Comparative genomic analyses of multi-drug resistant Mycobacterium tuberculosis from Nepal and other geographical locations.

Nepal exhibits a tuberculosis (TB) incidence rate that is comparable to neighbouring high TB incidence countries. In addition, it records >500 cases of multi-drug resistant (MDR) TB each year. The objective of this study was to perform whole-genome bioinformatic analysis on MDR-TB isolates from Nepal (n = 19) to identify the specific mutations underlying their phenotypic resistance. In addition, we examined the dominant genotype among the Nepal MDR-TB isolates, the East-Asian Beijing sub-lineage, to determine its relatedness to a panel of 1274 genomes of international strains available from public databases. These analyses provided evidence that the XDR-TB isolates in our collection were not derived from importation of primary XDR-TB to Nepal but were more likely the result of acquisition of second-line drug resistance in Nepal. Resistance to fluoroquinolones was detected among a high proportion of the Nepal isolates. This has implications for the management of TB, including appropriate antimicrobial stewardship and susceptibility testing for fluoroquinolones and other second-line TB drugs, to minimise the development of XDR-TB among Nepal TB cases.

Hypoxia-inducible factor and bacterial infections in chronic obstructive pulmonary disease.

COPD is a seriously disabling respiratory condition that inexorably progresses to disability and mortality. It affects approximately 10% of the population globally with a greater prevalence at advanced ages. Airway bacterial infections complicate the disease course in most COPD patients, leading to increased symptoms, more rapid decline in lung function, acute exacerbations and reduced quality of life. With increasing bacterial resistance to antibiotics and adverse effects of conventional treatments, new effective non-antibiotic antimicrobial therapies are urgently needed to manage COPD. Hypoxia-inducible factor (HIF)-1α is an important transcriptional regulator of cellular responses to hypoxia, oxidants and inflammation, and is overexpressed in the lungs of COPD patients. Recent evidence shows that increased HIF-1α expression can upregulate the platelet-activating factor receptor (PAFR) on the airway epithelial surface that is increased in smokers and particularly COPD patients. The receptor is utilized by PAFR-dependent bacteria (Streptococcus pneumoniae, Haemophilus influenzae and Pseudomonas aeruginosa) to induce infection in both the respiratory and gastrointestinal (GI) tracts. However, the importance and mechanism of HIF-1α in augmenting PAFR-dependent bacterial infections in COPD are poorly understood. Here, we review the evidence for the roles of local tissue hypoxia-induced inflammation, HIF-1α and PAFR in facilitating bacterial infections in COPD. Blocking PAFR may provide a novel antimicrobial approach to manage bacterial infections in COPD.

Growing the pool of rural general practitioners.

The critical importance of primary health care in maintaining a healthy population is well established internationally. Nevertheless, general practitioner care is not always easily accessible for some patients in Australia, particularly in rural regions. This is partly due to an insufficient number of medical graduates entering and being retained in the rural general practitioner workforce. Key elements of international and national programs designed to address this shortfall are discussed and include the use of entry requirements that preferentially select for applicants from a rural residence background, and immersion of medical students for a large share, or entire duration, of their training in rural communities. In addition, other factors that can influence decisions to enter and stay in rural practice are discussed.

The Link between Regional Tidal Stretch and Lung Injury during Mechanical Ventilation.

The aim of this study was to assess the association between regional tidal volume (Vt), regional functional residual capacity (FRC), and the expression of genes linked with ventilator-induced lung injury. Two groups of BALB/c mice (n = 8 per group) were ventilated for 2 hours using a protective or injurious ventilation strategy, with free-breathing mice used as control animals. Regional Vt and FRC of the ventilated mice was determined by analysis of high-resolution four-dimensional computed tomographic images taken at baseline and after 2 hours of ventilation and corrected for the volume of the region (i.e., specific [s]Vt and specific [s]FRC). RNA concentrations of 21 genes in 10 different lung regions were quantified using a quantitative PCR array. sFRC at baseline varied regionally, independent of ventilation strategy, whereas sVt varied regionally depending on ventilation strategy. The expression of IL-6 (P = 0.04), Ccl2 (P < 0.01), and Ang-2 (P < 0.05) was associated with sVt but not sFRC. The expression of seven other genes varied regionally (IL-1ß and RAGE [receptor for advanced glycation end products]) or depended on ventilation strategy (Nfe2l2 [nuclear factor erythroid-derived 2 factor 2], c-fos, and Wnt1) or both (TNF-α and Cxcl2), but it was not associated with regional sFRC or sVt. These observations suggest that regional inflammatory responses to mechanical ventilation are driven primarily by tidal stretch.

Streamlining an existing hip fracture patient pathway in an acute tertiary adult Irish hospital to improve patient experience and outcomes.

OBJECTIVE: To improve access for hip fracture patients to surgery within 48 h of presentation to the Emergency Department, and to increase the number of patients receiving pre-operative orthogeriatric review, through streamlining an existing hip fracture patient pathway. DESIGN: A pre-post design involving a multi-disciplinary team use of the Define, Measure, Analyse, Improve and Control framework integral to Lean Six Sigma (LSS) methodology, to assess and adapt the existing hip fracture pathway from presentation to Emergency Department to the initiation of surgery. SETTING: A 600-bed teaching hospital in Ireland. PARTICIPANTS: Nursing, medical, administrative and physiotherapy staff working across Emergency Medicine, Orthogeriatrics and Orthopaedic Specialities and Project management. INTERVENTIONS: LSS methodology was used to redesign an existing pathway, improving patient access to ortho-geriatrician assessment, pain relief and surgery in line with the Irish Hip Fracture Data Base Key performance indicators. MAIN OUTCOME MEASURES: Access to pain relief, access to surgery and volume of patients receiving ortho-geriatric assessment. RESULTS: The percentage of patients undergoing surgery within 48 h of presentation to Emergency Department increased from 55% to 79% at 3 months, and to 85% at 6 months. Improvements were also achieved in the secondary performance metrics relevant to quality of patient care. All care pathway changes were cost neutral. CONCLUSIONS: Hip fracture surgery within 48 h of presentation to hospital is a recognized standard of hip fracture care associated with decreased length of stay and decreased mortality. With respect to this performance metric, this intervention has contributed to improved patient outcomes.

Limitations of the Mycobacterium tuberculosis reference genome H37Rv in the detection of virulence-related loci.

The genome sequence of Mycobacterium tuberculosis strain H37Rv is an important and valuable reference point in the study of M. tuberculosis phylogeny, molecular epidemiology, and drug-resistance mutations. However, it is becoming apparent that use of H37Rv as a sole reference genome in analysing clinical isolates presents some limitations to fully investigating M. tuberculosis virulence. Here, we examine the presence of single locus variants and the absence of entire genes in H37Rv with respect to strains that are responsible for cases and outbreaks of tuberculosis. We discuss how these polymorphisms may affect phenotypic properties of H37Rv including pathogenicity. Based on our observations and those of other researchers, we propose that use of a single reference genome, H37Rv, is not sufficient for the detection and characterisation of M. tuberculosis virulence-related loci. We recommend incorporation of genome sequences of other reference strains, in particular, direct clinical isolates, in such analyses in addition to H37Rv.

Temporal upregulation of host surface receptors provides a window of opportunity for bacterial adhesion and disease.

Host surface receptors provide bacteria with a foothold from which to attach, colonize and, in some cases, invade tissue and elicit human disease. In this review, we discuss several key host receptors and cognate adhesins that function in bacterial pathogenesis. In particular, we examine the elevated expression of host surface receptors such as CEACAM-1, CEACAM-6, ICAM-1 and PAFR in response to specific stimuli. We explore how upregulated receptors, in turn, expose the host to a range of bacterial infections in the respiratory tract. It is apparent that exploitation of receptor induction for bacterial adherence is not unique to one body system, but is also observed in the central nervous, gastrointestinal and urogenital systems. Prokaryotic pathogens which utilize this mechanism for their infectivity include Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis and Escherichia coli. A number of approaches have been used, in both in vitro and in vivo experimental models, to inhibit bacterial attachment to temporally expressed host receptors. Some of these novel strategies may advance future targeted interventions for the prevention and treatment of bacterial disease.

Does upregulated host cell receptor expression provide a link between bacterial adhesion and chronic respiratory disease?

Expression of the platelet-activating factor receptor is upregulated in the respiratory epithelium of smokers and chronic obstructive pulmonary disease patients. We have recently determined that increased expression of PAFr correlates with higher levels of adhesion to human bronchial epithelial cells by non-typable Haemophilus influenzae and Streptococcus pneumoniae which are major bacterial pathogens in acute exacerbations of COPD. In addition, we found that a PAFr antagonist decreased the adhesion of both respiratory bacterial pathogens to non-cigarette exposure control levels. This highlights the possibility that epithelial receptors, that are upregulated in response to cigarette smoke, could be targeted to specifically block chronic bacterial infections of the lower respiratory tract. In this commentary, we explore the question of whether adhesion to a temporally-upregulated host receptor is a common event in chronic bacterial disease, and as such, could represent a putative therapeutic target for blocking infection by respiratory and other pathogens.

Convergence in the Epidemiology and Pathogenesis of COPD and Pneumonia.

Chronic obstructive pulmonary disease (COPD) is one of the main causes of human mortalities globally after heart disease and stroke. There is increasing evidence of an aetiological association between COPD and pneumonia, the leading infectious cause of death globally in children under 5 years. In this review, we discuss the known risk factors of COPD that are also shared with pneumonia including smoking, air pollution, age and immune suppression. We review how lung pathology linked to a previous history of pneumonia may heighten susceptibility to the development of COPD in later life. Furthermore, we examine how specific aspects of COPD immunology could contribute to the manifestation of pneumonia. Based on the available evidence, a convergent relationship is becoming apparent with respect to the pathogenesis of COPD and pneumonia. This has implications for the management of both diseases, and the development of new interventions.

Identification and bioactivity of 3-epi-xestoaminol C isolated from the New Zealand brown alga Xiphophora chondrophylla.

We report here the bioassay-guided isolation of a new 1-deoxysphingoid, 3-epi-xestoaminol C (1), isolated from the New Zealand brown alga Xiphophora chondrophylla. This is the first report of a 1-deoxysphingoid from a brown alga. We describe the isolation and full structure elucidation of this compound, including its absolute configuration, along with its bioactivity against mycobacteria and mammalian cell lines and preliminary mechanism of action studies using yeast chemical genomics.

Vancomycin-resistant Enterococcus faecium and the emergence of new sequence types associated with hospital infection.

Enterococcus faecium is a major species in infections by vancomycin-resistant enterococci (VRE). New variants of the pathogen have emerged and become dominant in healthcare settings. Two such examples, vanB ST796 and vanA ST1421 sequence types, originally arose in Australia and proceeded to cause VRE outbreaks in other countries. Of concern is the detection in Europe of vancomycin variable enterococci (VVE) belonging to ST1421 that exhibit a vancomycin-susceptible phenotype but can revert to resistant in the presence of vancomycin. The recent application of genome sequencing for increasing our understanding of the evolution and spread of VRE is also explored here.

Antibiotic resistance acquisition versus primary transmission in the presentation of extensively drug-resistant tuberculosis.

Mycobacterium tuberculosis is the leading cause of mortality worldwide due to a single bacterial pathogen. Of concern is the negative impact that the COVID-19 pandemic has had on the control of tuberculosis (TB) including drug-resistant forms of the disease. Antimicrobial resistance increases the likelihood of worsened outcomes in TB patients including treatment failure and death. Multidrug-resistant (MDR) strains, resistant to first-line drugs isoniazid and rifampin, and extensively drug-resistant (XDR) strains with further resistance to second-line drugs (SLD), threaten control programs designed to lower TB incidence and end the disease as a public health challenge by 2030, in accordance with UN Sustainable Development Goals. Tackling TB requires an understanding of the pathways through which drug resistance emerges. Here, the roles of acquired resistance mutation, and primary transmission, are examined with regard to XDR-TB. It is apparent that XDR-TB can emerge from MDR-TB through a small number of additional resistance mutations that occur in patients undergoing drug treatment. Rapid detection of resistance, to first-line drugs and SLD, at the initiation of and during treatment, and prompt adjustment of regimens are required to ensure treatment success in these patients. Primary transmission is predicted to make an increasing contribution to the XDR-TB caseload in the future. Much work is required to improve the implementation of the World Health Organization-recommended infection control practices and block onward transmission of XDR-TB patients to contacts including health-care workers. Finally, limiting background resistance to fluoroquinolones in pre-XDR strains of M. tuberculosis will necessitate better antimicrobial stewardship in the broader use of this drug class.

The interface between COVID-19 and bacterial healthcare-associated infections.

BACKGROUND: A wide range of bacterial infections occur in coronavirus disease 2019 (COVID-19) patients, particularly in those with severe coronaviral disease. Some of these are community-acquired co-infections. OBJECTIVE: To review recent data that indicate the occurrence of hospital-onset bacterial infections, including with antibiotic-resistant isolates, in COVID-19 patients. SOURCES: Using PubMed, the literature was searched using terms including: 'COVID-19'; 'SARS-CoV-2'; 'bacterial infection'; 'healthcare-associated infection'; 'antibiotic resistance'; 'antimicrobial resistance'; 'multi-drug resistance'; 'Streptococcus'; 'Staphylococcus'; 'Pseudomonas'; 'Escherichia'; 'Klebsiella'; 'Enterococcus'; 'Acinetobacter'; 'Haemophilus'; 'MRSA'; 'VRE'; 'ESBL'; 'NDM-CRE'; 'CR-Ab'; 'VRSA'; 'MDR'. CONTENT: There is a growing number of reports of bacterial infections acquired by patients with severe COVID-19 after hospital admission. Antibiotic-resistant pathogens found to cause healthcare-associated infections (HAIs) in COVID-19 patients include methicillin-resistant Staphylococcus aureus, New Delhi metallo-ß-lactamase-producing carbapenem-resistant Enterobacterales, carbapenem-resistant Acinetobacter baumannii, extended-spectrum ß-lactamase Klebsiella pneumoniae and vancomycin-resistant enterococci. COVID-19 has impacted bacterial HAIs in a number of ways with an increase in the incidence of New Delhi metallo-ß-lactamase-producing carbapenem-resistant Enterobacterales and carbapenem-resistant A. baumannii reported at some hospital sites compared with before the pandemic. Recommended guidelines for antimicrobial stewardship in COVID-19 patient treatment are discussed regarding minimization of empiric broad-spectrum antibiotic use. Other studies have reported a decrease in methicillin-resistant S. aureus and vancomycin-resistant enterococci cases, which has been attributed to enhanced infection prevention and control practices introduced to minimize intra-hospital spread of COVID-19. IMPLICATIONS: Poorer outcomes have been observed in hospitalized COVID-19 patients with an antibiotic-resistant infection. Although heightened IPC measures have been accompanied by a reduction in some HAIs at specific sites, in other situations, COVID-19 has been associated with an increase in bacterial HAI incidence. Further research is needed to define the cost-benefit relationship of maintaining COVID-19-related infection prevention and control protocols beyond the pandemic to reduce the burden of HAIs. In addition, the longer-term impact of high usage of certain broad-spectrum antibiotics during the COVID-19 pandemic requires evaluation.

Draft genome sequence of a nontypeable Haemophilus influenzae strain used in the study of human respiratory infection.

OBJECTIVES: Nontypeable Haemophilus influenzae (NTHi) is an important human respiratory bacterium that can cause a range of diseases including sinusitis, otitis media, conjunctivitis, pneumonia as well as acute exacerbations of chronic obstructive pulmonary disease (COPD). A number of studies have used NTHi clinical isolate RHH-3 as a laboratory strain for experimentation examining the effect of cigarette smoke and more recently, biomass smoke, on the susceptibility and response of cells lining the respiratory tract to infection. Therefore, definition of the genome content of RHH-3 is required to fully elucidate human-NTHi interactions associated with initial infection and subsequent development of respiratory disease. DATA DESCRIPTION: Here, we present the draft genome sequence of NTHi RHH-3 collected from the sputum of a patient at the Royal Hobart Hospital, Tasmania, Australia. The assembled genome size was 1,839,376 bp consisting of 61 contigs (> 500 bp), with a G+C content of 38.1%. This draft genome data can be accessed at DDBJ/ENA/GenBank under the accession number JADPRR000000000.

Smoking and COVID-19: What we know so far.

The ongoing COVID-19 pandemic has placed a spotlight on infectious diseases and their associations with host factors and underlying conditions. New data on the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus are entering the public domain at a rapid rate such that their distillation often lags behind. To minimise weak associations becoming perceived as established paradigms, it is imperative that methodologies and outputs from different studies are appropriately critiqued and compared. In this review, we examine recent data on a potential relationship between smoking and COVID-19. While the causal role of smoking has been firmly demonstrated in regard to lung cancer and chronic obstructive pulmonary disease, such associations have the benefit of decades' worth of multi-centre epidemiological and mechanistic data. From our analysis of the available studies to date, it appears that a relationship is emerging in regard to patients with a smoking history having a higher likelihood of developing more severe symptoms of COVID-19 disease than non-smokers. Data on whether COVID-19 has a greater incidence in smokers than non-smokers is thus far, contradictory and inconclusive. There is therefore a need for some caution to be exercised until further research has been conducted in a wider range of geographical settings with sufficient numbers of patients that have been carefully phenotyped in respect of smoking status and adequate statistical control for confounding factors.

Targeting the chromosome partitioning protein ParA in tuberculosis drug discovery.

OBJECTIVE: To identify inhibitors of the essential chromosome partitioning protein ParA that are active against Mycobacterium tuberculosis. METHODS: Antisense expression of the parA orthologue MSMEG_6939 was induced on the Mycobacterium smegmatis background. Screening of synthetic chemical libraries was performed to identify compounds with higher anti-mycobacterial activity in the presence of parA antisense. Differentially active compounds were validated for specific inhibition of purified ParA protein from M. tuberculosis (Rv3918c). ParA inhibitors were then characterized for their activity towards M. tuberculosis in vitro. RESULTS: Under a number of culture conditions, parA antisense expression in M. smegmatis resulted in reduced growth. This effect on growth provided a basis for the detection of compounds that increased susceptibility to expression of parA antisense. Two compounds identified from library screening, phenoxybenzamine and octoclothepin, also inhibited the in vitro ATPase activity of ParA from M. tuberculosis. Structural in silico analyses predict that phenoxybenzamine and octoclothepin undergo interactions compatible with the active site of ParA. Octoclothepin exhibited significant bacteriostatic activity towards M. tuberculosis. CONCLUSIONS: Our data support the use of whole-cell differential antisense screens for the discovery of inhibitors of specific anti-tubercular drug targets. Using this approach, we have identified an inhibitor of purified ParA and whole cells of M. tuberculosis.

Experimental models used to study human tuberculosis.

Mycobacterium tuberculosis causes more deaths in humans than any other bacterial pathogen. The most recent data from the World Health Organization reveal that over 9million new cases of tuberculosis occur each year and that the incidence appears to be increasing with population growth. Despite the global burden of tuberculosis, we are still reliant on relatively dated measures to prevent, diagnose, and treat the disease. New, more effective tools are needed to diminish the incidence of tuberculosis. M. tuberculosis lacks a natural host beyond humans and, hence, surrogate models have been employed in the study of the pathogen. The discovery and development of new vaccines, diagnostics, or antitubercular drugs are dependent upon the validity of any experimental model used and its relevance to tuberculosis in humans. In this review, a range of experimental models, from in vitro studies with fast-growing low-pathogenic species of mycobacteria to the infection of nonhuman primates with virulent M. tuberculosis, will be discussed.

Native New Zealand plants with inhibitory activity towards Mycobacterium tuberculosis.

BACKGROUND: Plants have long been investigated as a source of antibiotics and other bioactives for the treatment of human disease. New Zealand contains a diverse and unique flora, however, few of its endemic plants have been used to treat tuberculosis. One plant, Laurelia novae-zelandiae, was reportedly used by indigenous Maori for the treatment of tubercular lesions. METHODS: Laurelia novae-zelandiae and 44 other native plants were tested for direct anti-bacterial activity. Plants were extracted with different solvents and extracts screened for inhibition of the surrogate species, Mycobacterium smegmatis. Active plant samples were then tested for bacteriostatic activity towards M. tuberculosis and other clinically-important species. RESULTS: Extracts of six native plants were active against M. smegmatis. Many of these were also inhibitory towards M. tuberculosis including Laurelia novae-zelandiae (Pukatea). M. excelsa (Pohutukawa) was the only plant extract tested that was active against Staphylococcus aureus. CONCLUSIONS: Our data provide support for the traditional use of Pukatea in treating tuberculosis. In addition, our analyses indicate that other native plant species possess antibiotic activity.