Anaemia in Hospitalized Cancer Patients: A Retrospective Study of Two Cohorts before and after the Guideline Update.

INTRODUCTION: The incidence of anaemia and its consequences are often underestimated during cancer management. We propose to evaluate the situation before and after the recommendations were updated in order to assess their impact on the day-to-day practice. METHODS: In this single-centre retrospective study, eligible patients were treated for cancer and warranted overnight hospitalization over two periods (n = 206 in 2011, n = 143 in 2018). The diagnosis of anaemia was defined by a haemoglobin level below 12 and 13 g/dL for women and men, respectively. RESULTS: The prevalence of anaemia was 26% in 2011 and 16% in 2018 (p < 0.001). Biological assessment had changed between the two periods, with more tests of iron metabolism and measurements of inflammatory parameters. Patients hospitalized in 2018 had more advanced cancer and more severe anaemia (8.2 g/dL [±1.07] in 2011 vs. 7.9 g/dL [±1.18] in 2018). Rate of transfusion therapy did not change, but patients with mild and moderate anaemia were transfused less in 2018 (57% in 2011 vs. 44% in 2018). Intravenous iron and erythropoiesis-stimulating agent were used more frequently in 2018 (1 and 5 and 13 and 23% in 2011 and 2018, respectively), mainly for mild anaemia and life-threatening anaemia, respectively. Overall survival was poor in both cohorts at 24 months (15.4% in 2011 and 6.5% in 2018, p = 0.048). CONCLUSION: Practices have changed in the diagnosis of anaemia and prescriptions for erythropoiesis-stimulating agents and intravenous iron have increased. Efforts must continue to explore the causes of anaemia, optimize patients' quality of life, and reduce transfusions.

Diagnostic Strategy Using Color Doppler Ultrasound of Temporal Arteries in Patients With High Clinical Suspicion of Giant Cell Arteritis : A Prospective Cohort Study.

BACKGROUND: Giant cell arteritis (GCA) is the most prevalent systemic vasculitis in people older than 50 years. Any delay in diagnosis impairs patients' quality of life and can lead to permanent damage, particularly vision loss. OBJECTIVE: To evaluate a diagnostic strategy for GCA using color Doppler ultrasound of the temporal artery as a first-line diagnostic test, temporal artery biopsy (TAB) as a secondary test, and physician expertise as the reference method. DESIGN: Prospective multicenter study with a 2-year follow-up. (ClinicalTrials.gov: NCT02703922). SETTING: Patients were referred by their general practitioner or ophthalmologist to a physician with extensive experience in GCA diagnosis and management in one of the participating centers: 4 general and 2 university hospitals. PATIENTS: 165 patients with high clinical suspicion of GCA, aged 79 years (IQR, 73 to 85 years). INTERVENTION: The diagnostic procedure was ultrasound, performed less than 7 days after initiation of corticosteroid therapy. Only ultrasound-negative patients underwent TAB. MEASUREMENTS: Bilateral temporal halo signs seen on ultrasound were considered positive. Ultrasound and TAB results were compared with physician-diagnosed GCA based on clinical findings and other imaging. RESULTS: Diagnosis of GCA was confirmed in 44%, 17%, and 21% of patients by ultrasound, TAB, and clinical expertise and/or other imaging tests, respectively. Their diagnosis remained unchanged at 1 month, and 2 years for those with available follow-up data. An alternative diagnosis was made in 18% of patients. The proportion of ultrasound-positive patients among patients with a clinical GCA diagnosis was 54% (95% CI, 45% to 62%). LIMITATION: Small sample size, no blinding of ultrasound and TAB results, lack of an objective gold-standard comparator, and single diagnostic strategy. CONCLUSION: By using ultrasound of the temporal arteries as a first-line diagnostic tool in patients with high clinical suspicion of GCA, further diagnostic tests for patients with positive ultrasound were avoided. PRIMARY FUNDING SOURCE: Tender "Recherche CH-CHU Poitou-Charentes 2014."

Four typical pulmonary venous pressure curves displaying the level of occlusion during atrial fibrillation ablation by cryoballoon.

Background: Cryoballoon ablation is safe and effective for pulmonary vein isolation in patients with symptomatic drug-refractory paroxysmal atrial fibrillation. To monitor adhesion between the balloon and the pulmonary vein, an alternative technique to pulmonary venography is to analyze changes in the pressure curve. Methods: We have described the adhesion level characterized by four types of pressure waveforms. Results: These correlated with the extent of contrast agent leakage (Cohen's kappa of 0.81 [IC 95%: 0.63-0.99]). Conclusion: Monitoring the venous pressure curve is easy to perform and has the advantage of being able to detect balloon movement during the first few seconds of treatment.

ATE Score Diagnostic Accuracy for Predicting the Absence of Intra-Atrial Thrombi Before AF Ablation.

BACKGROUND: In a preliminary study in patients hospitalized for catheter ablation of atrial fibrillation (AF), the atrial thrombus exclusion (ATE) score (stroke, hypertension, heart failure, and D-dimers >270 ng/mL) was developed to rule out the diagnosis of intra-atrial thrombus, with a negative predictive value (NPV) of 100%, and to avoid performing transesophageal echocardiography (TEE). OBJECTIVES: The present study was designed to prospectively confirm the NPV of the ATE score in an independent population. METHODS: Consecutive patients hospitalized for catheter ablation of AF or left atrial tachycardia (LAT) were prospectively enrolled in a multicenter study. D-dimer levels were measured within 48 hours before ablation. An ATE score of 0 was considered predictive of no thrombus. TEE was routinely performed at the beginning or just before the ablation procedure. The primary endpoint was the presence of atrial thrombus diagnosed by TEE. RESULTS: The analysis included 3,072 patients (53.3% paroxysmal AF, 36.7% persistent AF, and 10% LAT). A thrombus was detected in 29 patients (0.94%; 95% CI: 0.63%-1.35%), all on appropriate anticoagulant therapy. An ATE score of 0 was observed in 818 patients (26.6%), and the sensitivity, specificity, positive predictive value, and NPV were 93.1%, 26.8%, 1.2%, and 99.8%, respectively. Follow-up of the 2 false negative patients revealed the persistence of chronic organized thrombi. CONCLUSIONS: In patients hospitalized for catheter ablation of AF or LAT, the ATE score identifies a population at very low risk for atrial thrombus. In consultation with the patient, the cardiologist may consider not performing a preoperative TEE in case of an ATE score of 0.

Prospective, single-centre evaluation of the safety and efficacy of percutaneous coronary interventions following a decision tree proposing a no-stent strategy in stable patients with coronary artery disease (SCRAP study).

AIM: We evaluated a decision algorithm for percutaneous coronary interventions (PCI) based on a no-stent strategy, corresponding to a combination of scoring balloon angioplasty (SCBA) and drug-coated balloon (DCB), as a first line approach. Stents were used only in unstable patients, or in case of mandatory bailout stenting (BO-stent). METHODS: From April 2019 to March 2020, 984 consecutive patients, including 1922 lesions, underwent PCI. The 12-month primary end-point was a composite of major adverse cardiac events (MACE) defined as all-cause death, nonfatal myocardial infarction, nonfatal stroke, and target lesion revascularization. Patients were classified into conventional or no-stent strategy groups according to the PCI strategy. In the no-stent strategy group, they were further classified into BO-stent or DCB-only groups. Their metal index was calculated by stent length divided by the total lesion length. RESULTS: The no-stent strategy was applied in 85% of the patients, and it was successful for 65% of them. MACE occurred in 7.1% of the study population, including 4.2% of all-cause death. Target lesion revascularization was required in 1.4%, 3.6%, and 1.5% of patients in the conventional DES, BO-stent, and DCB-only groups, respectively. MACE occurred more often in the elderly and in those treated with at least one stent (metal index greater than 0). CONCLUSIONS: The no-stent strategy, i.e., revascularization of coronary lesions by SCBA followed by DCB and with DES bailout stenting, was effective and safe at 1 year. This PCI approach was applicable on a daily practice in our cath lab. TRIAL REGISTRATION: This study was registered with clinicaltrials.gov (NCT03893396, first posted on March 28, 2019). Feasibility, safety and efficacy of percutaneous coronary interventions following a decision tree proposing a no-stent strategy in stable patients with coronary artery disease. DES: drug eluting stent; SCBA: scoring balloon angioplasty; BO-stent: at least one stent; DCB: drug coated balloon; BMS: bare metal stent; Bailout (dash lines); MACE: major adverse cardiac event.

Clinical and Epidemiologic Characteristics and Therapeutic Management of Patients with Vibrio Infections, Bay of Biscay, France, 2001-2019.

Noncholera vibriosis is a rare, opportunistic bacterial infection caused by Vibrio spp. other than V. cholerae O1/O139 and diagnosed mainly during the hot summer months in patients after seaside activities. Detailed knowledge of circulating pathogenic strains and heterogeneities in infection outcomes and disease dynamics may help in patient management. We conducted a multicenter case-series study documenting Vibrio infections in 67 patients from 8 hospitals in the Bay of Biscay, France, over a 19-year period. Infections were mainly caused by V. alginolyticus (34%), V. parahaemolyticus (30%), non-O1/O139 V. cholerae (15%), and V. vulnificus (10%). Drug-susceptibility testing revealed intermediate and resistant strains to penicillins and first-generation cephalosporins. The acute infections (e.g., those involving digestive disorder, cellulitis, osteitis, pneumonia, and endocarditis) led to a life-threatening event (septic shock), amputation, or death in 36% of patients. Physicians may need to add vibriosis to their list of infections to assess in patients with associated risk factors.

Evolution of Modeled Cortisol Is Prognostic of Death in Hospitalized Patients With COVID-19 Syndrome.

Introduction: Patients hospitalized with SARS-CoV-2 have an elevated risk of mortality related to a severe inflammatory response. We hypothesized that biological modeling with a complete blood count (CBC) would be predictive of mortality. Method: In 2020, 81 patients were randomly selected from La Rochelle Hospital, France for a simple blinded retrospective study. Demographic, vital signs, CBC and CRP were obtained on admission, at days 2-3 and 3-5. From a CBC, two biological modeling indexes were resulted: the neutrophil-to-lymphocyte ratio (NLR) and cortisol index adjusted (CA). Results: By ANOVA, in survivors vs. non-survivors there was statistical different at p < 0.01 for age (66.2 vs. 80), CRP (92 vs. 179 mg/dL, normal < 10), cortisol index adjusted (323 vs. 698, normal 3-7) and genito-thyroid indexes (7.5 vs. 18.2, normal 1.5-2.5), and at p = 0.02 creatinine (1.03 vs. 1.48, normal 0.73-1.8 mg/dL). By mixed model analysis, CA and NLR improved in those who survived across all three time points, but worsened again after 3-5 days in non-survivors. CRP continued to improve over time in survivors and non-survivors. Positive vs. Negative predictive value were: CRP (91.1%, 30.4%), NLR (94.5%, 22.7%), CA (100%, 0%). Discussion: Cortisol modeling and the neutrophil-to-lymphocyte ratio were more accurate in describing the course of non-survivors than CRP. Conclusion: In patients admitted for SARS CoV-2 infection, biological modeling with a CBC predicted risk of death better than CRP. This approach is inexpensive and easily repeated.

Deep amplicon sequencing for culture-free prediction of susceptibility or resistance to 13 anti-tuberculous drugs.

Conventional molecular tests for detecting Mycobacterium tuberculosis complex (MTBC) drug resistance on clinical samples cover a limited set of mutations. Whole-genome sequencing (WGS) typically requires culture.Here, we evaluated the Deeplex Myc-TB targeted deep-sequencing assay for prediction of resistance to 13 anti-tuberculous drugs/drug classes, directly applicable on sputum.With MTBC DNA tests, the limit of detection was 100-1000 genome copies for fixed resistance mutations. Deeplex Myc-TB captured in silico 97.1-99.3% of resistance phenotypes correctly predicted by WGS from 3651 MTBC genomes. On 429 isolates, the assay predicted 92.2% of 2369 first- and second-line phenotypes, with a sensitivity of 95.3% and a specificity of 97.4%. 56 out of 69 (81.2%) residual discrepancies with phenotypic results involved pyrazinamide, ethambutol and ethionamide, and low-level rifampicin or isoniazid resistance mutations, all notoriously prone to phenotypic testing variability. Only two out of 91 (2.2%) resistance phenotypes undetected by Deeplex Myc-TB had known resistance-associated mutations by WGS analysis outside Deeplex Myc-TB targets. Phenotype predictions from Deeplex Myc-TB analysis directly on 109 sputa from a Djibouti survey matched those of MTBSeq/PhyResSE/Mykrobe, fed with WGS data from subsequent cultures, with a sensitivity of 93.5/98.5/93.1% and a specificity of 98.5/97.2/95.3%, respectively. Most residual discordances involved gene deletions/indels and 3-12% heteroresistant calls undetected by WGS analysis or natural pyrazinamide resistance of globally rare "Mycobacterium canettii" strains then unreported by Deeplex Myc-TB. On 1494 arduous sputa from a Democratic Republic of the Congo survey, 14 902 out of 19 422 (76.7%) possible susceptible or resistance phenotypes could be predicted culture-free.Deeplex Myc-TB may enable fast, tailored tuberculosis treatment.

[The effect of therapeutic communication when washing patients]. / Effet de la communication thérapeutique pendant la toilette complète des patients.

There is a close link between care and communication. The purpose of the study is to evaluate therapeutic communication when bed washing patients, which dependent patients may experience as an aggressive treatment. Improved comfort, improved serenity, less intense pain, lower pulse and blood pressure have been observed in patients looked after by caregivers practising therapeutic communication.

Prevalence and Recovery From Olfactory and Gustatory Dysfunctions in Covid-19 Infection: A Prospective Multicenter Study.

BACKGROUND: Covid-19 is defined by an association of multiple symptoms, including frequently reported olfactory and gustatory disorders. OBJECTIVE: The main purpose of this study was to analyze the prevalence of these neurosensory impairments in patients with Covid-19, and to assess short-term recovery. METHODS: We performed a multicenter case series study during the Covid-19 epidemic. All patients presenting a RT-PCR-confirmed SARS-CoV-2 infection were included, whether hospitalized or treated at home. To analyze the prevalence and features of olfactory and gustatory dysfunctions, a phone interview was conducted 5 days after the positive PCR result. The questionnaire was submitted again 10 days later to patients having reported olfactory and gustatory disorders, in order to assess their recovery. RESULTS: 115 patients were included in our study. 81 patients (70%) reported olfactory and gustatory disorders without nasal obstruction or rhinorrhea. These impairments were more frequently reported in the female population, young people, and house-bound patients with mild symptomatic forms. Short-term recovery assessed at Day 15 was complete for 64% of the patients, and incomplete in 33%. Median recovery time was 15 days (4-27 days) after olfactory or gustatory symptom onset. CONCLUSION: Olfactory and gustatory dysfunctions related to Covid-19 are frequently reported and prevalent in mild symptomatic forms of the disease. Recovery in most cases seems rapid and complete.

Colour Doppler ultrasound of temporal arteries for the diagnosis of giant cell arteritis: a multicentre deep learning study.

OBJECTIVES: Giant cell arteritis (GCA) is the most common systemic vasculitis in adults. In recent years, colour Doppler ultrasound of the temporal arteries (CDU) has proven to be a powerful non-invasive diagnostic tool, but its place in the diagnosis of GCA remains to be defined. A limitation of the CDU is the inter-operator reproducibility. Image analysis from a different perspective is now possible with the development of artificial intelligence algorithms. We propose to assess this technology for the detection of the halo sign on CDU images. METHODS: Three public hospitals retrospectively collected data from 137 patients suspected of having GCA between January 2017 and April 2019. CDU images (n=1,311) were labelled with the VIA software. Three sets (training, validation and test) were created and analysed with a semantic segmentation technique using a U-Net convolutional neural network. RESULTS: The area under the curve (AUC) was 0.931 and 0.835 on the validation and test set, respectively. An image positivity threshold was determined by focusing on the specificity. With this threshold, a specificity of 95% and a sensitivity of 60% were obtained for the test set. The analysis of the false interpretation showed that the acquisition modalities and the presence of thrombus caused confusion for the algorithm. CONCLUSIONS: We propose an automated image analysis tool for GCA diagnosis. The 2018 EULAR guidelines for image acquisition must be respected before generalising this algorithm. After external validation, this tool could be used as an aid for diagnosis, staff training and student education.

Revision of hospital work organization using nurse and healthcare assistant workload indicators as decision aid tools.

BACKGROUND: Historically, governmental hospital organisation consisted in a heterogeneous distribution of staff and a fragmented logistical organisation without cross-functionality or sharing of resources between departments. This organisation could not last in a context of an evolving healthcare environment, changing patient profiles and hospital expenditure constraints. Cost-effective workforce regulation for optimal patient quality of care was urgently needed. The purpose of the study was to describe the reorganization that led to resource management no longer based on what has been achieved but based on a daily measured workload. METHODS: This prospective study used nursing intensity indicator, mirroring patient care needs, which was reported daily using VALPAReSO® software. Indirect care activities were recorded in departments of medicine, surgery and obstetrics. Based on data collected in 2012, a new organisation strategy was implemented and evaluated in 2015. RESULTS: Nursing intensity indicator analysis led to a reallocation of workforce per department, and the reinforcement unit (float pool) was managed based on this decision-aid tool for replacement and daily adequate staffing. The healthcare workflow audit resulted in the revision of five working tasks: time spent on handover, working time management, connections between services and the pharmacy, housekeeping, and food management. The reorganization took place at the same time as the transition to the development of very short-term care, resulting in a decrease in the number of full inpatient beds, which were therefore mainly occupied by heavier care profile patients. With the integrated strategy, this transition was achieved with constant staffing, and good overall patient satisfaction and working conditions were maintained. CONCLUSION: The reorganisation strategy was managed in a context of institutional commitment, coaching leadership built on close manager-employee interaction, a defragmented management between healthcare and all service providers, and a seamlessly dissemination and sharing of indicator information between healthcare managers, nurses and healthcare assistants. The process optimization allowed a better allocation of tasks and enabled nurses to refocus on patient care. Nursing intensity and indirect care indicators, when widely accepted, can be used as decision support tools for daily adequate staffing.

Exclusion of Intra-Atrial Thrombus Diagnosis Using D-Dimer Assay Before Catheter Ablation of Atrial Fibrillation.

OBJECTIVES: This study hypothesized that the association of D-dimer blood level and several clinical items in a new risk score could predict the absence of atrial thrombus. BACKGROUND: Symptomatic and drug resistant atrial fibrillation (AF) can be treated by catheter ablation. The procedure-related risk of thromboembolism is limited by the pre-operative use of transesophageal echocardiography (TEE) to detect atrial thrombi. METHODS: Patients admitted for catheter ablation of AF (n = 2,494) were prospectively included in a multicenter study. TEE was systematically performed before the procedure to search for atrial thrombus (primary endpoint). D-dimer level, CHADS2 score, left ventricular ejection fraction, pre-operative anticoagulation regimen, and medical history were collected. A logistic regression model was used to identify factors associated with the presence of atrial thrombus (hypertension, history of stroke, heart failure, D-dimer level >270 ng/ml). These factors were aggregated in a new score called atrial thrombus exclusion (ATE). RESULTS: The incidence of atrial thrombus was 1.92%. CHADS2 score and D-dimer level were significantly associated with atrial thrombus (p < 0.0001 and p < 0.0001, respectively). A zero CHADS2 score failed to exclude all atrial thrombi (5 false negatives; sensitivity: 89.58%, specificity: 52.2%). No false negative was found with a zero ATE score, which had a specificity of 37% and a higher sensitivity (100%) than the CHADS2 score (p < 0.031) to predict the absence of intra-atrial thrombi on TEE. Conversely, the positive predictive value was poor, and the ATE score should not be used to conclude a positive diagnosis of thrombus. CONCLUSIONS: An ATE score of zero was strongly associated with the absence of atrial thrombus. This new score could be useful to rule out a diagnosis of atrial thrombus before catheter ablation of AF.

Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing.

BACKGROUND: The World Health Organization recommends drug-susceptibility testing of Mycobacterium tuberculosis complex for all patients with tuberculosis to guide treatment decisions and improve outcomes. Whether DNA sequencing can be used to accurately predict profiles of susceptibility to first-line antituberculosis drugs has not been clear. METHODS: We obtained whole-genome sequences and associated phenotypes of resistance or susceptibility to the first-line antituberculosis drugs isoniazid, rifampin, ethambutol, and pyrazinamide for isolates from 16 countries across six continents. For each isolate, mutations associated with drug resistance and drug susceptibility were identified across nine genes, and individual phenotypes were predicted unless mutations of unknown association were also present. To identify how whole-genome sequencing might direct first-line drug therapy, complete susceptibility profiles were predicted. These profiles were predicted to be susceptible to all four drugs (i.e., pansusceptible) if they were predicted to be susceptible to isoniazid and to the other drugs or if they contained mutations of unknown association in genes that affect susceptibility to the other drugs. We simulated the way in which the negative predictive value changed with the prevalence of drug resistance. RESULTS: A total of 10,209 isolates were analyzed. The largest proportion of phenotypes was predicted for rifampin (9660 [95.4%] of 10,130) and the smallest was predicted for ethambutol (8794 [89.8%] of 9794). Resistance to isoniazid, rifampin, ethambutol, and pyrazinamide was correctly predicted with 97.1%, 97.5%, 94.6%, and 91.3% sensitivity, respectively, and susceptibility to these drugs was correctly predicted with 99.0%, 98.8%, 93.6%, and 96.8% specificity. Of the 7516 isolates with complete phenotypic drug-susceptibility profiles, 5865 (78.0%) had complete genotypic predictions, among which 5250 profiles (89.5%) were correctly predicted. Among the 4037 phenotypic profiles that were predicted to be pansusceptible, 3952 (97.9%) were correctly predicted. CONCLUSIONS: Genotypic predictions of the susceptibility of M. tuberculosis to first-line drugs were found to be correlated with phenotypic susceptibility to these drugs. (Funded by the Bill and Melinda Gates Foundation and others.).

Diagnostic performance of colour duplex ultrasonography along with temporal artery biopsy in suspicion of giant cell arteritis.

OBJECTIVES: Giant cell arteritis (GCA) is a vasculitis that occurs in older adults, affecting vessels of medium and large caliber. GCA diagnosis is a challenge for general practitioners and specialists. The aim of this study was to retrospectively analyse performances of temporal artery biopsy (TAB) and colour duplex ultrasonography (CDU) for GCA diagnosis. METHODS: All patients with suspicion of GCA and who underwent both TAB and CDU between April 2009 and March 2014 were included in the study. A positive CDU examination was defined by halos on both superficial temporal arteries. Patients were classified based on the physician final diagnosis. RESULTS: Among the 42 eligible patients, 12 had an alternative diagnosis and 30 were diagnosed with GCA. Sensitivities were 77% and 80% for TAB and CDU examinations, respectively. Specificities were 100% for both tests. Twenty-nine (96.7%) patients with GCA had their diagnosis confirmed either by CDU and/or by TAB. Time lengths between the first medical examination and results of TAB and CDU were 15 and 4.2 days (p<0.001), respectively. CONCLUSIONS: Our study suggests that in suspected GCA, CDU may be used as first line examination followed by TAB in case of CDU negative results. Such algorithm needs to be further assessed in a multicentre prospective study.

Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study.

BACKGROUND: Diagnosing drug-resistance remains an obstacle to the elimination of tuberculosis. Phenotypic drug-susceptibility testing is slow and expensive, and commercial genotypic assays screen only common resistance-determining mutations. We used whole-genome sequencing to characterise common and rare mutations predicting drug resistance, or consistency with susceptibility, for all first-line and second-line drugs for tuberculosis. METHODS: Between Sept 1, 2010, and Dec 1, 2013, we sequenced a training set of 2099 Mycobacterium tuberculosis genomes. For 23 candidate genes identified from the drug-resistance scientific literature, we algorithmically characterised genetic mutations as not conferring resistance (benign), resistance determinants, or uncharacterised. We then assessed the ability of these characterisations to predict phenotypic drug-susceptibility testing for an independent validation set of 1552 genomes. We sought mutations under similar selection pressure to those characterised as resistance determinants outside candidate genes to account for residual phenotypic resistance. FINDINGS: We characterised 120 training-set mutations as resistance determining, and 772 as benign. With these mutations, we could predict 89·2% of the validation-set phenotypes with a mean 92·3% sensitivity (95% CI 90·7-93·7) and 98·4% specificity (98·1-98·7). 10·8% of validation-set phenotypes could not be predicted because uncharacterised mutations were present. With an in-silico comparison, characterised resistance determinants had higher sensitivity than the mutations from three line-probe assays (85·1% vs 81·6%). No additional resistance determinants were identified among mutations under selection pressure in non-candidate genes. INTERPRETATION: A broad catalogue of genetic mutations enable data from whole-genome sequencing to be used clinically to predict drug resistance, drug susceptibility, or to identify drug phenotypes that cannot yet be genetically predicted. This approach could be integrated into routine diagnostic workflows, phasing out phenotypic drug-susceptibility testing while reporting drug resistance early. FUNDING: Wellcome Trust, National Institute of Health Research, Medical Research Council, and the European Union.

Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage.

Mycobacterium tuberculosis strains of the Beijing lineage are globally distributed and are associated with the massive spread of multidrug-resistant (MDR) tuberculosis in Eurasia. Here we reconstructed the biogeographical structure and evolutionary history of this lineage by genetic analysis of 4,987 isolates from 99 countries and whole-genome sequencing of 110 representative isolates. We show that this lineage initially originated in the Far East, from where it radiated worldwide in several waves. We detected successive increases in population size for this pathogen over the last 200 years, practically coinciding with the Industrial Revolution, the First World War and HIV epidemics. Two MDR clones of this lineage started to spread throughout central Asia and Russia concomitantly with the collapse of the public health system in the former Soviet Union. Mutations identified in genes putatively under positive selection and associated with virulence might have favored the expansion of the most successful branches of the lineage.

Proposal of a consensus set of hypervariable mycobacterial interspersed repetitive-unit-variable-number tandem-repeat loci for subtyping of Mycobacterium tuberculosis Beijing isolates.

Mycobacterium tuberculosis Beijing strains represent targets of special importance for molecular surveillance of tuberculosis (TB), especially because they are associated with spread of multidrug resistance in some world regions. Standard 24-locus mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing lacks resolution power for accurately discriminating closely related clones that often compose Beijing strain populations. Therefore, we evaluated a set of 7 additional, hypervariable MIRU-VNTR loci for better resolution and tracing of such strains, using a collection of 535 Beijing isolates from six world regions where these strains are known to be prevalent. The typeability and interlaboratory reproducibility of these hypervariable loci were lower than those of the 24 standard loci. Three loci (2163a, 3155, and 3336) were excluded because of their redundant variability and/or more frequent noninterpretable results compared to the 4 other markers. The use of the remaining 4-locus set (1982, 3232, 3820, and 4120) increased the number of types by 52% (from 223 to 340) and reduced the clustering rate from 58.3 to 36.6%, when combined with the use of the standard 24-locus set. Known major clonal complexes/24-locus-based clusters were all subdivided, although the degree of subdivision varied depending on the complex. Only five single-locus variations were detected among the hypervariable loci of an additional panel of 92 isolates, representing 15 years of clonal spread of a single Beijing strain in a geographically restricted setting. On this calibrated basis, we propose this 4-locus set as a consensus for subtyping Beijing clonal complexes and clusters, after standard typing.

Tuberculosis transmission among immigrants and autochthonous populations of the eastern province of Saudi Arabia.

BACKGROUND: Eastern province of Saudi Arabia is an industrial zone with large immigrant population and high level of tuberculosis case notification among immigrants. The impact of immigration and current trends of tuberculosis transmission among immigrants and autochthonous population in the region had not been investigated so far using molecular tools. METHODOLOGY: During 2009- 2011, a total of 524 Mycobacterium tuberculosis isolates were collected from the central tuberculosis reference laboratory, representing an estimated 79.2% of the culture-positive tuberculosis cases over the study period in the province. These isolates were genotyped by using 24 locus-based MIRU-VNTR typing and spoligotyping followed by first line drug susceptibility testing. The molecular clustering profiles and phylogenetic diversity of isolates were determined and compared to the geographical origins of the patients. PRINCIPLE FINDINGS: Genotyping showed an overall predominance of Delhi/CAS (29.4%), EAI (23.8%) and Ghana (13.3%) lineages, with slightly higher proportions of Delhi/CAS among autochthonous population (33.3 %) and EAI (30.9%) among immigrants. Rate of any drug resistance was 20.2% with 2.5% of multi-drug resistance. Strain cluster analysis indicated 42 clusters comprising 210 isolates, resulting in a calculated recent transmission index of 32.1%. Overall shared cluster ratio was 78.6% while 75.8% were shared between autochthonous population and immigrant population with a predominance of immigrants from South east Asia (40.7%). In contrast, cross national transmission within the immigrant population was limited (24.2%). Younger age (15-30- p value-0.043, 16-45, p value 0.030), Saudi nationality (p value-0.004) and South East Asian origin (p value-0.011) were identified as significant predisposing factors for molecular strain clustering. CONCLUSIONS: The high proportion of molecular clusters shared among the autochthonous and immigrant populations suggests a high permeability of tuberculosis transmission between both populations in the province. These results prompt for the need to strengthen the current tuberculosis control strategies and surveillance programs.