). Women in sub-Saharan Africa have a higher prevalence of these high-risk bacterial communities when compared to Western populations. However, the transition of cervicovaginal communities between high- and low-risk community states over time is not well described in African populations.

RESULTS

We profiled the bacterial composition of 316 cervicovaginal swabs collected at 3-month intervals from 88 healthy young Black South African women with a median follow-up of 9 months per participant and developed a Markov-based model of transition dynamics that accurately predicted bacterial composition within a broader cross-sectional cohort. We found that Lactobacillus iners-dominant, but not Lactobacillus crispatus-dominant, communities have a high probability of transitioning to high-risk states. Simulating clinical interventions by manipulating the underlying transition probabilities, our model predicts that the population prevalence of low-risk microbial communities could most effectively be increased by manipulating the movement between L. iners- and L. crispatus-dominant communities.

CONCLUSIONS

The Markov model we present here indicates that L. iners-dominant communities have a high probability of transitioning to higher-risk states. We additionally identify transitions to target to increase the prevalence of L. crispatus-dominant communities. These findings may help guide future intervention strategies targeted at reducing bacteria-associated adverse reproductive outcomes among women living in sub-Saharan Africa. Video Abstract.

Anti-salmonellosis agent for foodborne illness from Mangifera odorata (kuini) extracts

Salmonellosis infection caused by Salmonella bacteria is a public endemic problem in Malaysia with long-term morbidity and mortality effects. Thus, this study aimed to explore the antipathogenic activity of natural extracts from Mangifera odorata against two Salmonella species causing Salmonellosis. The extracts were derived from peel, flesh, and kernel seed of M. odorata. The inhibition performance of the extracts against both Salmonella enterica serovar Typhimurium and Salmonella enterica serovar Enteritidis bacteria were subsequently tested by using a bioassay-guided fractionation method. Results showed that the extracts derived from the kernel seed had the highest inhibition percentage of 83-90% against the Salmonellosis infection, followed by the peel with an inhibition of 61-67%, and lastly the flesh with an inhibition of 53-69%. The inhibition activities of hexane extracted flesh (FCH), methanol extracted peel (PCM), and methanol treated kernel seed (KTM) against S. enterica ser. Typhimurium bacteria were 59, 67 and 83%, respectively. Furthermore, the S. enterica ser. Enteritidis bacteria were found to be highly susceptible against the methanol extracted kernel seed (KCM), followed by the hexane extracted peel (PCH) and flesh (FTH) with the inhibition percentage of 90, 69 and 59%, respectively. The highly active anti-Salmonellosis performance of M. odorata extracts was attributed to its intrinsically high total phenolics content at 8-10 g GAE/g extract, high ferric reducing antioxidant power value (FRAP) at 18-22 g Fe2+/g extract and excellent scavenging activity with the inhibition performance ranges between 86% and 90%. This study revealed the antipathogenic activity of methanol extracts of M. odorata kernel seed inhibited the growth of both S. enterica ser. Typhimurium and S. enterica ser. Enteritidis bacteria. This study also discovered the prophylactic property of natural compounds in M. odorata kernel seed extracts and could be used as an anti-Salmonellosis agent. In the near future, M. odorata can be developed as an innovative functional food source for specific groups that are vulnerable to Salmonellosis

Early initiation of antiretroviral therapy following in utero HIV infection is associated with low viral reservoirs but other factors determine subsequent plasma viral rebound

Background

Early HIV diagnosis allows combination antiretroviral therapy (cART) initiation in the first days of life following in utero (IU) infection. The impact of early cART initiation on infant viral reservoir size in the setting of high-frequency cART nonadherence is unknown.

Methods

Peripheral blood total HIV DNA from 164 early treated (day 0–21 of life) IU HIV-infected South African infants was measured using droplet digital PCR at birth and following suppressive cART. We evaluated the impact of cART initiation timing on HIV reservoir size and decay, and on the risk of subsequent plasma viremia in cART-suppressed infants.

Results

Baseline HIV DNA (median 2.8 log₁₀ copies/million peripheral blood mononuclear cells, range 0.7–4.8) did not correlate with age at cART initiation (0–21 days) but instead with maternal antenatal cART use. In 98 infants with plasma viral suppression on cART, HIV DNA half-life was 28 days. However, the probability of maintenance of plasma aviremia was low (0.46 at 12 months) and not influenced by HIV DNA load. Unexpectedly, longer time to viral suppression was associated with protection against subsequent viral rebound.

Conclusions

With effective prophylaxis against mother-to-child transmission, cART initiation timing in the first 3 weeks of life is not critical to reservoir size.

Implementing novel regimens for drug-resistant TB in South Africa: what can the world learn?

Worldwide uptake of new drugs in the treatment of rifampicin-resistant tuberculosis (RR-TB) has been extremely low. In June 2018, ahead of the release of the updated WHO guidelines for the management of RR-TB, South Africa announced that bedaquiline (BDQ) would be provided to virtually all RR-TB patients on shorter or longer regimens. South Africa has been the global leader in accessing BDQ for patients with RR-TB, who now represent 60% of the global BDQ cohort. The use of BDQ within a shorter modified regimen has generated the programmatic data underpinning the most recent change in WHO guidelines endorsing a shorter, injectable-free regimen. Progressive policies on access to new drugs have resulted in improved favourable outcomes and a reduction in mortality among RR-TB patients in South Africa. This supported global policy change. The strategies underpinning these bold actions include close collaboration between the South African National TB Programme and partners, introduction of new TB diagnostic tools in closely monitored conditions and the use of locally generated programmatic evidence to inform country policy changes. In this paper, we summarise a decade´s work that led to the bold decision to use a modified, short, injectable-free regimen with BDQ and linezolid under carefully monitored programmatic conditions.

Gene-environment interaction in chronic kidney disease among people with type 2 diabetes from The Malaysian Cohort project: a case-control study

AIM

To examine the possible gene-environment interactions between 32 single nucleotide polymorphisms and environmental factors that could modify the probability of chronic kidney disease.

METHODS

A case-control study was conducted involving 600 people with type 2 diabetes (300 chronic kidney disease cases, 300 controls) who participated in The Malaysian Cohort project. Retrospective subanalysis was performed on the chronic kidney disease cases to assess chronic kidney disease progression from the recruitment phase. We genotyped 32 single nucleotide polymorphisms using mass spectrometry. The probability of chronic kidney disease and predicted rate of newly detected chronic kidney disease progression were estimated from the significant gene-environment interaction analyses.

RESULTS

Four single nucleotide polymorphisms (eNOS rs2070744, PPARGC1A rs8192678, KCNQ1 rs2237895 and KCNQ1 rs2283228) and five environmental factors (age, sex, smoking, waist circumference and HDL) were significantly associated with chronic kidney disease. Gene-environment interaction analyses revealed significant probabilities of chronic kidney disease for sex (PPARGC1A rs8192678), smoking (eNOS rs2070744, PPARGC1A rs8192678 and KCNQ1 rs2237895), waist circumference (eNOS rs2070744, PPARGC1A rs8192678, KCNQ1 rs2237895 and KCNQ1 rs2283228) and HDL (eNOS rs2070744 and PPARGC1A rs8192678). Subanalysis indicated that the rate of newly detected chronic kidney disease progression was 133 cases per 1000 person-years (95% CI: 115, 153), with a mean follow-up period of 4.78 (SD 0.73) years. There was a significant predicted rate of newly detected chronic kidney disease progression in gene-environment interactions between KCNQ1 rs2283228 and two environmental factors (sex and BMI).

CONCLUSIONS

Our findings suggest that the gene-environment interactions of eNOS rs2070744, PPARGC1A rs8192678, KCNQ1 rs2237895 and KCNQ1 rs2283228 with specific environmental factors could modify the probability for chronic kidney disease.

The developed Arabic version of the Hearing Handicap Inventory for the Elderly

Background

Hearing impairment ranks third on the list of chronic health conditions of the elderly, after arthritis and hypertension. As average lifespans increase, it is likely that the proportion of people with hearing loss will also increase. The purpose of the study was to develop, standardize, and apply an Arabic version of the Hearing Handicap Inventory for the Elderly (HHIE).

Results

The mean age of the 100 subjects included in the pretest was 64.92 ± 5.937 with age ranged from 60 to 84 years. The average score for each item (simple, clear, and relevant) for each separate question obtained more than 80% which is considered valid. One hundred percent of the participants reported that the entire inventory appeared simple, clear, and relevant, we further implied the jury opinion; the total score average of our jury for the entire inventory was calculated to determine the face validity of the questionnaire and found to be 89.81%. Responses of all participants for each question were collected and showed questions 8, 21, 6, 7, and 14 obtained the highest response results for both yes and sometimes. The HHIE showed high reliability (p value < 0.001) for all questions. The demographic data of the forty participants showed no statistically significant difference between the complaining group of hearing loss and the non-complaining group as regards age and gender. There was a highly statistically significant difference between the complaining group and the non-complaining group regarding the HHIE. The sensitivity of the HHIE was 79% for severe auditory handicapping and only 24% for mild-to-moderate auditory handicapping.

Conclusion

The developed Arabic version of the HHIE has high reliability, validity, simplicity, and clarity which found consistent with the original English questionnaire and it performed well in the detection of hearing loss in elderly Egyptians. It can be applied in a large population and for use in surveys.

Industrial enzymes-producing marine bacteria from marine resources

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Lipase is the most dominant industrial enzyme produced by cultivated marine bacteria.

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Genetic variation determines the yield of enzyme production.

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Proteobacteria (Vibrio spp.) is the main producer of industrial enzymes.

Industrial enzymes are important for various biotechnological applications. Currently, the diversity of industrial enzymes-producing marine bacteria from Malaysia remains mostly unknown. This study investigated the diversity of industrial enzyme-producing marine bacteria from culture collections at the Institute of Marine Biotechnology, Universiti Malaysia Terengganu. Out of 200 bacterial isolates revived, 163 bacteria isolate were successfully growth. Marine bacteria produced enzymes with total scoring higher than four were selected for molecular identification using 16S rDNA. About 161 bacteria isolate secreted amylase (68.7 %), lipase (88.3 %) and protease (68.7 %). The phylogenetic analysis led to the identification of three major phyla, namely Proteobacteria, Firmicutes and Bacteroidetes. These phyla were differentiated into nine genera consisted of Bacillus, Chryseomicrobium, Photobacterium, Pseudoalteromonas, Ruegeria, Shewanella, Solibacillus, Tenacibaculum and Vibrio. Genetic variation was more likely to occur within similar marine bacteria species. The microbial community was found to affect the production of industrial enzymes and the diversity of marine bacteria.

HIGH-FREQUENCY failure of combination antiretroviral therapy in paediatric HIV infection is associated with unmet maternal needs causing maternal NON-ADHERENCE

BACKGROUND

Early combination antiretroviral therapy (cART) reduces the size of the viral reservoir in paediatric and adult HIV infection. Very early-treated children may have higher cure/remission potential.

METHODS

In an observational study of 151 in utero (IU)-infected infants in KwaZulu-Natal, South Africa, whose treatment adhered strictly to national guidelines, 76 infants diagnosed via point-of-care (PoC) testing initiated cART at a median of 26 h (IQR 18-38) and 75 infants diagnosed via standard-of-care (SoC) laboratory-based testing initiated cART at 10 days (IQR 8-13). We analysed mortality, time to suppression of viraemia, and maintenance of aviraemia over the first 2 years of life.

FINDINGS

Baseline plasma viral loads were low (median 8000 copies per mL), with 12% of infants having undetectable viraemia pre-cART initiation. However, barely one-third (37%) of children achieved suppression of viraemia by 6 months that was maintained to >12 months. 24% had died or were lost to follow up by 6 months. Infant mortality was 9.3%. The high-frequency virological failure in IU-infected infants was associated not with transmitted or acquired drug-resistant mutations but with cART non-adherence (plasma cART undetectable/subtherapeutic, p<0.0001) and with concurrent maternal cART failure (OR 15.0, 95%CI 5.6-39.6; p<0.0001). High-frequency virological failure was observed in PoC- and SoC-tested groups of children.

INTERPRETATION

The success of early infant testing and cART initiation strategies is severely limited by subsequent cART non-adherence in HIV-infected children. Although there are practical challenges to administering paediatric cART formulations, these are overcome by mothers who themselves are cART-adherent. These findings point to the ongoing obligation to address the unmet needs of the mothers. Eliminating the particular barriers preventing adequate treatment for these vulnerable women and infants need to be prioritised in order to achieve durable suppression of viraemia on cART, let alone HIV cure/remission, in HIV-infected children.

FUNDING

Wellcome Trust, National Institutes of Health.

Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection

Cellular immunity is critical for controlling intracellular pathogens, but individual cellular dynamics and cell-cell cooperativity in evolving human immune responses remain poorly understood. Single-cell RNA-sequencing (scRNA-seq) represents a powerful tool for dissecting complex multicellular behaviors in health and disease1,2 and nominating testable therapeutic targets3. Its application to longitudinal samples could afford an opportunity to uncover cellular factors associated with the evolution of disease progression without potentially confounding inter-individual variability4. Here, we present an experimental and computational methodology that uses scRNA-seq to characterize dynamic cellular programs and their molecular drivers, and apply it to HIV infection. By performing scRNA-seq on peripheral blood mononuclear cells from four untreated individuals before and longitudinally during acute infection5, we were powered within each to discover gene response modules that vary by time and cell subset. Beyond previously unappreciated individual- and cell-type-specific interferon-stimulated gene upregulation, we describe temporally aligned gene expression responses obscured in bulk analyses, including those involved in proinflammatory T cell differentiation, prolonged monocyte major histocompatibility complex II upregulation and persistent natural killer (NK) cell cytolytic killing. We further identify response features arising in the first weeks of infection, for example proliferating natural killer cells, which potentially may associate with future viral control. Overall, our approach provides a unified framework for characterizing multiple dynamic cellular responses and their coordination.

Association between the cytokine storm, immune cell dynamics, and viral replicative capacity in hyperacute HIV infection

INTRODUCTION

Immunological damage in acute HIV infection (AHI) may predispose to detrimental clinical sequela. However, studies on the earliest HIV-induced immunological changes are limited, particularly in sub-Saharan Africa. We assessed the plasma cytokines kinetics, and their associations with virological and immunological parameters, in a well-characterized AHI cohort where participants were diagnosed before peak viremia.

METHODS

Blood cytokine levels were measured using Luminex and ELISA assays pre-infection, during the hyperacute infection phase (before or at peak viremia, 1-11 days after the first detection of viremia), after peak viremia (24-32 days), and during the early chronic phase (77-263 days). Gag-protease-driven replicative capacities of the transmitted/founder viruses were determined using a green fluorescent reporter T cell assay. Complete blood counts were determined before and immediately following AHI detection before ART initiation.

RESULTS

Untreated AHI was associated with a cytokine storm of 12 out of the 33 cytokines analyzed. Initiation of ART during Fiebig stages I-II abrogated the cytokine storm. In untreated AHI, virus replicative capacity correlated positively with IP-10 (rho = 0.84, P < 0.001) and IFN-alpha (rho = 0.59, P = 0.045) and inversely with nadir CD4⁺ T cell counts (rho = - 0.58, P = 0.048). Hyperacute HIV infection before the initiation of ART was associated with a transient increase in monocytes (P < 0.001), decreased lymphocytes (P = 0.011) and eosinophils (P = 0.003) at Fiebig stages I-II, and decreased eosinophils (P < 0.001) and basophils (P = 0.007) at Fiebig stages III-V. Levels of CXCL13 during the untreated hyperacute phase correlated inversely with blood eosinophils (rho = - 0.89, P < 0.001), basophils (rho = - 0.87, P = 0.001) and lymphocytes (rho = - 0.81, P = 0.005), suggesting their trafficking into tissues. In early treated individuals, time to viral load suppression correlated positively with plasma CXCL13 at the early chronic phase (rho = 0.83, P = 0.042).

CONCLUSION

While commencement of ART during Fiebig stages I-II of AHI abrogated the HIV-induced cytokine storm, significant depletions of eosinophils, basophils, and lymphocytes, as well as transient expansions of monocytes, were still observed in these individuals in the hyperacute phase before the initiation of ART, suggesting that even ART initiated during the onset of viremia does not abrogate all HIV-induced immune changes.

Extensively drug-resistant tuberculosis 'hotspots' and sociodemographic associations in Durban, South Africa

<sec> <title>BACKGROUND</title> In KwaZulu-Natal, South Africa, the incidence of extensively drug-resistant tuberculosis (XDR-TB) is driven by the transmission of resistant strains. As data suggest that cases may be spatially clustered, we sought to identify 'hotspots' and describe these communities. </sec> <sec> <title>METHODS</title> We enrolled XDR-TB patients diagnosed from 2011 to 2014 in eThekwini. Global positioning system (GPS) coordinates for participant homes were collected and hotspots were identified based on population-adjusted XDR-TB incidence. The sociodemographic features of hotspots were characterised using census data. For a subset of participants, we mapped non-home XDR-TB congregate locations and compared these with results including only homes. </sec> <sec> <title>RESULTS</title> Among 132 participants, 75 (57%) were female and 87 (66%) lived in urban or suburban locations. Fifteen of 197 census tracts were identified as XDR-TB hotspots with ≥95% confidence. Four spatial mapping methods identified one large hotspot in northeastern eThekwini. Hotspot communities had higher proportions of low educational attainment (12% vs. 9%) and unemployment (29.3% vs. 20.4%), and lower proportion of homes with flush toilets (36.4% vs. 68.9%). The case density shifted towards downtown Durban when congregate locations (e.g., workplaces) for 43 (33%) participants were mapped. </sec> <sec> <title>CONCLUSIONS</title> In eThekwini, XDR-TB case homes were clustered into hotspots with more poverty indicators than non-hotspots. Prevention efforts targeting hotspot communities and congregate settings may be effective in reducing community transmission. </sec>.

Chemical and antibacterial data of synthesized thioureido derivatives

This paper provided comprehensive data on spectroscopic and antibacterial activities of thioureido compounds which are relevant with research article entitled “Synthesis, Spectroscopic Studies and Antibacterial Activity of New Lauroyl Thiourea Amino Acid Derivatives” [1]. Based on the reported study, four new thioureido derivatives, namely 3-(3-dodecanoyl-thioureido)propionic acid (R1), 2-(3-dodecanoyl-thioureido)-3-methyl butyric acid (R2), (3-dodecanoyl-thioureido)acetic acid (R3) and 2-(3-dodecanoyl-thioureido)-3-phenyl propionic acid (R4) were characterized by elemental analysis, Fourier Transform Infrared (FTIR), ¹H Nuclear Magnetic Resonance (¹H NMR) and ¹³C Nuclear Magnetic Resonance (¹³C NMR), and Ultraviolet Visible spectroscopy (UV-Vis). The preliminary results from antibacterial assay which were tested against Gram-positive bacteria such as Bacillus subtilis, Staphylococcus epidermidis, Staphylococcus aureus and Gram-negative bacteria such as Escherichia coli, Salmonella typhimurium are also described.

Impact of austerity on prison health in England: a qualitative study involving national policymakers

Prisons offer states access to a population that is at high risk of morbidity. The UK austerity policy adopted in 2010 led to a 22% reduction (-£2.71bn) in prison spending by 2017. Whilst the number of prison officers dropped by 30%, the long-term impact of austerity on prison health in England has not been systematically contextualised. This research seeks to articulate the impact of austerity on prison health in England from the perspective of national policymakers.

Semi-structured interviews (X: 66 min) were conducted with 30 key prison policymakers. Constructivist grounded theory was used to assess the impact of austerity on prisoner health in England. Transcripts of 195,680 narrative texts were analysed using NVivo 11 until data saturation was achieved.

As a stealthy political ideology, austerity has caused societal disruption, which disproportionately affects prisons. The lack of access to services offered by the welfare state, including health-related provisions, precipitates societal unrest, increases prisoner numbers, and encourages harsher and longer sentences.

The prolonged constrained funding and the burgeoning population widen health inequalities in prisons. Healthcare provisions become increasingly limited, which unduly affects older and female prisoners who require more complex support. The degrading living conditions and lack of purposeful activities contribute to the increasing violence, self-harm and suicides in prisons, and reorient the healthcare provision from planned services to health emergencies. The excessive focus on Brexit and the perpetual changing political direction imposed on prisons reinforce the system’s instability.

Despite having the fifth largest economy in the world, England’s poorest population continues to bear the brunt of austerity. Initiating a more informed economic recovery policy and considering alternatives to imprisonment would help to ensure that England lives up to its view of itself as a progressive society.

Prevalence and characteristics of e-cigarette users among Malaysian current and ex-smokers

INTRODUCTION

Electronic cigarettes (ECs) are new devices that have been accepted widely by both smokers and non-smokers. However, the evidence on EC used in Malaysia is scarce. The objective of this study was to determine the prevalence of EC use and the socio-demographic and smoking characteristics associated with current EC use among Malaysian current and ex-smokers.

METHODS

This was a sub-analysis of data from a cross-sectional, national-population- based EC study conducted from May to June in 2016 in Malaysia. A detailed description of the sampling methods can be found in the National E-cigarette Survey (NECS) 2016 report. Briefly, data were obtained from 1396 individuals who had ever been smokers, i.e., 957 (68.6%) current smokers and 439 (31.4%) ex-smokers.

RESULTS

Current EC use was found predominantly among current smokers (8.0%) as compared with ex-smokers (4.3%). Among current smokers, the main reasons given for smoking ECs were wanting to try it (44.7%), followed by intention to quit tobacco smoking (15.8%) and to reduce tobacco smoking (10.5%). Using multiple logistic regression analysis, we found that among current smokers, current EC users were more likely to be younger, i.e., 18-44 years (aOR= 4.83, 95% CI= 1.97-11.86, p=0.001), urban residents (aOR= 1.89, 95% CI= 1.15-3.11, p=0.012), single/ divorced/ widowed (aOR= 2.11, 95% CI= 1.24-3.61, p=0.006) and students (aOR= 2.25, 95% CI= 1.01-5.01, p=0.048). Among exsmokers, only younger respondents (18-44 years old) was reported as being more likely to be current EC users (aOR= 3.81, 95% CI= 1.14-12.76, p=0.030).

CONCLUSION

This study showed that currently using and ever having used ECs were more prevalent among current smokers. The reasons given for initiating EC use among current smokers were mainly wanting to try it, followed by intention to quit and to reduce tobacco smoking. Current EC use appears to be common among current smokers who are younger, urban residents, single/divorced/widowed and students. Therefore, EC cessation intervention strategies and policies should target these high-prevalence groups.

Development and validation of TaqMan real-time PCR for the detection of Burkholderia pseudomallei isolates from Malaysia

Rapid detection of Burkholderia pseudomallei, the etiologic agent of melioidosis, allows for timely initiation of appropriate treatment and better clinical outcomes. In the current gold standard, the culture method is time consuming and suffers from low sensitivity. Meanwhile, previously reported molecular assays are fast and sensitive, but their performance on isolates from Malaysia, an endemic region of melioidosis is under reported. This study designed oligonucleotides targeting orf2 of Type III secretion system (TTSS) genes cluster for the detection of Malaysian B. pseudomallei isolates and evaluated the assay on 95 local B. pseudomallei strains, 58 other microorganisms and 71 clinical specimens from patients. The developed assay exclusively detected all tested B. pseudomallei isolates with a detection limit of 20 fg per reaction (equivalent to ~2.5 copies). Subsequent testing on clinical samples showed that the assay detected all confirmed specimens with the growth of B. pseudomallei (n = 10/10). None of the negative specimens had a detectable signal of our TTSS-orf2 assay (n = 0/61). In conclusion, the present study provides crucial preliminary data for a subsequent study and should be considered as a potential alternative to current time-consuming culture method for the detection of B. pseudomallei.

Broad-spectrum Antimicrobial Activity of Purified Hemocyanin Subunit IIIA Isolated from Asian Horseshoe Crab, Tachypleus gigas

BACKGROUND AND OBJECTIVES

Hemocyanin Subunit IIIA is believed to possess antimicrobial properties, but its efficacy against microbial pathogens is still unclarified. Thus, this study aimed to determine antimicrobial activities of hemocyanin subunit IIIA and to identify the best activator of this protein.

MATERIALS AND METHODS

The hemocyanin was partially purified using spin column affinity, its fraction was applied to Hi-Prep Sephacryl Exclusion 26/60 2-200 HR column, followed by Hi-Prep 26/10 Desalting Column on fast protein liquid chromatography. The purity of hemocyanin was validated by Matrix Assisted Laser Desorption Ionization-Time of Flight/Mass Spectrometry. The antimicrobial activity was performed by Disc Diffusion Test.

RESULTS

Purified hemocyanin subunit IIIA was identified to have a molecular weight of 72.9 kDa. SDS was found to be the best activator of hemocyanin, as indicated by elevated level of phenoloxidase. As for antimicrobial activity, hemocyanin was minimally inhibited by all bacteria strains tested (Escherichia coli, Staphylococcus aureus and Klebsiella pneumoniae), with relatively lower Minimum Inhibitory Concentration (MIC) at 0.005 g mL-1, than recorded MIC for fungal test strains. Two fungal strains (Penicillium sp. and A. niger) show susceptible response to phenoloxidase using MgSO4 as inducer. Whereas, lysate-treated CaCl2 induced susceptibility only to A. niger.

CONCLUSION

Hemocyanin shows better antimicrobial activity than phenoloxidase because of its broad-spectrum activity against bacterial and fungal strains tested. Hence, the hemocyanin may potentially become a new antimicrobial candidate to be discovered for a future use in treatment of resistant bacteria.

Dual HLA B*42 and B*81-reactive T cell receptors recognize more diverse HIV-1 Gag escape variants

Some closely related human leukocyte antigen (HLA) alleles are associated with variable clinical outcomes following HIV-1 infection despite presenting the same viral epitopes. Mechanisms underlying these differences remain unclear but may be due to intrinsic characteristics of the HLA alleles or responding T cell repertoires. Here we examine CD8⁺ T cell responses against the immunodominant HIV-1 Gag epitope TL9 (TPQDLNTML_180–188) in the context of the protective allele B*81:01 and the less protective allele B*42:01. We observe a population of dual-reactive T cells that recognize TL9 presented by both B*81:01 and B*42:01 in individuals lacking one allele. The presence of dual-reactive T cells is associated with lower plasma viremia, suggesting a clinical benefit. In B*42:01 expressing individuals, the dual-reactive phenotype defines public T cell receptor (TCR) clones that recognize a wider range of TL9 escape variants, consistent with enhanced control of viral infection through containment of HIV-1 sequence adaptation.

Closely related HLA alleles presenting similar HIV-1 epitopes can be associated with variable clinical outcome. Here the authors report their findings on CD8+ T cell responses to the HIV-1 Gag-p24 TL9 immunodominant epitope in the context of closely related protective and less protective HLA alleles, and their differential effect on viral control

Should we use a direct regulation to implement the Healthy Prisons Agenda in England? A qualitative study among prison key policy makers

Background

The Healthy Prisons Agenda seeks to reduce prisoners' health risks, balance prisoners' rights with a security regime, ensure equivalent prison health service provisions to community health services, and facilitate the whole-prison approach. There is an established assumption that legislation will ensure better implementation of health promotion programmes. This study aimed to examine whether a legislative framework, via a direct regulation, could lead to enhanced implementation of the Healthy Prisons Agenda in England.

Methods

A qualitative study design was conducted using semi-structured interviews with 30 key prison policy makers in England.

Findings

Our findings contradict the established assumption that legislation improves the implementation of health promotion programmes. A direct regulation was perceived as restrictive, manifesting excessive compliance and encouraging a risk-averse culture, whilst preoccupation with security, order and discipline amongst prison governors and custody staff was deemed an internal institutional barrier to implementing the Healthy Prisons Agenda. External barriers included diminishing resources, lengthier or delayed sentencing, and an unsympathetic public and political stance towards prisoner rehabilitation.

Conclusions

A direct regulation should not be used to operationalize the Healthy Prisons Agenda. Rather, self-regulation, along with proactive solutions for the identified barriers to implementing the Agenda, is the most appropriate path forward.

In vitro approaches for generation of Mycobacterium tuberculosis mutants resistant to bedaquiline, clofazimine or linezolid and identification of associated genetic variants

Bedaquiline, clofazimine and linezolid are pertinent drugs for drug-resistant tuberculosis. Drug-resistant mutants provide insight into important resistance acquisition mechanisms. Methods for in vitro Mycobacterium tuberculosis mutant generation are poorly described. Induction (serial passaging) and spontaneous (adapted Luria-Delbrück assay) approaches using M. tuberculosis ATCC reference strains (one fully-susceptible, four unique mono-resistant) were performed. Mutant MIC values were confirmed (MGIT960) and resultant RAVs compared between approaches and to a catalog of previously published RAVs. Mutant MIC values showed a 3-4-fold (induced) and a 1-4-fold (spontaneous) increase compared to baseline. The pyrazinamide-resistant strain had higher baseline MIC values and acquired resistance (≥4-fold) in fewer passages than other strains (induction approach) for bedaquiline. Previously described and novel RAVs in atpE (8 vs. 1) and rv0678 (4 vs. 12) genes were identified in bedaquiline- and clofazimine-resistant mutants. No rv1979c and rv2535c RAVs were identified. Previously described RAVs were identified in rplC and rrl genes for linezolid-resistant mutants. Both approaches successfully led to in vitro mutants with novel RAVs being described in atpE and rv0678 genes. It was observed that pre-existing resistance may influence mutant phenotypic and genotypic characteristics and warrants further attention.

Exploring finite-size effects in strongly correlated systems

Complexities greatly limit any study of strongly correlated systems to a small number of particles. Thus, any attempt at understanding infinite systems such as those arising from neutron matter (NM) must consider finite-size (FS) effects at play when below the thermodynamic limit (TL). In these conference proceedings we provide some examples of FS effects at work and discuss our prescription for extrapolating the physics of extended systems. We present our methodology and calculations performed for an assortment of strongly correlated (SC) systems. Ab initio, non-perturbative Quantum Monte Carlo (QMC) methods can be employed to accurately compute ground-state energies and finite-temperature properties. We apply these to periodically modulated NM and use our results to constrain phenomenological theories of nuclei and study the static response of NM.

Challenges for prison governors and staff in implementing the Healthy Prisons Agenda in English prisons

OBJECTIVES

In the two decades that have passed since the World Health Organisation established the Healthy Prisons Agenda, there has been no research conducted to investigate barriers and challenges prison managerial and operational staff encounter in implementing the Agenda in the English prison context. This article debates sectoral, institutional and occupational challenges perceived to hinder effective implementation of the Agenda, based on a qualitative study involving prison governors and operational staff.

STUDY DESIGN

Qualitative study taking a grounded theory approach.

METHODS

Semistructured interviews were conducted with 30 participants comprising prison governors, prison officers and external stakeholders with key strategic and operational roles across the prison estate. The interviews were analysed and coded into themes using constant comparative method.

RESULTS

The research identified a range of managerial and operational factors that impeded recognition, acceptance and successful implementation of the Healthy Prisons Agenda. These were found to be associated with scarcity of resources, low prioritisation, perceived low importance, and pressures at operational, managerial and strategic levels to adhere to standard operating procedures. Security, control and discipline tended to supersede other imperatives considered of secondary importance to the effective running of prisons.

CONCLUSIONS

Sustainability of the Healthy Prisons Agenda can only be assured by raising its significance and importance across prison hierarchies and within policies and practices through which operational and strategic objectives are realised. This means achieving wholesale commitment by prisons-among staff at all levels-towards public health goals that are fundamental to a successful and effective criminal justice system.