Search

The impact of the HIV/AIDS pandemic is mostly felt by adolescents as half of all new HIV/AIDS infections have occurred in people aged 15-24 years. Statistics show that campaigns implemented by the South African government have failed to bring about positive behavioural change among young people. The aim of this study was to determine the HIV/AIDS-related knowledge among students at a college and the association between knowledge, self-efficacy, self-concept in sexual practices. This study was conducted at a Further Education and Training College in Cape Town. Data were collected using self-administered questionnaires consisting of five sections including demographic information; sexual practices; knowledge of HIV/AIDS, levels of self-efficacy; and self-concept. Fifty four percent of the participants indicated no condom use when having sex, either by themselves or by a partner; 43% indicated that they had more than 2 sexual partners in the 12 months prior to the study. The odds that a person with higher HIV/AIDS knowledge will use a condom were 1.047 times greater than someone with less HIV/AIDS knowledge. The odd's ratio for self-efficacy indicates a positive relationship with the number of partners of an individual. The findings of the present study suggest adequate/high HIV/AIDS knowledge among the study sample. The study further highlights that for males, there is a greater likelihood that lower self-efficacy would predict more sexual partners in comparison to females. The results further suggest that although governmental organisations' efforts improved knowledge of HIV/AIDS, programmes avidly promoting self-efficacy for males should be implemented. [ABSTRACT FROM AUTHOR]

Background: We aimed to determine the prevalence and genetic characteristics of extended-spectrum beta-lactamase (ESBL)- and carbapenemase-producing Enterobacteriaceae in stools from healthy infants and their mothers, and to determine the risk factors associated with their carriage. Methods & Materials: This study was nested within the Drakenstein Child Health Study, South Africa. Maternal and infant faecal samples were collected at birth and at two additional time-points from the infants. Samples were screened for ESBLs and carbapenemase-producing organisms using ChromID ESBL and ChromID CARBA media, respectively. Vitek 2 was used for antibiotic susceptibility testing and identification of suspect ESBL/carbapenemase-producing isolates. ESBL production was confirmed using the combination disc test, and carbapenemase production using the modified Hodge test. Selected ESBL and carbapenemase genes were characterized by singleplex polymerase chain reaction and Sanger sequencing. Results: Maternal faecal carriage of ESBL-producing bacteria was 4.4%; 4/90 (95% confidence interval (CI): 1.5%-10.2%), and that of infants at birth was 3.5%; 4/116 (95% CI: 1.2%-8.0%). The infant faecal carriage of ESBL-producing bacteria at 5-12 and 20- 28 weeks was 4.4%; 3/68 (95% CI: 1.3%-11.3%) and 5.7%; 2/35 (95% CI: 1.2%-17.1%), respectively. ESBL genes were detected in six K. pneumoniae (blaCTX-M-15), five E. cloacae (blaSHV-12 and blaSHV-5) and three E. coli (blaCTX-M-14) isolates. No carbapenemaseproducing bacteria were identified in this study. Pulsed-field gel electrophoresis showed heterogeneous clones of CTX-M-15-producing K. pneumoniae isolates. In contrast, in a mother-infant pair, we observed clonal relations among ESBL-producing E. cloacae isolates. In addition, one infant was persistently colonized by SHV- 12-producing E. cloacae. Univariate analysis showed that infants born to HIV-positive mother, via elective caesarean section, and medication use before discharge were positively associated with ESBL faecal carriage. In contrast, breastfeeding prior to discharge was negatively associated with ESBL carriage. Conclusion: This is the first study to detect ESBL-producing bacteria inhumanmeconiumsamples in Africa, and raises questions on the source of such isolates and implications for community transmission. Further research is required to determine the spread of ESBL- and carbapenemase-producing bacteria in community settings in South Africa. [ABSTRACT FROM AUTHOR]

Background: There is concern regarding the increasing resistance of Group A streptococcus (GAS) to routinely used antibiotics. GAS is a common cause of bacterial pharyngitis and more severe invasive infections such as septicaemia. Furthermore, GAS pharyngitis is the antecedent for serious conditions such as rheumatic fever and rheumatic heart disease. The study aimed to determine the antimicrobial susceptibility patterns of GAS cultured from patients with invasive and non-invasive infections from Cape Town, as part of the AFRO Strep Registry., Methods: Samples were provided by the AFRO Strep Registry, a continental endeavour aiming to document Streptococcus pyogenes infection in Africa and create the first biorepository of its kind. Ninety-five GAS isolates (invasive, n = 40; non-invasive, n = 55) were evaluated for resistance to a panel of 20 antibiotics using the Sensititre® STP6F system with MICs interpreted by CLSI break points., Results: Amongst all isolates, highest levels of resistance were observed with respect to tetracycline (8.33 %), followed by azithromycin (1.04 %) and erythromycin (1.04 %). No resistance to the remaining antibiotics was detected amongst all isolates. No differences with regard to MIC values were observed between isolates from invasive and non-invasive infections (p-value >0.05 for all antibiotics)., Conclusion: GAS remains susceptible to routine-antimicrobial agents used in our low-resourced setting. Eight percent of the GAS isolates were resistant to tetracycline, and we did not observe macrolide resistance as reported in high income countries. This is the first study to report on the antimicrobial patterns of GAS in South Africa. These results address a critical gap in the available data on GAS in Africa and specifically South Africa and, thus, aid in avoiding therapeutic failures., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

Introduction: It is currently unclear what the role of Group A streptococcus (GAS) virulence factors (VFs) is in contributing to the invasive potential of GAS. This work investigated the evidence for the association of GAS VFs with invasive disease., Methods: We employed a broad search strategy for studies reporting the presence of GAS VFs in invasive and non-invasive GAS disease. Data were independently extracted by two reviewers, quality assessed, and meta-analyzed using Stata®., Results: A total of 32 studies reported on 45 putative virulence factors [invasive (n = 3,236); non-invasive (n = 5,218)], characterized by polymerase chain reaction (PCR) (n = 30) and whole-genome sequencing (WGS) (n = 2). The risk of bias was rated as low and moderate, in 23 and 9 studies, respectively. Meta-,analyses of high-quality studies (n = 23) revealed a significant association of speM [OR, 1.64 (95%CI, 1.06; 2.52)] with invasive infection. Meta-analysis of WGS studies demonstrated a significant association of hasA [OR, 1.91 (95%CI, 1.36; 2.67)] and speG [OR, 2.83 (95%CI, 1.63; 4.92)] with invasive GAS (iGAS). Meta-analysis of PCR studies indicated a significant association of speA [OR, 1.59 (95%CI, 1.10; 2.30)] and speK [OR, 2.95 (95%CI, 1.81; 4.80)] with invasive infection. A significant inverse association was observed between prtf1 [OR, 0.42 (95%CI, 0.20; 0.87)] and invasive infection., Conclusion: This systematic review and genomic meta-analysis provides evidence of a statistically significant association with invasive infection for the hasA gene, while smeZ , ssa , pnga3 , sda1 , sic , and NaDase show statistically significantly inverse associations with invasive infection. SpeA , speK , and speG are associated with GAS virulence; however, it is unclear if they are markers of invasive infection. This work could possibly aid in developing preventative strategies., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Rampersadh, Salie, Engel, Moodley, Zühlke and Engel.)

Background: The molecular epidemiology of carbapenem-resistant Enterobacterales in Cape Town remains largely unknown., Objectives: This study aimed to describe the molecular epidemiology, resistome, virulome and mobilome of carbapenem-resistant Klebsiella pneumoniae (CRKP) within Cape Town to guide therapy, antimicrobial stewardship and infection prevention and control practices., Methods: Eighty-five CRKP isolates from hospitalized patients underwent WGS as part of a prospective, multicentre, cross-sectional study, conducted between 1 November 2020 and 30 November 2022, across public-sector and private-sector hospitals in Cape Town, South Africa., Results: MLST revealed three novel types, ST6785, ST6786 and ST6787, while the most common were ST219, ST307, ST17, ST13 and ST2497. Different predominant clones were noted in each hospital. The most common carbapenemase gene was bla OXA-48-like , detected in 71% of isolates, with bla NDM detected in 5%. Notably, co-detection of two carbapenemase genes ( bla OXA-48-like and bla NDM ) occurred in 13% of isolates. The yersiniabactin siderophore was detected in 73% of isolates, and was most commonly associated with the ICE Kp 5 mobile element. All carbapenemases were located on plasmids. The genes bla OXA-181 and bla OXA-232 colocalized with a ColKP3 replicon type on assembled contigs in 83% and 100% of cases, respectively., Conclusions: CRKP epidemiology in Cape Town reflects institutionally dominant, rather than regional, clones. The most prevalent carbapenemase gene was bla OXA-48-like , in keeping with CRKP epidemiology in South Africa in general. Emerging clones harbouring both bla OXA-48-like and bla NDM , such as ST17, ST2497 and the novel ST6787, are a concern due to the limited availability of appropriate antimicrobial agents in South Africa., (© The Author(s) 2024. Published by Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy.)

Background: Carbapenem-resistant Enterobacterales (CRE) are a substantial problem in Cape Town. CRE epidemiology is largely unknown and mortality remains high., Objectives: To describe and characterize the clinical and microbiological epidemiology of CRE within Cape Town hospitals to better inform therapy with regard to current and novel antibiotics, as well as improve antimicrobial stewardship (AMS), and infection prevention and control (IPC)., Methods: This prospective, multicentre study performed between 1 November 2020 and 30 November 2022, across three public and three private hospitals included hospitalized participants with CRE from clinical cultures. Participant demographics, clinical information and microbiology results were collected and analysed., Results: Ninety percent of participants were from public hospitals. The age distribution ranged from 7 days to 88 years. Notable risk factors for CRE infection included recent exposure to antibiotics, medical devices and surgery. The most prevalent species was Klebsiella pneumoniae. However, a higher proportion of Serratia marcescens compared with previous reports was identified. The detected carbapenemases were bla OXA-48-like (80%) and bla NDM (11%). With the exception of amikacin (63%), tigecycline (65%), colistin (95%) and ceftazidime/avibactam (87%), susceptibility to antibiotics was low., Conclusions: This study identified common risk factors for CRE infection and generated a description of carbapenemase enzymes, species distribution and antibiograms, enabling a better understanding of CRE epidemiology. This provides insights into transmission patterns and resistance determinants of CREs, beneficial to informing data-driven regional patient management, AMS and IPC strategies., (© The Author(s) 2024. Published by Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy.)

The title compound, C 14 H 12 O 4 , comprises of two crystallographically independent mol-ecules in the asymmetric unit, linked via C-H⋯O inter-actions to form dimeric entities. The allylic groups are twisted out of the phenyl planes with dihedral angles varying between 7.92 (13) and 25.42 (8)°. In the crystal, the packing follows a zigzag pattern along the c -axis direction. The absolute configuration of the sample could not be determined reliably., (© Moodley et al. 2024.)

Computational methods have been established as cornerstones in optical imaging and holography in recent years. Every year, the dependence of optical imaging and holography on computational methods is increasing significantly to the extent that optical methods and components are being completely and efficiently replaced with computational methods at low cost. This roadmap reviews the current scenario in four major areas namely incoherent digital holography, quantitative phase imaging, imaging through scattering layers, and super-resolution imaging. In addition to registering the perspectives of the modern-day architects of the above research areas, the roadmap also reports some of the latest studies on the topic. Computational codes and pseudocodes are presented for computational methods in a plug-and-play fashion for readers to not only read and understand but also practice the latest algorithms with their data. We believe that this roadmap will be a valuable tool for analyzing the current trends in computational methods to predict and prepare the future of computational methods in optical imaging and holography., Supplementary Information: The online version contains supplementary material available at 10.1007/s00340-024-08280-3., Competing Interests: Conflict of interestThe authors declare no competing interests., (© The Author(s) 2024.)

Background: Sexually transmitted infections are among the most commonly occurring infections globally, with countries in sub-Saharan Africa exhibiting disproportionately higher prevalence rates. Numerous reports indicate the need for accurate detection, epidemiological characterisation, and appropriate management of these infections. This prospective observational laboratory study sought to determine the occurrence of STI, using a validated molecular assay as a diagnostic and surveillance tool in our setting., Methods: Urogenital swabs from symptomatic and asymptomatic patients, submitted to the National Health Laboratory Service, at Groote Schuur Hospital, from 04 August 2021-03 February 2022, for routine microbiological investigations, were subjected to the Allplex™ STI Essential Assay (Seegene Inc, South Korea) to determine the distribution of STI pathogens in our setting. This multiplex assay includes C. trachomatis, Mycoplasma genitalium, Mycoplasma hominis, N. gonorrhoeae, Trichomonas vaginalis, Ureaplasma parvum, and Ureaplasma urealyticum. Correlations between detected organisms and participant age and clinical indications for testing were determined using Stata® software., Results: A total of 148 urogenital swabs (91.2% from women) were included in the analysis, of which 56/148 (37.84%) were from symptomatic patients. Up to 83.8% of the samples tested positive for ≥1 organism, with all seven target organisms detected in at least one sample. Ureaplasma parvum was the most common organism detected, followed by N. gonorrhoeae, M. hominis, U. urealyticum, T. vaginalis, C. trachomatis, with M. genitalium being the least detected. All 25 samples submitted for routine antenatal Group B Streptococcal screening were positive for at least one STI organism, and one sample from sexual non-accidental injury tested positive for five different organisms., Conclusions: STIs comprise a variety of organisms in our setting, with many patients exhibiting coinfection with multiple organisms. This suggests the need for a critical evaluation of current syndromic testing and treatment guidelines so as to stem inadvertent spread of STI organisms and the development of resistance. The use of molecular testing methods may improve detection, especially in resource limited settings, providing speedy results, and thus allowing for guided therapy in only infected patients., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Moodley et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: Serratia marcescens is an opportunistic nosocomial pathogen, and recent reports have highlighted the rapid increase in multidrug resistance in this organism. There is a paucity in genomic data for carbapenem-resistant S. marcescens (CRSM)., Methods: A retrospective cohort study describing laboratory-confirmed CRSM from a tertiary academic hospital in Cape Town, South Africa, for the period 2015-20, was performed. Stored CRSM and contemporary isolates were submitted for WGS using Illumina MiSeq, with the Nextera DNA Flex Library Preparation Kit. Sequence data were analysed in-house using srst2 and Tychus, and CRSM and contemporary isolates were compared., Results: Twenty-one CRSM and four contemporary isolates were sequenced and analysed. Twenty-four different resistance genes were identified, with all isolates having at least two resistance genes, and seventeen isolates harbouring three or more genes. This correlated well with phenotypic results. The bla OXA-48-like carbapenemase was the most common carbapenemase identified, in 86% (18/21) of CRSM. A core SNP difference tree indicated that the CRSM could be grouped into three clusters. Eleven isolates had shared plasmids. Several genes and SNPs were identified in the CRSM, which may putatively augment virulence, but this requires further functional characterization., Conclusions: A diverse resistome was observed in CRSM, which was also reflected phenotypically, with bla OXA-48-like the most commonly carbapenemase. Though distinct clusters were observed, no clonality was noted, and a limited number of isolates shared plasmids. This study provides genomic data for emerging CRSM and highlights the importance of ongoing genomic surveillance to inform infection prevention control and antimicrobial stewardship initiatives., (© The Author(s) 2023. Published by Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy.)

The expression of indoleamine 2,3-dioxygenase (IDO), a robust immunosuppressant, is significantly induced in macaque tuberculosis (TB) granulomas, where it is expressed on IFN-responsive macrophages and myeloid-derived suppressor cells. IDO expression is also highly induced in human TB granulomas, and products of its activity are detected in patients with TB. In vivo blockade of IDO activity resulted in the reorganization of the granuloma with substantially greater T cells being recruited to the core of the lesions. This correlated with better immune control of TB and reduced lung M. tuberculosis burdens. To study if the IDO blockade strategy can be translated to a bona fide host-directed therapy in the clinical setting of TB, we studied the effect of IDO inhibitor 1-methyl-d-tryptophan adjunctive to suboptimal anti-TB chemotherapy. While two-thirds of controls and one-third of chemotherapy-treated animals progressed to active TB, inhibition of IDO adjunctive to the same therapy protected macaques from TB, as measured by clinical, radiological, and microbiological attributes. Although chemotherapy improved proliferative T cell responses, adjunctive inhibition of IDO further enhanced the recruitment of effector T cells to the lung. These results strongly suggest the possibility that IDO inhibition can be attempted adjunctive to anti-TB chemotherapy in clinical trials.

Background: Determining lower respiratory tract infection (LRTI) aetiology is complex. Culture-based methods are laborious with poor sensitivity. Molecular assays improve detection of potential pathogens, but incorrect interpretation of results may lead to inappropriate antimicrobial therapy., Methods: The utility of the BioFire ® FilmArray ® Pneumonia Panel plus (FA-PP) to detect LRTI pathogens, and the potential impact on antimicrobial stewardship in a low-resource setting, were assessed. Routine LRT samples were included from adult patients with clinically suspected LRTI or with a concomitant blood culture at Groote Schuur Hospital and referring facilities. Culture and FA-PP results were compared, and pharmacy data analysed to determine appropriateness of antibiotic therapy., Results: There was an 80% correlation between cultured LRTI pathogens and the FA-PP bin ≥10 7 results. Compared with culture, the FA-PP detected substantially more pathogens (86.6% versus 17.9%) and produced a combined 100% positive percent agreement, and 88% negative percent agreement. The FA-PP detected bacterial/viral coinfections in 27% of samples. Correlation of FA-PP results with pharmacy data ( n  = 69) indicated a potential antibiotic change in 75% of cases, but this is difficult to accurately characterize without a 'gold standard' for treatment or complete clinical data., Conclusions: The FA-PP increased the number of positive samples with typical bacteria, but the semi-quantitative reporting algorithm does not describe the correlation between the different bin values and colonization versus infection. This complicates result interpretation and may lead to inappropriate antimicrobial treatment. This study highlights the potential positive impact of rapid molecular assays for routine care in lower-income settings, but also underscores the interpretive challenges associated with these tests., (© The Author(s) 2023. Published by Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy.)

Here in we report the development of a Pt-V/CeO 2 catalyst performing under mild conditions in amide hydrogenation. Ceria with different morphologies was employed as support in this study. We further developed a glycol-thermal technique that yields thermally stable quantum dot ceria, which can be applied as a support. A systematic investigation revealed the importance of proximity between the small crystalline hydrogenating sites (Pt) and oxophilic sites (V). The study showed that oxygen vacancies on the ceria surface oxidize both Pt and V, poisoning the hydrogenation reaction. In contrast, the absence of oxygen vacancies promoted the hydrogenating ability of Pt sites and also improved their ability to participate in the H 2 spillover mechanism and in situ formation of oxophilic V 3+ . This study demonstrates how the engineering of the oxygen vacancies on the surface of the redox support can manipulate the nature of active sites toward specific reactions., Competing Interests: The authors declare no conflicts of interest., (© 2022 The Author(s).)

Rationale: Different Mycobacterium tuberculosis ( Mtb ) strains exhibit variable degrees of virulence in humans and animal models. Differing stress response strategies used by different strains of Mtb could influence virulence. Objectives: We compared the virulence of two strains of Mtb with use in animal model research: CDC1551 and Erdman. Methods: Rhesus macaques, which develop human-like tuberculosis attributes and pathology, were infected with a high dose of either strain via aerosol, and virulence was compared by bacterial burden and pathology. Measurements and Main Results: Infection with Erdman resulted in significantly shorter times to euthanasia and higher bacterial burdens and greater systemic inflammation and lung pathology relative to those infected with CDC1551. Macaques infected with Erdman also exhibited significantly higher early inflammatory myeloid cell influx to the lung, greater macrophage and T cell activity, and higher expression of lung remodeling (extracellular matrix) genes, consistent with greater pathology. Expression of NOTCH4 (neurogenic locus notch homolog 4) signaling, which is induced in response to hypoxia and promotes undifferentiated cellular state, was also higher in Erdman-infected lungs. The granulomas generated by Erdman, and not CDC1551, infection appeared to have larger regions of necrosis, which is strongly associated with hypoxia. To better understand the mechanisms of differential hypoxia induction by these strains, we subjected both to hypoxia in vitro . Erdman induced higher concentrations of DosR regulon relative to CDC1551. The DosR regulon is the global regulator of response to hypoxia in Mtb and critical for its persistence in granulomas. Conclusions: Our results show that the response to hypoxia is a critical mediator of virulence determination in Mtb , with potential impacts on bacillary persistence, reactivation, and efficiency of therapeutics.

Quantum ghost imaging offers many advantages over classical imaging, including low photon fluxes and non-degenerate object and image wavelengths for imaging light sensitive structures, but suffers from slow image reconstruction speeds. Image reconstruction times depend on the resolution of the required image which scale quadratically with the image resolution. Here, we propose a super-resolved imaging approach based on neural networks where we reconstruct a low resolution image, which we denoise and super-resolve to a high resolution image. To test the approach, we implemented both a generative adversarial network as well as a super-resolving autoencoder in conjunction with an experimental quantum ghost imaging setup, demonstrating its efficacy across a range of object and imaging projective mask types. We achieved super-resolving enhancement of [Formula: see text] the measured resolution with a fidelity close to 90[Formula: see text] at an acquisition time of N[Formula: see text] measurements, required for a complete N [Formula: see text] N pixel image solution. This significant resolution enhancement is a step closer to a common ghost imaging goal, to reconstruct images with the highest resolution and the shortest possible acquisition time., (© 2022. The Author(s).)

Despite a century of research into tuberculosis (TB), there is a dearth of reproducible, easily quantifiable, biomarkers that can predict disease onset and differentiate between host disease states. Due to the challenges associated with human sampling, nonhuman primates (NHPs) are utilized for recapitulating the closest possible modelling of human TB. To establish a predictive peripheral biomarker profile based on a larger cohort of rhesus macaques (RM), we analyzed results pertaining to peripheral blood serum chemistry and cell counts from RMs that were experimentally exposed to Mtb in our prior studies and characterized as having either developed active TB (ATB) disease or latent TB infection (LTBI). We compared lung CFU burdens and quantitative pathologies with a number of measurables in the peripheral blood. Based on our results, the investigations were then extended to the study of specific molecules and cells in the lung compartments of a subset of these animals and their immune responses. In addition to the elevated serum C-reactive protein (CRP) levels, frequently used to discern the level of Mtb infection in model systems, reduced serum albumin-to-globulin (A/G) ratios were also predictive of active TB disease. Furthermore, higher peripheral myeloid cell levels, particularly those of neutrophils, kynurenine-to-tryptophan ratio, an indicator of induced expression of the immunosuppressive molecule indoleamine dioxygenase, and an influx of myeloid cell populations could also efficiently discriminate between ATB and LTBI in experimentally infected macaques. These quantifiable correlates of disease were then used in conjunction with a regression-based analysis to predict bacterial load. Our results suggest a potential biomarker profile of TB disease in rhesus macaques, that could inform future NHP-TB research. Our results thus suggest that specific biomarkers may be developed from the myeloid subset of peripheral blood or plasma with the ability to discriminate between active and latent Mtb infection.

Background: Outbreaks of community-acquired Pseudomonas aeruginosa are typically small and localized. We investigated an increase in community-acquired infections with P. aeruginosa in Cape Town, South Africa., Methods: Cases were defined as P. aeruginosa isolated from any clinical sample, and "wild-type" as those susceptible to all antibiotics tested. The residential addresses of community-acquired wild-type cases were mapped. Whole-genome sequencing and multilocus sequence typing were used to determine clonality and identify virulence genes. A clinical study in a subset of patients with bloodstream infection compared demographic and clinical characteristics between sequence types (STs)., Results: The outbreak lasted 10 months from December 2016 to September 2017 with 3,321 documented cases. At the peak, cases reached 2.3-fold baseline rates. Cases were distributed widely across the city. Multilocus ST 303 was predominant during the outbreak. A total of 51 virulence genes were differentially present in ST303 compared with other STs, including genes involved in biofilm formation, iron uptake, and gut penetration., Conclusion: The investigation confirmed a citywide outbreak of P. aeruginosa. We identified a predominant outbreak-associated clone, ST303, which harbored genes that could contribute to virulence and survival in adverse environmental conditions such as those associated with drought., Competing Interests: Conflict of interest The authors have no competing conflict of interest to declare with regards to the material discussed in the article., (Copyright © 2022 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Emergence of mutant SARS-CoV-2 strains associated with an increased risk of COVID-19-related death necessitates better understanding of the early viral dynamics, host responses and immunopathology. Single cell RNAseq (scRNAseq) allows for the study of individual cells, uncovering heterogeneous and variable responses to environment, infection and inflammation. While studies have reported immune profiling using scRNAseq in terminal human COVID-19 patients, performing longitudinal immune cell dynamics in humans is challenging. Macaques are a suitable model of SARS-CoV-2 infection. Our longitudinal scRNAseq of bronchoalveolar lavage (BAL) cell suspensions from young rhesus macaques infected with SARS-CoV-2 (n = 6) demonstrates dynamic changes in transcriptional landscape 3 days post- SARS-CoV-2-infection (3dpi; peak viremia), relative to 14-17dpi (recovery phase) and pre-infection (baseline) showing accumulation of distinct populations of both macrophages and T-lymphocytes expressing strong interferon-driven inflammatory gene signature at 3dpi. Type I interferon response is induced in the plasmacytoid dendritic cells with appearance of a distinct HLADR + CD68 + CD163 + SIGLEC1 + macrophage population exhibiting higher angiotensin-converting enzyme 2 (ACE2) expression. These macrophages are significantly enriched in the lungs of macaques at 3dpi and harbor SARS-CoV-2 while expressing a strong interferon-driven innate anti-viral gene signature. The accumulation of these responses correlated with decline in viremia and recovery., (© 2022. The Author(s).)

Smoking is known to be an added risk factor for tuberculosis (TB), with nearly a quarter of the TB cases attributed to cigarette smokers in the 22 countries with the highest TB burden. Many studies have indicated a link between risk of active TB and cigarette smoke. Smoking is also known to significantly decrease TB cure and treatment completion rate and increase mortality rates. Cigarette smoke contains thousands of volatile compounds including carcinogens, toxins, reactive solids, and oxidants in both particulate and gaseous phase. Yet, to date, limited studies have analyzed the impact of cigarette smoke components on Mycobacterium tuberculosis ( Mtb ), the causative agent of TB. Here we report the impact of cigarette smoke condensate (CSC) on survival, mutation frequency, and gene expression of Mtb in vitro . We show that exposure of virulent Mtb to cigarette smoke increases the mutation frequency of the pathogen and strongly induces the expression of the regulon controlled by SigH-a global transcriptional regulator of oxidative stress. SigH has previously been shown to be required for Mtb to respond to oxidative stress, survival, and granuloma formation in vivo . A high-SigH expression phenotype is known to be associated with greater virulence of Mtb . In patients with pulmonary TB who smoke, these changes may therefore play an important, yet unexplored, role in the treatment efficacy by potentially enhancing the virulence of tubercle bacilli., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Willemse, Moodley, Mehra and Kaushal.)

Here we outline a description of paraxial light propagation from a modal perspective. By decomposing the initial transverse field into a spatial basis whose elements have known and analytical propagation characteristics, we are able to analytically propagate any desired field, making the calculation fast and easy. By selecting a basis other than that of planes waves, we overcome the problem of numerical artifacts in the angular spectrum approach and at the same time are able to offer an intuitive understanding for why certain classes of fields propagate as they do. We outline the concept theoretically, compare it to the numerical angular spectrum approach, and confirm its veracity experimentally using a range of instructive examples. We believe that this modal approach to propagating light will be a useful addition to the toolbox for propagating optical fields.

In vitro MICs and in vivo pharmacodynamics of ceftazidime and cefepime human-simulated regimens (HSR) against modified carbapenem inactivation method (mCIM)-positive Pseudomonas aeruginosa isolates harboring different OXA-10-like subtypes were described. The murine thigh model assessed ceftazidime (2 g every 8 h [q8h] HSR) and cefepime (2 g and 1 g q8h HSR). Phenotypes were similar despite possessing OXA-10-like subtypes with differing spectra. Ceftazidime produced ≥1-log 10 killing in all isolates. Cefepime activity was dose dependent and MIC driven. This approach may be useful in assessing the implications of β-lactamase variants.

Background: Pertussis is an acute respiratory tract disease caused by Bordetella pertussis. In 2014, 24.1 million pertussis cases, resulting in 160,700 deaths, were estimated to have occurred worldwide. This study aimed to determine the epidemiology of pertussis among patients with clinically compatible illness who visited selected hospitals in the Amhara Regional State of Ethiopia., Methods: A cross-sectional study design was used to review pertussis patients with clinically compatible illness. Nasopharyngeal swabs were collected from 515 patients from July 2018 through February 2019. DNA was extracted from all nasopharyngeal swabs and samples were analyzed using real-time (RT-) PCR. Crude and adjusted odds ratios with corresponding 95% confidence intervals were estimated using bivariable and multivariable logistic regression analysis, respectively., Results: The overall prevalence of Bordetella species among the study participants was 156 of 515 (30.3%) [95% CI = 26.4-34.6] as determined by Bordetella RT-PCR, including: 65 (41.7%) B. pertussis, 89 (57.1%) indeterminate B. pertussis, one (0.6%) Bordetella holmesii and one (0.6%) Bordetella parapertussis., Conclusions: This study found that pertussis is potentially endemic and a common health problem among patients visiting health institutions in the Amhara Regional State of Ethiopia. More data regarding pertussis in Ethiopia could inform development of effective prevention strategies., (Copyright © 2021. Published by Elsevier Ltd.)

Quantum ghost imaging offers many advantages over classical imaging, including the ability to probe an object with one wavelength and record the image with another (non-degenerate ghost imaging), but suffers from slow image reconstruction due to sparsity and probabilistic arrival positions of photons. Here, we propose a two-step deep learning approach to establish an optimal early stopping point based on object recognition, even for sparsely filled images. In step one we enhance the reconstructed image after every measurement by a deep convolutional auto-encoder, followed by step two in which a classifier is used to recognise the image. We test this approach on a non-degenerate ghost imaging setup while varying physical parameters such as the mask type and resolution. We achieved a fivefold decrease in image acquisition time at a recognition confidence of [Formula: see text]. The significant reduction in experimental running time is an important step towards real-time ghost imaging, as well as object recognition with few photons, e.g., in the detection of light sensitive structures.

Background: Culture remains the diagnostic standard for Streptococcus pneumoniae bacteraemia but is limited by time to identification, prior antibiotics and bacterial autolysis. Culture-independent methods for detecting S. pneumoniae include PCR and antigen tests. We evaluated an antigen test on blood culture broth for the rapid detection of S. pneumoniae bacteraemia., Method: We collected 212 signal-positive blood cultures, with gram-positive cocci in pairs, chains or with uncertain morphology. The BinaxNOW S. pneumoniae urinary antigen test, Gram stain, culture and lytA PCR were performed on all samples. Diagnostic accuracy of the antigen test and Gram stain with gram-positive cocci in pairs were compared with culture, polymerase chain reaction (PCR) and the composite of culture and PCR., Results: Streptococcus pneumoniae was isolated in 26% of samples, 66% cultured other gram-positive organisms and 8% of samples had no growth. Sensitivity and negative predictive values of the antigen test were 100%, specificity and positive predictive values were 87% - 88% and 76% - 81%, but increased to 93% - 96% and 96% - 98% when applied to subsets with gram-positive cocci in pairs, or history compatible with respiratory illness or meningitis. Sensitivity (69% - 75%) and specificity (81%) of Gram stain (gram-positive cocci in pairs) were lower than the antigen test even when applied to the same subsets., Conclusion: Accurate and rapid diagnosis of S. pneumoniae bacteraemia is challenging. Specificity of this antigen test is limited by cross-reactivity with other gram-positive organisms, but could be improved if Gram stain morphology and clinical history are available. The antigen test is a useful adjunct for rapid diagnosis of S. pneumoniae bacteraemia., Competing Interests: The authors declare that they have no financial or personal relationships that may have inappropriately influenced them in writing this research article., (© 2021. The Authors.)

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb) latently infects approximately one-fourth of the world's population. The immune mechanisms that govern progression from latent (LTBI) to active pulmonary TB (PTB) remain poorly defined. Experimentally Mtb-infected non-human primates (NHP) mirror the disease observed in humans and recapitulate both PTB and LTBI. We characterized the lung immune landscape in NHPs with LTBI and PTB using high-throughput technologies. Three defining features of PTB in macaque lungs include the influx of plasmacytoid dendritic cells (pDCs), an Interferon (IFN)-responsive macrophage population, and activated T cell responses. In contrast, a CD27 + Natural killer (NK) cell subset accumulated in the lungs of LTBI macaques. This NK cell population was also detected in the circulation of LTBI individuals. This comprehensive analysis of the lung immune landscape will improve the understanding of TB immunopathogenesis, providing potential targets for therapies and vaccines for TB control., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Introduction: There are few studies describing colonisation with extended spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) and carbapenem-resistant Enterobacterales (CRE) among children in sub-Saharan Africa. Colonisation often precedes infection and multi-drug-resistant Enterobacterales are important causes of invasive infection., Methods: In this prospective cross-sectional study, conducted between April and June 2017, 200 children in a tertiary academic hospital were screened by rectal swab for EBSL-PE and CRE. The resistance-conferring genes were identified using polymerase chain reaction technology. Risk factors for colonisation were also evaluated., Results: Overall, 48% (96/200) of the children were colonised with at least one ESBL-PE, 8.3% (8/96) of these with 2 ESBL-PE, and one other child was colonised with a CRE (0.5% (1/200)). Common colonising ESBL-PE were Klebsiella pneumoniae (62.5%, 65/104) and Escherichia coli (34.6%, 36/104). The most frequent ESBL-conferring gene was blaCTX-M in 95% (76/80) of the isolates. No resistance- conferring gene was identified in the CRE isolate (Enterobacter cloacae). Most of the Klebsiella pneumoniae isolates were susceptible to piperacillin/tazobactam (86.2%) and amikacin (63.9%). Similarly, 94.4% and 97.2% of the Escherichia coli isolates were susceptible to piperacillin/tazobactam and amikacin, respectively. Hospitalisation for more than 7 days before study enrolment was associated with ESBL-PE colonisation., Conclusion: Approximately half of the hospitalised children in this study were colonised with ESBL-PE. This highlights the need for improved infection prevention and control practices to limit the dissemination of these microorganisms., Competing Interests: The authors have declared that no competing interests exist.

Background: There remains a significant proportion of deaths due to pneumococcal pneumonia in infants from low- and middle-income countries despite the marginal global declines recorded in the past decade. Monitoring changes in pneumococcal carriage is key to understanding vaccination-induced shifts in the ecology of carriage, patterns of antimicrobial resistance, and impact on health. We longitudinally investigated pneumococcal carriage dynamics in PCV-13 vaccinated infants by collecting nasopharyngeal (NP) samples at 2-weekly intervals from birth through the first year of life from 137 infants. As a proof of concept, 196 NP samples were retrieved from a subset of 23 infants to explore strain-level pneumococcal colonization patterns and associated antimicrobial-resistance determinants. These were selected on the basis of changes in serotype and antibiogram over time. NP samples underwent short-term enrichment for streptococci prior to total nucleic acid extraction and whole metagenome shotgun sequencing (WMGS). Reads were assembled and aligned to pneumococcal reference genomes for the extraction of pneumococcal and non-pneumococcal bacterial reads. Pneumococcal contigs were aligned to the Antibiotic Resistance Gene-ANNOTation database of acquired AMR genes. In silico pneumococcal capsular and multilocus sequence typing were performed. Results: Of the 196 samples sequenced, 174 had corresponding positive cultures for pneumococci, of which, 152 were assigned an in silico serotype. Metagenomic sequencing detected a single pneumococcal serotype in 85% (129/152), and co-colonization in 15% (23/152) of the samples. Twenty-two different pneumococcal serotypes were identified, with 15B/15C and 16F being the most common non-PCV13 serotypes, while 23F and 19A were the most common PCV13 serotypes. Twenty-six different sequence types (STs), including four novel STs were identified in silico . Mutations in the fol A and fol P genes, associated with cotrimoxazole resistance, were detected in 89% (87/98) of cotrimoxazole-non-susceptible pneumococci, as well as in the pbp 1a and pbp 2x genes, in penicillin non-susceptible ST7052 15B/15C isolates. Conclusions: Metagenomic sequencing of NP samples is a valuable culture-independent technique for a detailed evaluation of the pneumococcal component and resistome of the NP microbiome. This method allowed for the detection of novel STs, as well as co-colonization, with a predominance of non-PCV13 serotypes in this cohort. Forty-eight resistance genes, as well as mutations associated with resistance were detected, but the correlation with phenotypic non-susceptibility was lower than expected., (Copyright © 2020 Manenzhe, Dube, Wright, Lennard, Mounaud, Lo, Zar, Nierman, Nicol and Moodley.)

Introduction: Nasopharyngeal (NP) colonization with antimicrobial-resistant bacteria is a global public health concern. Antimicrobial-resistance (AMR) genes carried by the resident NP microbiota may serve as a reservoir for transfer of resistance elements to opportunistic pathogens. Little is known about the NP antibiotic resistome. This study longitudinally investigated the composition of the NP antibiotic resistome in Streptococcus-enriched samples in a South African birth cohort., Methods: As a proof of concept study, 196 longitudinal NP samples were retrieved from a subset of 23 infants enrolled as part of broader birth cohort study. These were selected on the basis of changes in serotype and antibiogram over time. NP samples underwent short-term enrichment for streptococci prior to total nucleic acid extraction and whole metagenome shotgun sequencing (WMGS). Reads were assembled and aligned to pneumococcal reference genomes for the extraction of streptococcal and non-streptococcal bacterial reads. Contigs were aligned to the Antibiotic Resistance Gene-ANNOTation database of acquired AMR genes., Results: AMR genes were detected in 64% (125/196) of the samples. A total of 329 AMR genes were detected, including 36 non-redundant genes, ranging from 1 to 14 genes per sample. The predominant AMR genes detected encoded resistance mechanisms to beta-lactam (52%, 172/329), macrolide-lincosamide-streptogramin (17%, 56/329), and tetracycline antibiotics (12%, 38/329). MsrD, ermB, and mefA genes were only detected from streptococcal reads. The predominant genes detected from non- streptococcal reads included blaOXA-60, blaOXA-22, and blaBRO-1. Different patterns of carriage of AMR genes were observed, with only one infant having a stable carriage of mefA, msrD and tetM over a long period., Conclusion: This study demonstrates that WMGS can provide a broad snapshot of the NP resistome and has the potential to provide a comprehensive assessment of resistance elements present in this niche., Competing Interests: The authors have no conflict of interest to declare related to the content of this paper.

The immunometabolic mechanisms underlying suboptimal T cell immunity in tuberculosis remain undefined. Here, we examine how chronic Mycobacterium tuberculosis (Mtb) and M. bovis BCG infections rewire metabolic circuits and alter effector functions in lung CD8 + T cells. As Mtb infection progresses, mitochondrial metabolism deteriorates in CD8 + T cells, resulting in an increased dependency on glycolysis that potentiates inflammatory cytokine production. Over time, these cells develop bioenergetic deficiencies that reflect metabolic "quiescence." This bioenergetic signature coincides with increased mitochondrial dysfunction and inhibitory receptor expression and was not observed in BCG infection. Remarkably, the Mtb-triggered decline in T cell bioenergetics can be reinvigorated by metformin, giving rise to an Mtb-specific CD8 + T cell population with improved metabolism. These findings provide insights into Mtb pathogenesis whereby glycolytic reprogramming and compromised mitochondrial function contribute to the breakdown of CD8 + T cell immunity during chronic disease, highlighting opportunities to reinvigorate immunity with metabolically targeted pharmacologic agents., (Copyright © 2019 The Author(s). Published by Elsevier Inc. All rights reserved.)

Background: Phenotypic detection of extended-spectrum beta-lactamases (ESBLs) is based on the inhibition of ESBL enzymes by β-lactamase inhibitors and on the comparison of cephalosporin activity with or without a β-lactamase inhibitor. Many South African diagnostic laboratories rely on the Vitek 2 for automated susceptibility testing and for ESBL detection. However, the Gram-negative susceptibility card currently used locally (AST-N255) has been modified and its accuracy for ESBL detection is not known., Methods: We randomly selected 50 isolates of Klebsiella pneumoniae and Escherichia coli from a collection of clinical bloodstream isolates from Groote Schuur Hospital from 2015 to 2016, including ESBL-producing and non-ESBL-producing strains. We used standardised phenotypic (disc diffusion and broth microdilution) and genotypic (conventional polymerase chain reaction (PCR) for bla CTX-M , bla SHV and bla TEM ) methods for detection of ESBLs. We compared ESBL detection by Vitek 2 to a composite reference standard comprising ESBL detection either by both phenotypic methods or by one phenotypic method together with genotypic detection., Results: The sensitivity of Vitek 2 system for detection of ESBLs was 33/36 or 92% (78% - 97%) for E. coli , and 40/40 or 100% (91% - 100%) for K. pneumoniae , whilst specificity was 10/10 or 100% (72% - 100%) and 9/10 or 90% (60% - 98%), respectively. This is comparable with previous studies., Conclusion: Using a composite reference standard of the phenotypic and genotypic methods employed in this study, no Vitek-categorised ESBL E. coli or K. pneumoniae was found to be a non-ESBL with the exception of possible misinterpretation with K. pneumoniae SHV-hyper-producing isolates., Competing Interests: The authors have declared that no competing interests exist., (© 2019. The Authors.)

Introduction: Nasopharyngeal (NP) colonization by Streptococcus pneumoniae (pneumococcus) precedes the development of respiratory tract infection. Colonization by antimicrobial-resistant pneumococci, especially in infants, is a major public health concern. We longitudinally investigated antimicrobial-resistance amongst pneumococci colonizing the nasopharynx of South African infants immunized with the 13-valent pneumococcal conjugate vaccine (PCV13). Methods: NP swabs were collected every second week from birth through the first year of life from 137 infants. Pneumococci were identified and serotyped using conventional microbiological techniques, and their antibiotic susceptibility profiles determined by disk diffusion and E -test. Results: All infants were immunized with 3 doses of PCV13. 1520 pneumococci (760 non-repeat) isolates were recovered from 137 infants; including non-typeable ( n = 99), PCV13 ( n = 133) and non-PCV13 serotypes ( n = 528). The prevalence of penicillin, erythromycin, and cotrimoxazole non-susceptibility was 19% (95% CI 17-22%) (3% fully resistant), 18% (95% CI 15-21%) (14% fully resistant), and 45% (95% CI 42-49%) (36% fully resistant), respectively. The predominant penicillin-non-susceptible serotypes included 19A, 19F, 15B/15C, 15A, and 21, while susceptible serotypes included 23A, 34, and 17A. Multidrug-resistance (MDR) was observed in 9% (95% CI 7-11%) of the isolates. PCV13 serotypes were more likely to be non-susceptible, compared to non-PCV13 serotypes, to penicillin (26% vs. 16%, p = 0.007), erythromycin (23% vs. 15%, p = 0.027) and cotrimoxazole (62% vs. 41%, p < 0.001). Non-susceptibility to penicillin, erythromycin, and cotrimoxazole remained relatively constant through the first year of life ( X 2 test for trend: p = 0.184, p = 0.171, and p = 0.572, respectively). Overall, penicillin or erythromycin-non-susceptible pneumococci were carried for a shorter duration than susceptible pneumococci [penicillin (mean days, 18 vs. 21, p = 0.013) and erythromycin (mean days, 18 vs. 21, p = 0.035)]. Within individual infants carrying the same serotype longitudinally, changes in antibiotic susceptibility were observed over time in 45% (61/137) of infants and these changes were predominantly for penicillin (76%, 79/104). Conclusion: Prevalence of NP carriage with antibiotic-non-susceptible pneumococci was relatively constant throughout the first year of life. PCV13 serotypes were more commonly non-susceptible to penicillin, erythromycin, and cotrimoxazole. Penicillin or erythromycin-non-susceptible pneumococci were carried for a shorter duration than penicillin or erythromycin-susceptible pneumococci.

The antileprosy drug clofazimine was recently repurposed as part of a newly endorsed short-course regimen for multidrug-resistant tuberculosis. It also enables significant treatment shortening when added to the first-line regimen for drug-susceptible tuberculosis in a mouse model. However, clofazimine causes dose- and duration-dependent skin discoloration in patients, and the optimal clofazimine dosing strategy in the context of the first-line regimen is unknown. We utilized a well-established mouse model to systematically address the impacts of duration, dose, and companion drugs on the treatment-shortening activity of clofazimine in the first-line regimen. In all studies, the primary outcome was relapse-free cure (culture-negative lungs) 6 months after stopping treatment, and the secondary outcome was bactericidal activity, i.e., the decline in the lung bacterial burden during treatment. Our findings indicate that clofazimine activity is most potent when coadministered with first-line drugs continuously throughout treatment and that equivalent treatment-shortening results are obtained with half the dose commonly used in mice. However, our studies also suggest that clofazimine at low exposures may have negative impacts on treatment outcomes, an effect that was evident only after the first 3 months of treatment. These data provide a sound evidence base to inform clofazimine dosing strategies to optimize the antituberculosis effect while minimizing skin discoloration. The results also underscore the importance of conducting long-term studies to allow the full evaluation of drugs administered in combination over long durations., (Copyright © 2018 American Society for Microbiology.)

Tuberculosis (TB) has been the scourge of the human race for many decades, claiming countless number of lives. This is further complicated by the ability of Mycobacterium tuberculosis to infect extrapulmonary sites, specifically the brain. These extrapulmonary forms of TB are difficult to treat owing to problems associated with drug delivery across the blood-brain barrier. Linezolid (LIN) and clofazimine (CFZ) are two of the more promising anti-TB drugs in recent times. In this study, BALB/c mice were aerosol-infected with M. tuberculosis H37Rv and were treated for 4 weeks with LIN [100 mg/kg body weight (BW)] or CFZ (100 mg/kg BW). Concurrently, it was investigated whether an aerosol TB infection would lead to dissemination of TB bacilli into the brain. Post-treatment brain and lung CFUs were determined together with serum, lung and brain drug concentrations. CFZ displayed a strong bactericidal effect in the lung, whilst LIN had a bacteriostatic effect. Mycobacterium tuberculosis appeared at 2 weeks post-infection in the untreated group (2.38 ± 0.43 log 10 CFU) and more surprisingly at 3 weeks post-infection in the LIN-treated group (1.14 ± 0.99 log 10 CFU). TB bacilli could not be detected in the brains of the CFZ-treated group. To the best of our knowledge, this is the first study showing the appearance of M. tuberculosis in the brain following a murine aerosol TB infection. This study may advocate the use of CFZ as prophylactic treatment to prevent the development of extrapulmonary TB of the central nervous system using a two-pronged approach., (Copyright © 2017 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.)

Objectives: The anti-leprosy drug clofazimine has been shown to have antimicrobial activity against Mycobacterium tuberculosis and has been associated with treatment-shortening activity in both clinical and preclinical studies of TB chemotherapy. However, a reported lack of early bactericidal activity (EBA) in TB patients has raised questions regarding the usefulness of clofazimine as an anti-TB drug. Our objective was to systematically evaluate the EBA of clofazimine in vitro and in vivo to provide insight into how and when this drug exerts its antimicrobial activity against M. tuberculosis., Methods: We evaluated the 14 day EBA of clofazimine (i) in vitro at concentrations ranging from 4 times below to 4 times above the MIC for M. tuberculosis and (ii) in vivo in infected BALB/c mice at doses ranging from 1.5 to 100 mg/kg/day, and serum clofazimine levels were measured. In both experiments, isoniazid was used as the positive control., Results: In vitro, clofazimine, at any concentration tested, did not exhibit bactericidal activity during the first week of exposure; however, in the second week, it exhibited concentration-dependent antimicrobial activity. In vivo, clofazimine, at any dose administered, did not exhibit bactericidal activity during the first week, and limited antimicrobial activity was observed during the second week of administration. While serum clofazimine levels were clearly dose dependent, the antimicrobial activity was not significantly related to the dose administered., Conclusions: Our data suggest that clofazimine's delayed antimicrobial activity may be due more to its mechanism of action rather than to host-related factors., (© The Author 2016. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)

Human brucellosis in South Africa (SA) is under-diagnosed and under-reported. This is because many clinicians have little or no experience in managing affected patients, and in part because of the nonspecific and insidious nature of the disease. A case of human brucellosis caused by Brucella melitensis in a patient from the Western Cape Province of SA is described, and the resulting exposure of staff members at two medical microbiology laboratories, as well as the public health investigation that was conducted, are discussed. This article aims to highlight the need for strengthening integration between public health, medical and veterinary services and exposing deficiencies in public health, veterinary and laboratory practices.

Background: During 2013, the haematology/oncology unit at a tertiary level paediatric hospital in South Africa experienced the emergence of infection with vancomycin-resistant Enterococcus (VRE)., Objective: To describe the clinical and molecular aspects of the cases identified., Methods: VRE isolates identified from blood culture specimens processed at the National Health Laboratory Service were screened for the presence of the vancomycin resistance genes vanA, B and C1, 2 and 3. Further characterisation of these isolates was carried out using pulsed-field gel electrophoresis (PGFE) and multilocus sequence typing (MLST). Clinical records of infected patients were reviewed to identify possible risk factors, while surveillance with rectal swabs was performed to identify VRE-colonised patients., Results: Four patients with haematological malignancies were identified with VRE bloodstream infections. Patients were immunocompromised at the time of the bloodstream infection (BSI), with receipt of vancomycin prior to VRE-BSI, and infections were treated with linezolid. Colonisation with VRE was found in 8 of 55 patients screened. Infected and colonised patients were isolated in the unit during their admission and strict contact precaution infection control practices were instituted. The vanA gene was identified in all of the isolates but one. PFGE and MLST results showed a degree of genetic relatedness between certain isolates obtained from rectal swab and blood culture samples, suggesting possible patient-to-patient transmission or persistence of the isolates in the unit., Conclusion: Strict infection control practices are necessary to prevent infection and transmission of resistant organisms among vulnerable patients.

Experimental and clinical studies have indicated that the antileprosy drug clofazimine may contribute treatment-shortening activity when included in tuberculosis treatment regimens. Clofazimine accumulates to high levels in tissues, has a long half-life, and remains in the body for months after administration is stopped. We hypothesized that in tuberculosis treatment, accumulated clofazimine may contribute sustained antimicrobial activity after treatment cessation, and we used the BALB/c mouse model of chronic tuberculosis chemotherapy to address this hypothesis. Mycobacterium tuberculosis-infected mice were treated for 4 weeks or 8 weeks with either isoniazid alone, clofazimine alone, the first-line regimen rifampin-isoniazid-pyrazinamide-ethambutol, or a first-line regimen where clofazimine was administered in place of ethambutol. To evaluate posttreatment antimicrobial activity, bacterial regrowth in the lungs and spleens was assessed at the day of treatment cessation and 2, 4, 6, and 8 weeks after treatment was stopped. Bacterial regrowth was delayed in all mice receiving clofazimine, either alone or in combination, compared to the mice that did not receive clofazimine. This effect was especially evident in mice receiving multidrug therapy. In mice not receiving clofazimine, bacterial regrowth began almost immediately after treatment was stopped, while in mice receiving clofazimine, bacterial regrowth was delayed for up to 6 weeks, with the duration of sustained antimicrobial activity being positively associated with the time that serum clofazimine levels remained at or above the 0.25-μg/ml MIC for M. tuberculosis Thus, sustained activity of clofazimine may be important in the treatment-shortening effect associated with this drug., (Copyright © 2016, American Society for Microbiology. All Rights Reserved.)

Background: Klebsiella pneumoniae is an opportunistic pathogen often associated with nosocomial infections. A suspected outbreak of K. pneumoniae isolates, exhibiting reduced susceptibility to carbapenem antibiotics, was detected during the month of May 2012 among patients admitted to a haematology unit of a tertiary academic hospital in Cape Town, South Africa (SA)., Objectives: An investigation was done to determine possible epidemiological links between the case patients and to describe the mechanisms of carbapenem resistance of these bacterial isolates., Methods: Relevant demographic, clinical and laboratory information was extracted from hospital records and an observational review of infection prevention and control practices in the affected unit was performed. Antimicrobial susceptibility testing including phenotypic testing and genotypic detection of the most commonly described carbapenemase genes was done. The phylogenetic relationship of all isolates containing the blaOXA-181 carbapenemase gene was determined by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing., Results: Polymerase chain reaction analysis identified a total of seven blaOXA-181-positive, carbapenem-resistant K. pneumoniae isolates obtained from seven patients, all from a single unit. These isolates were indistinguishable using PFGE analysis and belonged to sequence type ST-14. No other carbapenemase enzymes were detected., Conclusion: This is the first documented laboratory-confirmed outbreak of OXA-181-producing K. pneumoniae in SA, and highlights the importance of enforcing strict adherence to infection control procedures and the need for ongoing surveillance of antibiotic-resistant pathogens in local hospitals.

This is the first report of clofazimine (CFZ) penetration and distribution in normal mouse brain. Mice were administered 25 mg/kg CFZ or 100 mg/kg CFZ orally, daily for 2 weeks. Animals were sacrificed and blood and brain tissues were harvested. Liquid chromatography tandem mass spectrometry showed high concentrations of CFZ in homogenized brain, with 100 mg/kg dose having significantly higher concentration than 25 mg/kg. Matrix-assisted laser desorption/ionization spectrometric imaging of brain sections showed widespread tissue distribution of CFZ. Our results show dose dependent localization in brain.

Administration of probiotic bacteria such as Bifidobacterium spp. can prevent antibiotic associated diarrhoea since they can survive the often harsh conditions of the gut. In Bifidobacterium longum subsp. longum(T) NCIMB 702259, two gene clusters, with homology to the ATP-binding cassette (ABC) family of efflux transporters, were identified and studied to assess their functional contribution to antibiotic resistance. Both gene clusters contained two genes encoding putative efflux transporters and a regulator gene, upstream of the structural genes. Reverse transcriptase analysis indicated that the genes in each cluster were transcribed as operons, one where all three genes, including a putative MarR-type regulator were transcribed together (BLLJ&#95;1496/1495/1494), and the other where the two ABC-type transporter genes (BLLJ&#95;1837/1836) were co-transcribed, but excluded the putative regulator (BLLJ&#95;1838). Heterologous expression of the cloned BLLJ&#95;1837/1836 transporter genes in Lactococcus lactis conferred resistance to erythromycin and tetracycline by increasing the minimum inhibitory concentration between 1.5 and 3 fold. The presence of these genes also allowed a 16% increase in the efflux of Hoechst 33342 from L. lactis cells containing the two transporter genes, BLLJ&#95;1837-6. In B. longum, an increase in the levels of transcription of 3.3 fold was observed for BLLJ&#95;1837 in the presence of erythromycin, as measured by multiplex quantitative PCR. In contrast to this, the expression of the genes of the BLLJ&#95;1495/1494 operon in L. lactis did not show significant drug resistance functionality. Gel shift experiments showed that in the BLLJ&#95;1495/1494 operon, the putative MarR-type regulator protein (BLLJ&#95;1496) bound with high affinity to the DNA sequence upstream of the operon in which it was located but this was not erythromycin dependent. This study demonstrated the occurrence of a drug inducible, ABC-type transporter system (BLLJ&#95;1837/1836) in B. longum as well as a putative MarR-type DNA binding protein (BLLJ&#95;1496)., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

The antileprosy drug clofazimine has shown potential for shortening tuberculosis treatment; however, the current dosing of the drug is not evidence based, and the optimal dosing is unknown. Our objective was to conduct a preclinical evaluation of the pharmacokinetics and pharmacodynamics of clofazimine in the mouse model of tuberculosis, with the goal of providing useful information on dosing for future studies. Pharmacokinetic parameters were evaluated in infected and uninfected BALB/c mice. Pharmacodynamic parameters were evaluated in Mycobacterium tuberculosis-infected mice that were treated for 12 weeks with one of six different clofazimine dosing regimens, i.e., doses of 6.25, 12.5, and 25 mg/kg of body weight/day and 3 regimens with loading doses. Clofazimine progressively accumulated in the lungs, livers, and spleens of the mice, reaching levels of greater than 50 μg/g in all tissues by 4 weeks of administration, while serum drug levels remained low at 1 to 2 μg/ml. Elimination of clofazimine was extremely slow, and the half-life was dependent on the duration of drug administration. Clofazimine exhibited dose-dependent tissue and serum concentrations. At any dose, clofazimine did not have bactericidal activity during the first 2 weeks of administration but subsequently demonstrated potent, dose-independent bactericidal activity. The antituberculosis activity of clofazimine was dependent on neither the dose administered nor the drug concentrations in the tissues, suggesting that much lower doses could be effectively used for tuberculosis treatment., (Copyright © 2015, American Society for Microbiology. All Rights Reserved.)

Objectives: To determine the genotypes of serogroup Y meningococcus (MenY), and to determine the prevalence of and identify factors associated with MenY lpxL1 variants., Methods: Isolates, collected from 2003 to 2007 through national surveillance for invasive meningococcal disease, were characterized by multilocus sequence typing and screened for interleukin-6 induction. LpxL1 genes were sequenced from low IL-6 inducers., Results: MenY represented 13% (n = 219/1702) of meningococcal disease. Clonal complex (cc) 175, ST-23/Cluster A3 (cc23), cc11 and cc167 accounted for 82% (176/214), 11% (24/214), 3% (6/214) and 3% (7/214) respectively. Low cytokine induction was evident in 15% (32/218). Cc23 isolates (24/24) had an lpxL1 mutation, while among the remaining isolates the proportion of lpxL1 variants was 4% (8/189, p < 0.001), and these were all cc175. Compared to wild type isolates, lpxL1 variants were associated with patients aged 5-14 years [unadjusted OR (95% CI): 4.3 (1.5-12)] or 15-24 years [unadjusted OR (95% CI): 9.1 (2.8-29)] compared to children <5 years; and were more likely have been isolated from CSF than blood [unadjusted OR (95% CI): 3.5 (1-11.9)]. On multivariable analysis, age remained significant [adjusted OR (95% CI), 5-14 years: 4.2 (1.5-12); 15-24 years: 8.9 (2.7-29)]., Conclusion: LpxL1 variants were associated with cc23 among young adults., (Copyright © 2014 The British Infection Association. All rights reserved.)

Differences in the composition of the gut microbiota have been associated with a range of diseases using culture-independent methods. Reliable extraction of nucleic acid is a key step in identifying the composition of the faecal microbiota. Five widely used commercial deoxyribonucleic acid (DNA) extraction kits (QIAsymphony® Virus/Bacteria Midi Kit (kit QS), ZR Fecal DNA MiniPrep™ (kit Z), QIAamp® DNA Stool Mini Kit (kit QA), Ultraclean® Fecal DNA Isolation Kit (kit U) and PowerSoil® DNA Isolation Kit (kit P)) were evaluated, using human faecal samples. Yield, purity and integrity of total genomic DNA were compared spectrophotometrically and using gel electrophoresis. Three bacteria, commonly found in human faeces were quantified using real time polymerase chain reaction (qPCR) and total bacterial diversity was studied using denaturing gradient gel electrophoresis (DGGE) as well as terminal restriction fragment length polymorphism (T-RFLP). The measurements of DNA yield and purity exhibited variations between the five kits tested in this study. Automated kit QS exhibited the best quality and highest quantity of DNA. All kits were shown to be reproducible with CV values≤0.46 for DNA extraction. qPCR results showed that all kits were uniformly efficient for extracting DNA from the selected target bacteria. DGGE and T-RFLP produced the highest diversity scores for DNA extracted using kit Z (H'=2.30 and 1.27) and kit QS (H'=2.16 and 0.94), which also extracted the highest DNA yields compared to the other kits assessed., (Copyright © 2013 Elsevier B.V. All rights reserved.)

From August 1999 through July 2002, hyperinvasive Neisseria meningitidis serogroup B (MenB) clonal complexes (CCs), namely, ST-32/ET-5 (CC32) and ST-41/44/lineage 3 (CC41/44), were predominant in the Western Cape Province of South Africa. This study analyzed MenB invasive isolates from a national laboratory-based surveillance system that were collected from January 2002 through December 2006. Isolates were characterized by pulsed-field gel electrophoresis (PFGE) (n = 302), and multilocus sequence typing (MLST) and PorA and FetA typing were performed on randomly selected isolates (34/302, 11%). In total, 2,400 cases were reported, with the highest numbers from Gauteng Province (1,307/2,400, 54%) and Western Cape Province (393/2,400, 16%); 67% (1,617/2,400) had viable isolates and 19% (307/1,617) were identified as serogroup B. MenB incidence remained stable over time (P = 0.77) (average incidence, 0.13/100,000 population [range, 0.10 to 0.16/100,000 population]). PFGE (302/307, 98%) divided isolates (206/302, 68%) into 13 clusters and 96 outliers. The largest cluster, B1, accounted for 25% of isolates (76/302) over the study period; its prevalence decreased from 43% (20/47) in 2002 to 13% (8/62) in 2006 (P < 0.001), and it was common in the Western Cape (58/76, 76%). Clusters B2 and B3 accounted for 10% (31/302) and 6% (19/302), respectively, and showed no significant change over time and were predominant in Gauteng. Randomly selected isolates from clusters B1, B2, and B3 belonged to CC32, CC41/44, and the new CC4240/6688, respectively. Overall, 15 PorA and 12 FetA types were identified. MenB isolates were mostly diverse with no single dominant clone; however, CC32 and CC41/44 accounted for 35% and the new CC4240/6688 was the third most prevalent clone.