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Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates.

Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates.

BMC Genomics. 2015;16(1):857

Authors: Black PA, de Vos M, Louw GE, van der Merwe RG, Dippenaar A, Streicher EM, Abdallah AM, Sampson SL, Victor TC, Dolby T, Simpson JA, van Helden PD, Warren RM, Pain A

Abstract
BACKGROUND: Whole genome sequencing has revolutionised the interrogation of mycobacterial genomes. Recent studies have reported conflicting findings on the genomic stability of Mycobacterium tuberculosis during the evolution of drug resistance. In an age where whole genome sequencing is increasingly relied upon for defining the structure of bacterial genomes, it is important to investigate the reliability of next generation sequencing to identify clonal variants present in a minor percentage of the population. This study aimed to define a reliable cut-off for identification of low frequency sequence variants and to subsequently investigate genetic heterogeneity and the evolution of drug resistance in M. tuberculosis.
METHODS: Genomic DNA was isolated from single colonies from 14 rifampicin mono-resistant M. tuberculosis isolates, as well as the primary cultures and follow up MDR cultures from two of these patients. The whole genomes of the M. tuberculosis isolates were sequenced using either the Illumina MiSeq or Illumina HiSeq platforms. Sequences were analysed with an in-house pipeline.
RESULTS: Using next-generation sequencing in combination with Sanger sequencing and statistical analysis we defined a read frequency cut-off of 30 % to identify low frequency M. tuberculosis variants with high confidence. Using this cut-off we demonstrated a high rate of genetic diversity between single colonies isolated from one population, showing that by using the current sequencing technology, single colonies are not a true reflection of the genetic diversity within a whole population and vice versa. We further showed that numerous heterogeneous variants emerge and then disappear during the evolution of isoniazid resistance within individual patients. Our findings allowed us to formulate a model for the selective bottleneck which occurs during the course of infection, acting as a genomic purification event.
CONCLUSIONS: Our study demonstrated true levels of genetic diversity within an M. tuberculosis population and showed that genetic diversity may be re-defined when a selective pressure, such as drug exposure, is imposed on M. tuberculosis populations during the course of infection. This suggests that the genome of M. tuberculosis is more dynamic than previously thought, suggesting preparedness to respond to a changing environment.

PMID: 26496891 [PubMed – as supplied by publisher]

Study on Association of Peroxisome Proliferator-Activated Receptor α with C-Reactive Protein, and Additional Gene-Gene Interaction in Chinese Han.

Study on Association of Peroxisome Proliferator-Activated Receptor α with C-Reactive Protein, and Additional Gene-Gene Interaction in Chinese Han.

Arch Iran Med. 2015 Nov;18(11):765-769

Authors: Zhang SQ, Li GL, Liu YF, Li YQ

Abstract
BACKGROUND: The aim was to examine the association between 6 single nucleotide polymorphisms (SNPs) of peroxisome proliferator-activated receptors α (PPAR α) poly morphisms and C-reactive protein (CRP) level, as well as  additional gene-gene interaction among the 6 SNPs.
METHODS: A total of 1260 subjects (583 men, 677 women), with a mean age of 41.3 ± 14.6 years old, were selected. Six SNPs of PPAR α were selected for genotyping in the study including: rs135539, rs135551, rs135549, rs1800206, rs1800243 and rs4253623. Linear regression analysis was performed to verify the polymorphism association between SNP with CRP levels. Generalized MDR (GMDR) was employed to analysis the interaction among six SNPs.
RESULTS: Linear regression results indicated a significant negative correlation between mutation of rs1800206 and CRP level. The carriers of the V allele (LV + VV) of rs1800206 were associated with a significant decreased level of CRP (regression coefficients was -0.533, standard error was 0.148 (P < 0.001)). However, the other 5 SNPs in PPAR α were not significantly associated with CRP level before or after covariate adjustment. GMDR model indicated that there was a significant two-locus model (P = 0.0107) involving rs1800206 and rs135539, indicating a potential gene-gene interaction between rs1800206 and rs135539. Overall, the two- locus models had a cross-validation consistency of 10 of 10, respectively, and had the testing accuracy of 55.9%, respectively.
CONCLUSIONS: Our results support an important association between rs1800206 minor allele (V) of PPAR α and lower CRP level. The interaction analysis showed a combined effect between rs1800206 and rs135539 on the lower CRP level.

PMID: 26497374 [PubMed – as supplied by publisher]

Light Emitting Diode Fluorescence Microscopy increased the detection of smear-positives during follow-up of Tuberculosis patients in India: program implications.

Light Emitting Diode Fluorescence Microscopy increased the detection of smear-positives during follow-up of Tuberculosis patients in India: program implications.

BMC Res Notes. 2015;8(1):596

Authors: Thapa B, Reza LW, Kumar AM, Pandey A, Satyanarayana S, Chadha S

Abstract
BACKGROUND: In India, since July 2012, at designated Microscopy Centers (DMCs) in 200 medical colleges, sputum smear examination for tuberculosis bacilli changed from Ziehl Neelsen (ZN) method to auramine based Light Emitting Diode Fluorescent Microscopy (LED-FM) method. We assessed the additional yield of smear positives among patients undergoing follow-up sputum examination during TB treatment before and after deploying LED-FM.
METHODS: This was a before and after comparison study in eight conveniently selected medical college DMCs across North India. We extracted data from TB laboratory registers on number of TB patients examined for follow-up and their smear microscopy results including the grades by ZN (before; July-December 2011) and LED-FM (after; July-December 2012) and compared them.
RESULTS: Altogether, 2868 TB patients were examined by LED-FM and 2740 were examined by ZN during follow-up. LED-FM increased the proportion of follow-up smear positives from 5.0 % (n = 136) to 7.4 % (n = 213) with an additional yield of 77 follow-up smear-positives-with the highest increase in smears graded scanty (2.6 vs 1.2 %) (p value <0.05).
CONCLUSIONS: Since all smear positives during follow-up are considered ‘presumptive multidrug resistant (MDR)-TB patients’ in India, introduction of LED-FM would result in additional number of patients eligible for MDR-TB testing, which would have otherwise been missed by ZN.

PMID: 26499322 [PubMed – as supplied by publisher]

Development, Maintenance, and Reversal of Multiple Drug Resistance: At the Crossroads of TFPI1, ABC Transporters, and HIF1.

Development, Maintenance, and Reversal of Multiple Drug Resistance: At the Crossroads of TFPI1, ABC Transporters, and HIF1.

Cancers (Basel). 2015;7(4):2063-2082

Authors: Arnason T, Harkness T

Abstract
Early detection and improved therapies for many cancers are enhancing survival rates. Although many cytotoxic therapies are approved for aggressive or metastatic cancer; response rates are low and acquisition of de novo resistance is virtually universal. For decades; chemotherapeutic treatments for cancer have included anthracyclines such as Doxorubicin (DOX); and its use in aggressive tumors appears to remain a viable option; but drug resistance arises against DOX; as for all other classes of compounds. Our recent work suggests the anticoagulant protein Tissue Factor Pathway Inhibitor 1α (TFPI1α) plays a role in driving the development of multiple drug resistance (MDR); but not maintenance; of the MDR state. Other factors; such as the ABC transporter drug efflux pumps MDR-1/P-gp (ABCB1) and BCRP (ABCG2); are required for MDR maintenance; as well as development. The patient population struggling with therapeutic resistance specifically requires novel treatment options to resensitize these tumor cells to therapy. In this review we discuss the development, maintenance, and reversal of MDR as three distinct phases of cancer biology. Possible means to exploit these stages to reverse MDR will be explored. Early molecular detection of MDRcancers before clinical failure has the potential to offer new approaches to fightingMDRcancer.

PMID: 26501324 [PubMed – as supplied by publisher]

Improving hospital hygiene to reduce the impact of multidrug-resistant organisms in health care-a prospective controlled multicenter study.

Related Articles

Improving hospital hygiene to reduce the impact of multidrug-resistant organisms in health care-a prospective controlled multicenter study.

BMC Infect Dis. 2015;15(1):441

Authors: Gerlich MG, Piegsa J, Schäfer C, Hübner NO, Wilke F, Reuter S, Engel G, Ewert R, Claus F, Hübner C, Ried W, Flessa S, Kramer A, Hoffmann W

Abstract
BACKGROUND: Nosocomial infections are the most common complication during inpatient hospital care. An increasing proportion of these infections are caused by multidrug-resistant organisms (MDROs). This report describes an intervention study which was designed to address the practical problems encountered in trying to avoid and treat infections caused by MDROs. The aim of the HARMONIC (Harmonized Approach to avert Multidrug-resistant Organisms and Nosocomial Infections) study is to provide comprehensive support to hospitals in a defined study area in north-east Germany, to meet statutory requirements. To this end, a multimodal system of hygiene management was implemented in the participating hospitals.
METHODS/DESIGN: HARMONIC is a controlled intervention study conducted in eight acute care hospitals in the ‘Health Region Baltic Sea Coast’ in Germany. The intervention measures include the provision of written recommendations on methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococci (VRE) and multi-resistant Gram-negative bacteria (MRGN), supplemented by regional recommendations for antibiotic prescriptions. In addition, there is theoretical and practical training of health care workers (HCWs) in the prevention and handling of MDROs, as well as targeted and critically gauged applications of antibiotics. The main outcomes of the implementation and analysis of the HARMONIC study are: (i) screening rates for MRSA, VRE and MRGN in high-risk patients, (ii) the frequency of MRSA decolonization, (iii) the level of knowledge of HCWs concerning MDROs, and (iv) specific types and amounts of antibiotics used. The data are predominantly obtained by paper-based questionnaires and documentation sheets. A computer-assisted workflow-based documentation system was developed in order to provide support to the participating facilities. The investigation includes three nested studies on risk profiles of MDROs, health-related quality of life, and cost analysis. A six-month follow-up study investigates the quality of life after discharge, the long-term costs of the treatment of infections caused by MDROs, and the sustainability of MRSA eradication.
DISCUSSION: The aim of this study is to implement and evaluate an area-wide harmonized hygiene program to control the nosocomial spreading of MDROs. Comparability between the intervention and control group is ensured by matching the hospitals according to size (number of discharges per year / number of beds) and level of care (standard or maximum). The results of the study may provide important indications for the implementation of regional MDRO management programs.

PMID: 26493394 [PubMed – as supplied by publisher]

How do physicians cope with controversial topics in existing guidelines for the management of infective endocarditis? Results of an international survey.

Related Articles

How do physicians cope with controversial topics in existing guidelines for the management of infective endocarditis? Results of an international survey.

Clin Microbiol Infect. 2015 Oct 19;

Authors: Béraud G, Pulcini C, Paño-Pardo JR, Hoen B, Beovic B, Nathwani D, ESGAP

Abstract
International guidelines are available to help physicians prescribe appropriate antibiotic regimens to patients with infective endocarditis (IE). However some topics of these guidelines are controversial. We conducted an international survey to assess physicians’ adherence to these guidelines, focusing on these controversial items. An invitation to participate to a 15-question online survey was sent in 2012-2013 to ESCMID members, scientific societies and corresponding authors of publications on IE mentioned in Pubmed from 1990 to 2012, inclusive. Eight hundred and thirty-seven physicians participated in the survey and 625 (74.7%) completed it over the first question. The results showed great heterogeneity of practices. Claiming to follow guidelines was marginally associated with more guidelines-based strategies. Gentamicin use depended on causative pathogens (p<0.001) and physician’s specialty (p=0.02). Eighty-six percent of the physicians favoured vancomycin alone or in combination with gentamicin or rifampicin as a first-line treatment for left-sided native valve MRSA IE, 31% considered switching to oral therapy as a therapeutic option and 33% used the ampicillin and ceftriaxone combination for enterococcal IE as a first-line therapy. Physician’s specialty significantly impacted the choice of a therapeutic strategy, while practicing in a university hospital or the number of years of practice had virtually no impact. Our survey, the largest on infective endocarditis treatment, underscores important heterogeneity in practices for treatment of IE. Nonetheless, physicians who do not follow guidelines can have very rational strategies based on literature. These results could inform the revision of future guidelines, and identify unmet need for future studies.

PMID: 26493845 [PubMed – as supplied by publisher]