HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities.

Shotgun metagenomics is a powerful tool to identify antimicrobial resistance (AMR) genes in microbiomes but has the limitation that extrachromosomal DNA, such as plasmids, cannot be linked with the host bacterial chromosome. Here we present a comprehensive laboratory and bioinformatics pipeline HAM-ART (Hi-C Assisted Metagenomics for Antimicrobial Resistance Tracking) optimised for the generation of metagenome-assembled genomes including both chromosomal and extrachromosomal AMR genes. We demonstrate the performance of the pipeline in a study comparing 100 pig faecal microbiomes from low- and high-antimicrobial use pig farms (organic and conventional farms). We found significant differences in the distribution of AMR genes between low- and high-antimicrobial use farms including a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial use farms in three species of Lactobacilli. The bioinformatics pipeline code is available at https://github.com/lkalmar/HAM-ART.

Multiclonal human origin and global expansion of an endemic bacterial pathogen of livestock.

Most new pathogens of humans and animals arise via switching events from distinct host species. However, our understanding of the evolutionary and ecological drivers of successful host adaptation, expansion, and dissemination are limited. Staphylococcus aureus is a major bacterial pathogen of humans and a leading cause of mastitis in dairy cows worldwide. Here we trace the evolutionary history of bovine S. aureus using a global dataset of 10,254 S. aureus genomes including 1,896 bovine isolates from 32 countries in 6 continents. We identified 7 major contemporary endemic clones of S. aureus causing bovine mastitis around the world and traced them back to 4 independent host-jump events from humans that occurred up to 2,500 y ago. Individual clones emerged and underwent clonal expansion from the mid-19th to late 20th century coinciding with the commercialization and industrialization of dairy farming, and older lineages have become globally distributed via established cattle trade links. Importantly, we identified lineage-dependent differences in the frequency of host transmission events between humans and cows in both directions revealing high risk clones threatening veterinary and human health. Finally, pangenome network analysis revealed that some bovine S. aureus lineages contained distinct sets of bovine-associated genes, consistent with multiple trajectories to host adaptation via gene acquisition. Taken together, we have dissected the evolutionary history of a major endemic pathogen of livestock providing a comprehensive temporal, geographic, and gene-level perspective of its remarkable success.

Advancing the quantitative characterization of farm animal welfare.

Animal welfare is usually excluded from life cycle assessments (LCAs) of farming systems because of limited consensus on how to measure it. Here, we constructed several LCA-compatible animal-welfare metrics and applied them to data we collected from 74 diverse breed-to-finish systems responsible for 5% of UK pig production. Some aspects of metric construction will always be subjective, such as how different aspects of welfare are aggregated, and what determines poor versus good welfare. We tested the sensitivity of individual farm rankings, and rankings of those same farms grouped by label type (memberships of quality-assurance schemes or product labelling), to a broad range of approaches to metric construction. We found farms with the same label types clustered together in rankings regardless of metric choice, and there was broad agreement across metrics on the rankings of individual farms. We found woodland and Organic systems typically perform better than those with no labelling and Red tractor labelling, and that outdoor-bred and outdoor-finished systems perform better than indoor-bred and slatted-finished systems, respectively. We conclude that if our goal is to identify relatively better and worse farming systems for animal welfare, exactly how LCA welfare metrics are constructed may be less important than commonly perceived.

Predicting effects of multiple interacting global change drivers across trophic levels.

Global change encompasses many co-occurring anthropogenic drivers, which can act synergistically or antagonistically on ecological systems. Predicting how different global change drivers simultaneously contribute to observed biodiversity change is a key challenge for ecology and conservation. However, we lack the mechanistic understanding of how multiple global change drivers influence the vital rates of multiple interacting species. We propose that reaction norms, the relationships between a driver and vital rates like growth, mortality, and consumption, provide insights to the underlying mechanisms of community responses to multiple drivers. Understanding how multiple drivers interact to affect demographic rates using a reaction-norm perspective can improve our ability to make predictions of interactions at higher levels of organization-that is, community and food web. Building on the framework of consumer-resource interactions and widely studied thermal performance curves, we illustrate how joint driver impacts can be scaled up from the population to the community level. A simple proof-of-concept model demonstrates how reaction norms of vital rates predict the prevalence of driver interactions at the community level. A literature search suggests that our proposed approach is not yet used in multiple driver research. We outline how realistic response surfaces (i.e., multidimensional reaction norms) can be inferred by parametric and nonparametric approaches. Response surfaces have the potential to strengthen our understanding of how multiple drivers affect communities as well as improve our ability to predict when interactive effects emerge, two of the major challenges of ecology today.

A Markovian arrival stream approach to stochastic gene expression in cells.

We analyse a generalisation of the stochastic gene expression model studied recently in Fromion et al. (SIAM J Appl Math 73:195-211, 2013) and Robert (Probab Surv 16:277-332, 2019) that keeps track of the production of both mRNA and protein molecules, using techniques from the theory of point processes, as well as ideas from the theory of matrix-analytic methods. Here, both the activity of a gene and the creation of mRNA are modelled with an arbitrary Markovian Arrival Process governed by finitely many phases, and each mRNA molecule during its lifetime gives rise to protein molecules in accordance with a Poisson process. This modification is important, as Markovian Arrival Processes can be used to approximate many types of point processes on the nonnegative real line, meaning this framework allows us to further relax our assumptions on the overall process of transcription.

Historical Lattice Trees.

We prove that the rescaled historical processes associated to critical spread-out lattice trees in dimensions d>8 converge to historical Brownian motion. This is a functional limit theorem for measure-valued processes that encodes the genealogical structure of the underlying random trees. Our results are applied elsewhere to prove that random walks on lattice trees, appropriately rescaled, converge to Brownian motion on super-Brownian motion.

Natural ballistic gelatine ultrasound phantoms are suitable to be used for student education and can be produced cheaply and effectively.

Practical experience in ultrasonography at medical and veterinary schools is difficult to achieve using live models due to ethical considerations. A solution to this problem has been the creation of synthetic ultrasound phantoms that allow simulation of both ultrasound scans and ultrasound-guided procedures. Whilst commercially available phantoms are expensive in a resource-limited environment, it would be desirable to create affordable, reusable, homemade phantoms which could be used to aid student learning. Recent studies have indicated that ballistic gelatine is an excellent material for this. A prospective, experimental study was performed with three ultrasound phantoms for student use. Vascular, bladder, and liver parenchymal models were produced with a natural ballistic gel, along with instructions for their construction and maintenance. Model efficacy was evaluated by assessing students' performance in completing a set of tasks when performing ultrasound on a dog. Group one received training with the models, group two received prior training without the models and the group three received no training. Entry and exit questionnaires assessed students' confidence in ultrasound scanning having used the models. Student questionnaires showed that students enjoyed using the models and found them more useful than existing teaching aids. It was also found that the models produced better practical skills in students that trained with them, in comparison to existing teaching. The models were easy to make, produced good images, and are reusable.

COPD is associated with increased pro-inflammatory CD28null CD8 T and NKT-like cells in the small airways.

We previously showed increased steroid-resistant CD28null CD8+ senescent lymphocyte subsets in the peripheral blood from patients with chronic obstructive pulmonary disease (COPD). These cells expressed decreased levels of the glucocorticoid receptor (GCR), suggesting their contribution to the steroid-resistant property of these cells. COPD is a disease of the small airways (SA). We, therefore, hypothesized that there would be a further increase in these steroid-resistant lymphocytes in the lung, particularly in the SA. We further hypothesized that the pro-inflammatory/cytotoxic potential of these cells could be negated using prednisolone with low-dose cyclosporin A. Blood, bronchoalveolar lavage, large proximal, and small distal airway brushings were collected from 11 patients with COPD and 10 healthy aged-matched controls. The cytotoxic mediator granzyme b, pro-inflammatory cytokines IFNγ/TNFα, and GCR were determined in lymphocytes subsets before and after their exposure to 1µM prednisolone and/or 2.5 ng/mL cyclosporin A. Particularly in the SA, COPD subjects showed an increased percentage of CD28null CD8 T-cells and NKT-like cells, with increased expression of granzyme b, IFNγ and TNFα and a loss of GCR, compared with controls. Significant negative correlations between SA GCR expression and IFNγ/TNFα production by T and NKT-like cells (eg, T-cell IFNγ R = -0.834, P = 0.031) and with FEV1 (R = -0.890) were shown. Cyclosporine A and prednisolone synergistically increased GCR expression and inhibited pro-inflammatory cytokine production by CD28null CD8- T and NKT-like cells. COPD is associated with increased pro-inflammatory CD28null CD8+ T and NKT-like cells in the SA. Treatments that increase GCR in these lymphocyte subsets may improve the efficacy of clinical treatment.

Genomic insights of beta-lactamase producing Klebsiella quasipneumoniae subsp. similipneumoniae belonging to sequence type 1699 from retail market fish, India.

Klebsiella quasipneumoniae is a recently described species and often misidentified as Klebsiella pneumoniae. Here, we report the genomic characterization of Klebsiella quasipneumoniae subsp. similipneumoniae (India238 strain) isolated from fish. The annotated genome acknowledged the presence of blaCTX-M-15, blaOKP-B-1, fosA5, oqxAB and virulence genes. The strain with ST1699 and serotypes KL52 and OL103 also harboured insertion sequences (ISs): ISKpn26 and ISEc9. Three complete phage genomes were identified in contigs 1 and 6 of the bacterial genome, enhancing the prospects of genome manipulation. The study highlights the pitfall of conventional microbiological identification methods to distinguish K. pneumoniae and K. quasipneumoniae. This is the first Indian study documenting the incidence of extended-spectrum beta-lactamase (ESBL)-producing K. quasipneumoniae subsp. similipneumoniae from a non-clinical environment, equipped with virulomes and associated mobile genetic elements. Given that fish can act as a potential vector for transmission of antimicrobial resistance genes, our findings have paramount importance on human health.

Comparative Analysis of Rural-Urban Definitions in Predicting Surgeon Workforce Supply.

BACKGROUND: There are multiple different systems that define a rural area in health services research, but few studies compare their ability to measure access to health resources. Our objective was to compare various definitions of rurality to determine which system best measures local surgeon supply. MATERIALS AND METHODS: In this retrospective observational study, we used the 2019 Area Health Resource File to obtain the 2017 county-level supply of general surgeons, surgical subspecialists, and total physicians for all counties in the United States. Physicians per 100,000 population were calculated for each physician measure and were the primary outcomes. The rural-urban measurements included were the Office of Management and Budget 2017 definition, Urban Influence Codes (UIC), Rural-Urban Commuting Codes (RUCCs), and Census urban population within the county. We also developed and tested a measure combining the RUCCs and Census urban population. Linear regression was used to compare performance of these definitions for each outcome using adjusted R2 values. RESULTS: In 3138 counties included in the study, dichotomous measures of rural-urban using the UIC/RUCC had the lowest adjusted R2 values across all outcomes. Quartiles using the Census urban population and the RUCC/Census urban population combined measure had the highest adjusted R2 values for all outcomes. CONCLUSIONS: The Census urban population had the best performance in measuring geographic access to surgical care. This study can inform surgical health services researchers who want to include measures of rurality in their analysis.

Temporal Changes in Treatment Patterns for Rural and Urban Patients With Early-Stage Non-Small Cell Lung Cancer.

BACKGROUND Our objectives were to evaluate geographic access to lung cancer treatment modalities in North Carolina and to characterize how practice patterns are changing over time. We hypothesized that rural patients would be less likely to undergo treatment compared to urban patients, with widening disparities over time.METHODS We identified patients with Stage I non-small cell lung cancer (NSCLC) from 2006 to 2015 using the North Carolina Central Cancer Registry linked with Medicaid, Medicare, and private insurance claims. The primary outcome was first-course treatment: surgery, radiation, or no treatment. Calendar years were split into earlier (2006-2010) and later (2011-2015) periods. We estimated the adjusted odds ratio (OR) of rural/urban status and time period with 1) surgery and 2) any treatment (surgery or radiation) using multivariable logistic regression.RESULTS Among 5504 patients, 3206 (58%) underwent surgery as initial therapy, 1309 (24%) received radiation as initial therapy, and 989 (18%) had no therapy. There were no rural-urban disparities in treatment patterns. For rural and urban patients, the odds of surgery decreased over time and the odds of radiation increased. We also found that only 48% of those receiving no treatment ever reached a surgeon or radiation oncologist.LIMITATIONS This was an insured, single-state population. Treatment preferences are unknown.CONCLUSIONS Among all treated patients, whether urban or rural, there was increasing use of radiation and decreasing use of surgery over time. Many patients without treatment never had a consultation with a surgeon/radiation oncologist, and this is an actionable target for improving treatment access for early-stage NSCLC.

Short-term inhalation exposure evaluations of airborne antibiotic resistance genes in environments.

Antibiotic resistance is a sword of Damocles that hangs over humans. In regards to airborne antibiotic resistance genes (AARGs), critical knowledge gaps still exist in the identification of hotspots and quantification of exposure levels in different environments. Here, we have studied the profiles of AARGs, mobile genetic elements (MGEs) and bacterial communities in various atmospheric environments by high throughput qPCR and 16S rRNA gene sequencing. We propose a new AARGs exposure dose calculation that uses short-term inhalation (STI). Swine farms and hospitals were high-risk areas where AARGs standardised abundance was more abundant than suburbs and urban areas. Additionally, resistance gene abundance in swine farm worker sputum was higher than that in healthy individuals in other environments. The correlation between AARGs with MGEs and bacteria was strong in suburbs but weak in livestock farms and hospitals. STI exposure analysis revealed that occupational intake of AARGs (via PM10) in swine farms and hospitals were 110 and 29 times higher than in suburbs, were 1.5 × 104, 5.6 × 104 and 5.1 × 102 copies, i.e., 61.9%, 75.1% and 10.7% of the overall daily inhalation intake, respectively. Our study comprehensively compares environmental differences in AARGs to identify high-risk areas, and forwardly proposes the STI exposure dose of AARGs to guide risk assessment.

Rural representation of the surveillance, epidemiology, and end results database.

PURPOSE: SEER data are widely used to study rural-urban disparities in cancer. However, no studies have directly assessed how well the rural areas covered by SEER represent the broader rural United States. METHODS: Public data sources were used to calculate county level measures of sociodemographics, health behaviors, health access and all cause cancer incidence. Driving time from each census tract to nearest Commission on Cancer certified facility was calculated and analyzed in rural SEER and non-SEER areas. RESULTS: Rural SEER and non-SEER counties were similar with respect to the distribution of age, race, sex, poverty, health behaviors, provider density, and cancer screening. Overall cancer incidence was similar in rural SEER vs non-SEER counties. However, incidence for White, Hispanic, and Asian patients was higher in rural SEER vs non-SEER counties. Unadjusted median travel time was 53 min (IQR 34-82) in rural SEER tracts and 54 min (IQR 35-82) in rural non-SEER census tracts. Linear modeling showed shorter travel times across all levels of rurality in SEER vs non-SEER census tracts when controlling for region (Large Rural: 13.4 min shorter in SEER areas 95% CI 9.1;17.6; Small Rural: 16.3 min shorter 95% CI 9.1;23.6; Isolated Rural: 15.7 min shorter 95% CI 9.9;21.6). CONCLUSIONS: The rural population covered by SEER data is comparable to the rural population in non-SEER areas. However, patients in rural SEER regions have shorter travel times to care than rural patients in non-SEER regions. This needs to be considered when using SEER-Medicare to study access to cancer care.

Predicting moisture content during maize nixtamalization using machine learning with NIR spectroscopy.

KEY MESSAGE: Moisture content during nixtamalization can be accurately predicted from NIR spectroscopy when coupled with a support vector machine (SVM) model, is strongly modulated by the environment, and has a complex genetic architecture. Lack of high-throughput phenotyping systems for determining moisture content during the maize nixtamalization cooking process has led to difficulty in breeding for this trait. This study provides a high-throughput, quantitative measure of kernel moisture content during nixtamalization based on NIR scanning of uncooked maize kernels. Machine learning was utilized to develop models based on the combination of NIR spectra and moisture content determined from a scaled-down benchtop cook method. A linear support vector machine (SVM) model with a Spearman's rank correlation coefficient of 0.852 between wet laboratory and predicted values was developed from 100 diverse temperate genotypes grown in replicate across two environments. This model was applied to NIR spectra data from 501 diverse temperate genotypes grown in replicate in five environments. Analysis of variance revealed environment explained the highest percent of the variation (51.5%), followed by genotype (15.6%) and genotype-by-environment interaction (11.2%). A genome-wide association study identified 26 significant loci across five environments that explained between 5.04% and 16.01% (average = 10.41%). However, genome-wide markers explained 10.54% to 45.99% (average = 31.68%) of the variation, indicating the genetic architecture of this trait is likely complex and controlled by many loci of small effect. This study provides a high-throughput method to evaluate moisture content during nixtamalization that is feasible at the scale of a breeding program and provides important information about the factors contributing to variation of this trait for breeders and food companies to make future strategies to improve this important processing trait.

Virulence and intermediate resistance to high-end antibiotic (teicoplanin) among coagulase-negative staphylococci sourced from retail market fish.

This study reports the distribution of enterotoxigenic determinants among staphylococci and the susceptibility of staphylococci to various classes of antibiotics. We observed all the isolates as resistant to beta-lactam antibiotics and a few as resistant to non-beta-lactam antibiotics such as clindamycin (47.4%), erythromycin (44.7%), gentamicin (23.7%), norfloxacin (34.2%), tetracycline (26.3%), trimethoprim-sulfamethoxazole (15.8%) etc. The resistance of S. sciuri (n = 1) and S. haemolyticus (n = 1) to rifampicin and intermediate resistance of S. gallinarum (n = 2) to teicoplanin, a high-end antibiotic, are also observed in this study. The multidrug-resistance (≥ 3 classes of antibiotics) was recorded in 23 (60.5%) isolates. The virulomes such as sea, seb, seg and sei were identified predominantly in S. haemolyticus. Surprisingly, certain isolates which were phenotypically confirmed as biofilm-producers by Congo red agar (CRA) test did not harbor biofilm-associated loci. This implies the protein-mediated mechanism of biofilm formation as an alternative to polysaccharide intercellular adhesin (PIA) in staphylococci. However, icaAD locus which encodes PIA was identified in 10 (26.3%) isolates and the eno locus, encoding elastin-binding protein which can accelerate the biofilm production, is identified in all the isolates. The possession of type V SCCmec elements by the S. haemolyticus (15.8%) raised the concern about the rapid dissemination of mecA gene to other species of staphylococci including the virulent S. aureus. In short, this study acknowledges the toxigenicity of coagulase-negative staphylococci (CoNS). Through this study, surveillance of antimicrobial resistance and transference of virulomes in staphylococci is warranted.

A One Health Study of the Genetic Relatedness of Klebsiella pneumoniae and Their Mobile Elements in the East of England.

BACKGROUND: Klebsiella pneumoniae is a human, animal, and environmental commensal and a leading cause of nosocomial infections, which are often caused by multiresistant strains. We evaluate putative sources of K. pneumoniae that are carried by and infect hospital patients. METHODS: We conducted a 6-month survey on 2 hematology wards at Addenbrooke's Hospital, Cambridge, United Kingdom, in 2015 to isolate K. pneumoniae from stool, blood, and the environment. We conducted cross-sectional surveys of K. pneumoniae from 29 livestock farms, 97 meat products, the hospital sewer, and 20 municipal wastewater treatment plants in the East of England between 2014 and 2015. Isolates were sequenced and their genomes compared. RESULTS: Klebsiella pneumoniae was isolated from stool of 17/149 (11%) patients and 18/922 swabs of their environment, together with 1 bloodstream infection during the study and 4 others over a 24-month period. Each patient carried 1 or more lineages that was unique to them, but 2 broad environmental contamination events and patient-environment transmission were identified. Klebsiella pneumoniae was isolated from cattle, poultry, hospital sewage, and 12/20 wastewater treatment plants. There was low genetic relatedness between isolates from patients/their hospital environment vs isolates from elsewhere. Identical genes encoding cephalosporin resistance were carried by isolates from humans/environment and elsewhere but were carried on different plasmids. CONCLUSION: We identified no patient-to-patient transmission and no evidence for livestock as a source of K. pneumoniae infecting humans. However, our findings reaffirm the importance of the hospital environment as a source of K. pneumoniae associated with serious human infection.

Molecular assessment of antimicrobial resistance and virulence in multi drug resistant ESBL-producing Escherichia coli and Klebsiella pneumoniae from food fishes, Assam, India.

The present study investigated the prevalence of Extended-Spectrum Beta Lactamase (ESBL) -producing E. coli and K. pneumoniae from the food fishes in retail markets in Assam, India. A total of 54 ESBL-producing E. coli and 12 K. pneumoniae isolates were recovered from 79 fish samples and were analyzed for antimicrobial resistance genes (ARGs) and virulence genes. E. coli isolates were categorized as multi drug resistant with resistance up to 12 different antibiotics with multiple antibiotic resistances (MAR) index ranging from 0.26 to 0.63. In E. coli, 100% resistance to cefotaxime along with 6% resistance to ceftazidime (third-generation cephalosporins) was observed. Moreover, 85% of the E. coli isolates were resistant to cefepime, a fourth-generation cephalosporin. K. pneumoniae showed resistance to 11 different antibiotics with MAR index value ranging from 0.21 to 0.57. All K. pneumoniae isolates showed 100% resistance to cefotaxime, 67% resistance to ceftazidime and 75% resistance to cefepime. Molecular characterization of ARGs revealed the presence of CTX-M group 1(CTX-M-15) in almost all E. coli isolates (98%, n = 53) and 100% in K. pneumoniae. A combination of uniplex and multiplex PCRs revealed fewer ARGs in E. coli isolates, with each isolate carrying 3 to 5 genes (tetA, dfrA1, sul1, sul2, qnrB, qnrS, aac(6')-Ib-cr). Majority of the E. coli were assigned to low-virulence phylogroup B1 and A while 8% of them belonged to pathogenic phylogroup D. 31 unique genetic profiles were identified for E. coli isolates by Pulsed-Field Gel Electrophoresis (PFGE) typing. K. pneumoniae isolates were highly diverse with 11 unique genetic profiles and a substantial ARG profile (blaTEM, blaSHV, blaOXA-1-like, tetA, strA, strB, dfrA1, sul1, sul2, qnrB, qnrS, aac(6')-Ib-cr, oqxA, oqxB). The frequency of ARGs ranged between 4 and 11. All K. pneumoniae isolates belonged to capsular serotype with wzi gene. Virulence gene iutA was prominent in all isolates while ybtS and kfu were confirmed in two isolates. Our findings raise concerns that fishes bought for consumption may serve as potential reservoirs of AMR genes and pose serious threat to public health. The study emphasizes the need for extensive surveillance of resistant strains in aquaculture and related settings, their in-depth analysis of population structure and transmission dynamics.

BK virus-associated nephropathy in a lung transplant patient: case report and literature review.

BACKGROUND: BK virus-associated nephropathy (BKVAN) is a relatively common cause of renal dysfunction in the first six months after renal transplantation. It arises from reactivation of the latent and usually harmless BK virus (BK virus) due to immunosuppression and other factors including some that are unique to renal transplantation such as allograft injury. BKVAN is much rarer in non-renal solid organ transplantation, where data regarding diagnosis and management are extremely limited. CASE PRESENTATION: We report a case of a 58-year-old man found to have worsening renal dysfunction nine months after bilateral sequential lung transplantation for chronic obstructive pulmonary disease (COPD). He had required methylprednisolone for acute allograft rejection but achieved good graft function. Urine microscopy and culture and renal ultrasound were normal. BK virus PCR was positive at high levels in urine and blood. Renal biopsy subsequently confirmed BKVAN. The patient progressed to end-stage renal failure requiring haemodialysis despite reduction in immunosuppression, including switching mycophenolate for everolimus, and the administration of intravenous immunoglobulin (IVIG). CONCLUSIONS: This very rare case highlights the challenges presented by BK virus in the non-renal solid organ transplant population. Diagnosis can be difficult, especially given the heterogeneity with which BKV disease has been reported to present in such patients, and the optimal approach to management is unknown. Balancing reduction in immunosuppression against prevention of allograft rejection is delicate. Improved therapeutic options are clearly required.

Progressive multifocal leukoencephalopathy in a lung transplant recipient presenting with memory impairment: Case report and literature review.

BACKGROUND: Progressive multifocal leukoencephalopathy (PML) is a rare demyelinating disease of the central nervous system caused by JC virus (JCV). The disease occurs in the setting of significant immunocompromise and has now been reported in many different settings, although only very rarely after lung transplantation. The mortality rate is high and therapeutic options are limited. CASE PRESENTATION: We report a case of a 66-year-old man who presented with non-specific memory disturbance at 19 months after lung transplantation for chronic hypersensitivity pneumonitis. He had required methylprednisolone for acute allograft rejection but achieved good graft function. Physical examination was unremarkable. CT revealed hypodensity in the left frontal lobe. MR demonstrated significant hyperintense white-matter abnormalities on T2-weighted and fluid-attenuated inversion recovery (FLAIR) sequences, mainly focused on the periventricular region adjacent the frontal horn of the left lateral ventricle. Brain biopsy confirmed PML. The patient had his immunosuppression reduced but then developed antibody-mediated rejection four months later. Despite re-escalation of immunosuppression, he remains neurologically stable on mirtazapine at eight months post-diagnosis. CONCLUSIONS: This very rare case highlights the challenges presented by PML, especially in the lung transplant population. It reveals the difficult balance between reducing immunosuppression to protect the brain versus prevention of lung allograft rejection. It clearly highlights the need for improved therapeutic modalities.

Diagnosis and treatment of lung disease associated with alpha one-antitrypsin deficiency: A position statement from the Thoracic Society of Australia and New Zealand.

AATD is a common inherited disorder associated with an increased risk of developing pulmonary emphysema and liver disease. Many people with AATD-associated pulmonary emphysema remain undiagnosed and therefore without access to care and counselling specific to the disease. AAT augmentation therapy is available and consists of i.v. infusions of exogenous AAT protein harvested from pooled blood products. Its clinical efficacy has been the subject of some debate and the use of AAT augmentation therapy was recently permitted by regulators in Australia and New Zealand, although treatment is not presently subsidized by the government in either country. The purpose of this position statement is to review the evidence for diagnosis and treatment of AATD-related lung disease with reference to the Australian and New Zealand population. The clinical efficacy and adverse events of AAT augmentation therapy were evaluated by a systematic review, and the GRADE process was employed to move from evidence to recommendation. Other sections address the wide range of issues to be considered in the care of the individual with AATD-related lung disease: when and how to test for AATD, changing diagnostic techniques, monitoring of progression, disease in heterozygous AATD and pharmacological and non-pharmacological therapy including surgical options for severe disease. Consideration is also given to broader issues in AATD that respiratory healthcare staff may encounter: genetic counselling, patient support groups, monitoring for liver disease and the need to establish national registries for people with AATD in Australia and New Zealand.