Keeping up with the pathogens: improved antimicrobial resistance detection and prediction from Pseudomonas aeruginosa genomes.

BACKGROUND: Antimicrobial resistance (AMR) is an intensifying threat that requires urgent mitigation to avoid a post-antibiotic era. Pseudomonas aeruginosa represents one of the greatest AMR concerns due to increasing multi- and pan-drug resistance rates. Shotgun sequencing is gaining traction for in silico AMR profiling due to its unambiguity and transferability; however, accurate and comprehensive AMR prediction from P. aeruginosa genomes remains an unsolved problem. METHODS: We first curated the most comprehensive database yet of known P. aeruginosa AMR variants. Next, we performed comparative genomics and microbial genome-wide association study analysis across a Global isolate Dataset (n = 1877) with paired antimicrobial phenotype and genomic data to identify novel AMR variants. Finally, the performance of our P. aeruginosa AMR database, implemented in our AMR detection and prediction tool, ARDaP, was compared with three previously published in silico AMR gene detection or phenotype prediction tools-abritAMR, AMRFinderPlus, ResFinder-across both the Global Dataset and an analysis-naïve Validation Dataset (n = 102). RESULTS: Our AMR database comprises 3639 mobile AMR genes and 728 chromosomal variants, including 75 previously unreported chromosomal AMR variants, 10 variants associated with unusual antimicrobial susceptibility, and 281 chromosomal variants that we show are unlikely to confer AMR. Our pipeline achieved a genotype-phenotype balanced accuracy (bACC) of 85% and 81% across 10 clinically relevant antibiotics when tested against the Global and Validation Datasets, respectively, vs. just 56% and 54% with abritAMR, 58% and 54% with AMRFinderPlus, and 60% and 53% with ResFinder. ARDaP's superior performance was predominantly due to the inclusion of chromosomal AMR variants, which are generally not identified with most AMR identification tools. CONCLUSIONS: Our ARDaP software and associated AMR variant database provides an accurate tool for predicting AMR phenotypes in P. aeruginosa, far surpassing the performance of current tools. Implementation of ARDaP for routine AMR prediction from P. aeruginosa genomes and metagenomes will improve AMR identification, addressing a critical facet in combatting this treatment-refractory pathogen. However, knowledge gaps remain in our understanding of the P. aeruginosa resistome, particularly the basis of colistin AMR.

Treatment Approaches to Mycobacterium abscessus Pulmonary Disease.

Mycobacterium abscessus pulmonary disease is highly antibiotic-resistant, and the current armamentarium of antibiotics yields poor treatment outcomes with significant drug toxicity. Macrolide susceptibility is a key prognostic factor. Optimal drug combinations, duration of therapy, and management of refractory disease are unknown. Surgical resection, performed at centers with experience in surgical management of nontuberculous mycobacterial pulmonary disease, may produce favorable outcomes in select patients. Multiple emerging therapeutic candidates hold promise for more efficacious and tolerable treatment options.

Cystic Fibrosis-Related Nontuberculous Mycobacterial Pulmonary Disease.

Non-tuberculous mycobacteria (NTM) infection is a major cause of morbidity in people with cystic fibrosis (pwCF) with rates of infection increasing worldwide. Accurate diagnosis and decisions surrounding best management remain challenging. Treatment guidelines have been developed to assist physicians in managing NTM in pwCF, but involve prolonged and complex mycobacterial regimens, often associated with significant toxicity. Fortunately, current management and outcomes of NTM in CF are likely to evolve due to improved understanding of disease acquisition, better diagnostics, emerging antimycobacterial therapies, and the widespread uptake of cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapies.

A mariner's tale: Invasive endotracheal Mycobacterium marinum infection.

Mycobacterium marinum is a ubiquitous water-borne non-tuberculous mycobacterial (NTM) pathogen. In humans, M. marinum infections are acquired through direct inoculation of skin wounds and are almost exclusively localized to skin and soft tissues. Pulmonary infection with M. marinum is extremely rare, and to our knowledge, invasive endobronchial disease has not been reported. Here, we present a case of a 71-year-old immunocompetent male surfer with invasive endotracheal M. marinum granulomatous disease. The patient was successfully cured with a regimen of azithromycin 250 mg daily, ethambutol 900 mg (15 mg/kg) daily and rifampicin 600 mg daily for 12 months following culture conversion. This case highlights several important concepts: Firstly, M. marinum infection, including invasive endobronchial infection, should be considered a rare cause of NTM pulmonary disease. Secondly, endotracheal infection can be successfully eradicated with this selected therapeutic regimen. Finally, the absence of M. marinum skin or soft-tissue infection in this patient, raises the possibility that human disease might also be acquired via inhalation of M. marinum contaminated water in rare circumstances.

Rapid fluoroquinolone resistance detection in Pseudomonas aeruginosa using mismatch amplification mutation assay-based real-time PCR.

Background. Antimicrobial resistance (AMR) is an ever-increasing global health concern. One crucial facet in tackling the AMR epidemic is earlier and more accurate AMR diagnosis, particularly in the dangerous and highly multi-drug-resistant ESKAPE pathogen, Pseudomonas aeruginosa.Objectives. We aimed to develop two SYBR Green-based mismatch amplification mutation assays (SYBR-MAMAs) targeting GyrA T83I (gyrA248) and GyrA D87N, D87Y and D87H (gyrA259). Together, these variants cause the majority of fluoroquinolone (FQ) AMR in P. aeruginosa.Methods. Following assay validation, the gyrA248 and gyrA259 SYBR-MAMAs were tested on 84 Australian clinical P. aeruginosa isolates, 46 of which demonstrated intermediate/full ciprofloxacin resistance according to antimicrobial susceptibility testing.Results. Our two SYBR-MAMAs correctly predicted an AMR phenotype in the majority (83%) of isolates with intermediate/full FQ resistance. All FQ-sensitive strains were predicted to have a sensitive phenotype. Whole-genome sequencing confirmed 100 % concordance with SYBR-MAMA genotypes.Conclusions. Our GyrA SYBR-MAMAs provide a rapid and cost-effective method for same-day identification of FQ AMR in P. aeruginosa. An additional SYBR-MAMA targeting the GyrB S466Y/S466F variants would increase FQ AMR prediction to 91 %. Clinical implementation of our assays will permit more timely treatment alterations in cases where decreased FQ susceptibility is identified, leading to improved patient outcomes and antimicrobial stewardship.

Express Yourself: Quantitative Real-Time PCR Assays for Rapid Chromosomal Antimicrobial Resistance Detection in Pseudomonas aeruginosa.

The rise of antimicrobial-resistant (AMR) bacteria is a global health emergency. One critical facet of tackling this epidemic is more rapid AMR diagnosis in serious multidrug-resistant pathogens like Pseudomonas aeruginosa. Here, we designed and then validated two multiplex quantitative real-time PCR (qPCR) assays to simultaneously detect differential expression of the resistance-nodulation-division efflux pumps MexAB-OprM, MexCD-OprJ, MexEF-OprN, and MexXY-OprM, the AmpC ß-lactamase, and the porin OprD, which are commonly associated with chromosomally encoded AMR. Next, qPCRs were tested on 15 sputa from 11 participants with P. aeruginosa respiratory infections to determine AMR profiles in vivo. We confirmed multiplex qPCR testing feasibility directly on sputa, representing a key advancement in in vivo AMR diagnosis. Notably, comparison of sputa with their derived isolates grown in Luria-Bertani broth (±2.5% NaCl) or a 5-antibiotic cocktail showed marked expression differences, illustrating the difficulty in replicating in vivo expression profiles in vitro. Cystic fibrosis sputa showed significantly reduced mexE and mexY expression compared with chronic obstructive pulmonary disease sputa, despite harboring fluoroquinolone- and aminoglycoside-resistant strains, indicating that these loci do not contribute to AMR in vivo. oprD was also significantly downregulated in cystic fibrosis sputa, even in the absence of contemporaneous carbapenem use, suggesting a common adaptive trait in chronic infections that may affect carbapenem efficacy. Sputum ampC expression was highest in participants receiving carbapenems (6.7 to 15×), some of whom were simultaneously receiving cephalosporins, the latter of which would be rendered ineffective by the upregulated ampC. Our qPCR assays provide valuable insights into the P. aeruginosa resistome, and their use on clinical specimens will permit timely treatment alterations that will improve patient outcomes and antimicrobial stewardship measures.

Genomic diversity and antimicrobial resistance of Prevotella species isolated from chronic lung disease airways.

Cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) are characterized by increasingly frequent acute pulmonary exacerbations that reduce life quality and length. Human airways are home to a rich polymicrobial environment, which includes members of the obligately anaerobic genus Prevotella. Despite their commonness, surprisingly little is known about the prevalence, role, genomic diversity and antimicrobial resistance (AMR) potential of Prevotella species and strains in healthy and diseased airways. Here, we used comparative genomics to develop a real-time PCR assay to permit rapid Prevotella species identification and quantification from cultures and clinical specimens. Assay specificity was validated across a panel of Prevotella and non-Prevotella species, followed by PCR screening of CF and COPD respiratory-derived cultures. Next, 35 PCR-positive isolates were subjected to whole-genome sequencing. Of eight identified Prevotella species, P. histicola, P. melaninogenica, P. nanceiensis, P. salivae and P. denticola overlapped between participant cohorts. Phylogenomic analysis revealed considerable interhost but limited intrahost diversity, suggesting patient-specific lineages in the lower airways, probably from oral cavity aspirations. Correlation of phenotypic AMR profiles with AMR genes identified excellent correlation between tetQ presence and decreased doxycycline susceptibility, and ermF presence and decreased azithromycin susceptibility and clindamycin resistance. AMR rates were higher in the CF isolates, reflecting greater antibiotic use in this cohort. All tested Prevotella isolates were tobramycin-resistant, providing a potential selection method to improve Prevotella culture retrieval rates. Our addition of 35 airway-derived Prevotella genomes to public databases will enhance ongoing efforts to unravel the role of this diverse and enigmatic genus in both diseased and healthy lungs.

Performance of myositis-specific antibodies detected on myositis line immunoassay to diagnose and sub-classify patients with suspected idiopathic inflammatory myopathy, a retrospective records-based review.

AIM: To evaluate myositis line immunoassay (LIA) for diagnosis and sub-classification of suspected idiopathic inflammatory myopathy (IIM). To investigate if test performance is improved by increasing signal strength cut-off for myositis-specific antibody (MSA) or combining MSA with indirect immunofluorescence (IIF). METHODS: A retrospective, consecutive case series of patients investigated for MSAs from June 2013 to June 2020 for suspected IIM. Specificity, sensitivity, positive predictive value, and negative predictive value were calculated with 95% confidence intervals for diagnosis of IIM. Association of IIM diagnosis with increased signal strength and presence of an expected IIF pattern on Hep-2 cells was assessed by Fisher's exact test in MSA-positive patients. RESULTS: A total of 195 patients were evaluated. IIM was diagnosed in 32/195 (16.4%) patients. MSAs were detected in 41/195 (21%) patients, 18/41 (43.9%) patients with an MSA had a diagnosis of IIM. The probability of an IIM diagnosis was increased in MSA-positive patients with high compared with low signal strength (83.3% vs 43.5%; P = 0.01) and an expected compared with unexpected IIF pattern (61.5% vs 23.8%; P = 0.04). Specificity for IIM was not significantly improved by increasing signal strength cut-off (85.9% vs 93.8%). Positive predictive value of myositis LIA was only modest and not significantly improved by either increasing signal strength cut-off or requiring an expected IIF pattern for determination of MSA positivity (43.9% vs 60% vs 61.5%). Sub-classification of IIM correlated closely for respective MSAs (88.9%). CONCLUSION: Increased MSA signal strength on myositis LIA and the presence of an expected IIF pattern were associated with IIM diagnosis. Test performance was non-significantly improved by these methods. Prevalence of IIM in this patient cohort was low; it is not excluded that LIA performance could be improved by these methods in a higher prevalence cohort.

Mobile phone use is associated with higher smallholder agricultural productivity in Tanzania, East Africa.

Mobile phone use is increasing in Sub-Saharan Africa, spurring a growing focus on mobile phones as tools to increase agricultural yields and incomes on smallholder farms. However, the research to date on this topic is mixed, with studies finding both positive and neutral associations between phones and yields. In this paper we examine perceptions about the impacts of mobile phones on agricultural productivity, and the relationships between mobile phone use and agricultural yield. We do so by fitting multilevel statistical models to data from farmer-phone owners (n = 179) in 4 rural communities in Tanzania, controlling for site and demographic factors. Results show a positive association between mobile phone use for agricultural activities and reported maize yields. Further, many farmers report that mobile phone use increases agricultural profits (67% of respondents) and decreases the costs (50%) and time investments (47%) of farming. Our findings suggest that there are opportunities to target policy interventions at increasing phone use for agricultural activities in ways that facilitate access to timely, actionable information to support farmer decision making.

COVID-19 in a complex obstetric patient with cystic fibrosis.

We report the first case of COVID-19 in a pregnant patient with cystic fibrosis. We describe the diagnosis, clinical course and management of the patient and their family with regards to clinical, social and infection control measures around delivery. This case highlights the importance of the cooperation of multidisciplinary teams to achieve good clinical outcomes in complex patients with COVID-19.

Detailed Polysomnography in Australian Vietnam Veterans With and Without Posttraumatic Stress Disorder.

STUDY OBJECTIVES: Recent results from the PTSD Initiative, a cross-sectional cohort study in Australian Vietnam veterans (VV) with and without posttraumatic stress disorder (PTSD), demonstrated an increased prevalence of self-reported sleep disturbances in those with PTSD. This study aimed to objectively assess the prevalence of sleep disorders in the same cohort using detailed polysomnography (PSG). METHODS: Participants from the PTSD Initiative were recruited to undergo PSG. PTSD status was determined with the Clinician Administered PTSD Scale for DSM-5 (CAPS-5). Subjective sleep information was attained via structured questionnaires. Data from single night PSG were compared between trauma-exposed VV with and without PTSD. RESULTS: A total of 74 trauma-exposed male VV (40 with PTSD) underwent PSG (prospective n = 59, retrospective n = 15). All PSG parameters were similar between groups. No difference was seen in PSG-diagnosed obstructive sleep apnea (OSA) or periodic limb movements of sleep (PLMS). VV with PTSD showed a trend toward increased duration of sleep with oxygen saturations < 90% (10% versus 1.8%; P = .07). VV with PTSD reported increased sleep onset latency (42.4 versus 13.3 minutes; P < .01); were less likely to report sleeping well (32.5% versus 67.5%; P < .01); had higher OSA risk using Berlin Questionnaire (BQ) (70% versus 38.2%; P < .01); and had higher rates of partner-reported limb movements (56.4% versus 17.6%; P < .01). No association between PSG-diagnosed OSA and PTSD severity was evident. CONCLUSIONS: In Australian VV with and without PTSD, no difference was seen across all PSG parameters including the diagnosis and severity of OSA and PLMS. However, VV with PTSD demonstrated an increased perception of sleep disturbances.

Sleep Disturbances in Australian Vietnam Veterans With and Without Posttraumatic Stress Disorder.

STUDY OBJECTIVES: Posttraumatic stress disorder (PTSD) is a condition that may develop after a traumatic event, particularly combat-related trauma. Although sleep disturbance is a hallmark of PTSD, the prevalence of sleep disturbances in Australian veterans with PTSD remains uncertain. This study aimed to subjectively compare the prevalence of sleep disturbances in Australian Vietnam veterans with and without PTSD. METHODS: A cross-sectional cohort study compared trauma-exposed Australian Vietnam veterans with and without PTSD. PTSD diagnosis was confirmed using the Clinician Administered PTSD Scale for DSM-5. Sleep information was evaluated using supervised structured questionnaires, including Epworth Sleepiness Scale (ESS) and Berlin and Mayo Questionnaires. RESULTS: Two hundred fourteen male Vietnam veterans (108 with PTSD) were included. Participants with PTSD had higher body mass index (30.3 versus 29 kg/m2; P < .05), higher ESS score (9.2 versus 7.6; P < .05), and increased alcohol or medication use to assist with sleep (19% versus 6%; P < .01; and 44% versus 14%; P < .01). Those with PTSD were less likely to sleep well (32% versus 72%; P < .01) and reported higher rates of restless legs (45% versus 25%; P < .01), nightmares (91% versus 29%; P < .01), nocturnal screaming (73% versus 18%; P < .01), sleep terrors (61% versus 13%; P < .01) and dream enactment (78% versus 11.8%; P < .01). The PTSD group had higher rates of diagnosed OSA (42% versus 21%; P < .01) and an increased risk of OSA on the Berlin Questionnaire (69% versus 43%; P < .01). CONCLUSIONS: Compared to trauma-exposed controls, Australian Vietnam veterans with PTSD demonstrated an increased prevalence of a wide range of sleep disturbances, including OSA. In veterans with PTSD, detailed sleep assessment, including consideration of polysomnography, is paramount.

Pulmonary schistosomiasis mimicking IgG4-related lung disease.

IgG4-related disease (IgG4-RD) is a systemic fibroinflammatory disease characterized by tumefactive lesions in various organ systems, including the lungs. Clinical and radiological manifestations of IgG4-RD are relatively non-specific, and we report a case highlighting the importance of histopathological confirmation in cases of suspected IgG4-related lung disease. A 44-year-old male with significantly elevated serum IgG4 levels, patchy consolidation on thoracic CT imaging, and cough was referred with suspected IgG4-related lung disease. However, surgical lung biopsy revealed an unexpected diagnosis of pulmonary schistosomiasis, and following treatment with praziquantel, cough resolved and IgG4 levels significantly declined. This case highlights the potentially diverse array of conditions that may mimic IgG4-related lung disease and the importance of comprehensive evaluation including histopathological confirmation where possible.

Artificial stone-associated silicosis: a rapidly emerging occupational lung disease.

INTRODUCTION: Artificial stone is an increasingly popular material used to fabricate kitchen and bathroom benchtops. Cutting and grinding artificial stone is associated with generation of very high levels of respirable crystalline silica, and the frequency of cases of severe silicosis associated with this exposure is rapidly increasing. AIM: To report the characteristics of a clinical series of Australian workers with artificial stone-associated silicosis. METHODS: Respiratory physicians voluntarily reported cases of artificial stone-associated silicosis identified in their clinical practices. Physicians provided information including occupational histories, respiratory function tests, chest radiology and histopathology reports, when available. RESULTS: Seven male patients were identified with a median age of 44 years (range 26-61). All were employed in small kitchen and bathroom benchtop fabrication businesses with an average of eight employees (range 2-20). All workplaces primarily used artificial stone, and dust control measures were poor. All patients were involved in dry cutting artificial stone. The median duration of exposure prior to symptoms was 7 years (range 4-10). Six patients demonstrated radiological features of progressive massive fibrosis. These individuals followed up over a median follow-up period of 16 months (IQR 21 months) demonstrated rapid decline in prebronchodilator forced expiratory volume in 1 s of 386 mL/year (SD 204 mL) and forced vital capacity of 448 mL/year (SD 312 mL). CONCLUSIONS: This series of silicosis in Australian workers further demonstrates the risk-associated high-silica content artificial stone. Effective dust control and health surveillance measures need to be stringently implemented and enforced in this industry.

Mycobacterium shimoidei, a Rare Pulmonary Pathogen, Queensland, Australia.

Nontuberculous mycobacteria are human pathogens with increasing incidence and prevalence worldwide. Mycobacterium shimoidei is a rare cause of pulmonary disease, with only 15 cases previously reported. This series documents an additional 23 cases of M. shimoidei from Queensland, Australia, and highlights the pathogenicity and clinical role of this species.

A stonemason with accelerated silicosis in the setting of tumour necrosis factor alpha inhibitor therapy.

We present the case of a 26-year-old stonemason with accelerated silicosis in the setting of treatment for psoriasis with the tumour necrosis factor alpha (TNF-alpha) inhibitor adalimumab. Accelerated silicosis is an important occupational lung disease with a poor prognosis and limited treatment options [1]. Although the exact pathogenesis remains unknown, it is suggested that secretion of cytokines, including TNF-alpha, plays a central role in disease progression [1,2]. Importantly, however, TNF-alpha inhibitors, in addition to resulting in an increased risk of infection, are also now being seen to cause interstitial lung disease [3,4]. To our knowledge, this is the first documented patient to develop silicosis whilst on TNF-alpha inhibitor therapy. This case challenges the theory behind TNF-alpha's exact role in the pathogenesis of silicosis and lung fibrosis, highlights the importance of monitoring individuals with both occupational and drug exposures, and illustrates the increasing difficulties physicians face in investigating patients with pulmonary infiltrates and multiple possible aetiologies.

Mobile Phone Use and Human-Wildlife Conflict in Northern Tanzania.

Throughout the developing world, mobile phones are spreading rapidly into rural areas where subsistence livelihoods, biodiversity conservation, and human-wildlife conflict (HWC) are each common. Despite this trend, little is known about the relationship between mobile phones and HWC in conservation landscapes. This paper examines this relationship within ethnically Maasai communities in northern Tanzania on the border of Tarangire National Park. Mixed qualitative and quantitative methods of data collection and analysis are used to (1) describe how Maasai agro-pastoralists use phones to manage human-wildlife interactions; and (2) assess the relationship between phone use and measures of HWC, controlling for other factors. The findings indicate that households use phones to reduce the number and severity of HWC events and that the relationship between phones and HWC varies according to the type of HWC.

Use of single large or several small policies as strategies to manage people-park interactions.

Biodiversity conservation has been criticized for undermining or ignoring social well-being. Currently efforts to mutually promote social justice, rural development, and biodiversity conservation, which have been contentious and yielded mixed results, continue to spread despite a general dearth of effective management strategies. We contend that social and economic concerns should be integral to conservation planning and propose that the scale of these phenomena is also critical. To evaluate the merit of this proposal, we adopted and expanded a conservation management strategy framework developed by Joel Heinen and examined how population density, economic disparity, and ethnic heterogeneity vary spatially surrounding 2 contrasting protected areas in East Africa: Kibale National Park in Uganda and Tarangire National Park in Tanzania. Analyses of demographic, wealth, and ethnicity data from regional censuses and household surveys conducted in 2009 and 2010 indicated that choice of scale (landscape or community) changed the management strategies recommended by the model. Therefore, "several small" people-park management strategies varying around a given protected area may be more appropriate than a "single large" people-park strategy applied across an entire protected area. Correspondingly, scale adjusted Heinen recommendations offered new strategies for effective conservation management within these human landscapes not incorporated in current in situ management plans.

Livelihood Diversification and Shifting Social Networks of Exchange: A Social Network Transition?

In the developing world, traditional social networks of exchange and reciprocity are critical components of household security, disaster relief, and social wellbeing especially in rural areas. This research asks the question: How are traditional social networks of exchange related to emerging household strategies to diversify livelihoods? Within this context, this study uses a mixed methods design to examine the character of inter-household exchanges of material goods (IHE) and the association between IHE and livelihood diversification, in ethnically Maasai communities in northern Tanzania. Findings show that IHE are both evolving and declining and are negatively associated with livelihood diversification.