Top 10 Biorxiv Papers Today in Microbiology


2.01 Mikeys
#1. Comparative genomic analysis of the emerging pathogen Streptococcus pseudopneumoniae: novel insights into virulence determinants and identification of a novel species-specific molecular marker
Genevieve Garriss, Priyanka Nannapaneni, Alexandra S. Simoes, Sarah Brovall, Raquel Sa-Leao, Herman Goossens, Herminia de Lencastre, Birgitta Henriques-Normark
Streptococcus pseudopneumoniae is a close relative of the major human pathogen S. pneumoniae. While initially considered as a commensal species, it has been increasingly associated with lower-respiratory tract infections and high prevalence of antimicrobial resistance (AMR). S. pseudopneumoniae is difficult to identify using traditional typing methods due to similarities with S. pneumoniae and other members of the mitis group (SMG). Using phylogenetic and comparative genomic analyses of SMG genomes, we identified a new molecular marker specific for S. pseudopneumoniae and absent from any other bacterial genome sequenced to date. We found that a large number of known virulence and colonization genes are present in the core S. pseudopneumoniae genome and we reveal the impressive number of known and new surface-exposed proteins encoded by this species. Phylogenetic analyses of S. pseudopneumoniae show that specific clades are associated with allelic variants of core proteins. Resistance to tetracycline and macrolides, the two most...
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biorxivpreprint: Comparative genomic analysis of the emerging pathogen Streptococcus pseudopneumoniae: novel insights into virulence determinants and identification of a novel species-specific molecular marker https://t.co/MkNMclX6nx #bioRxiv
biorxiv_micrbio: Comparative genomic analysis of the emerging pathogen Streptococcus pseudopneumoniae: novel insights into virulence determinants and ... https://t.co/7hfSgo3CDf #biorxiv_micrbio
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Sample Sizes : [16, 3, 5, 4, 4, 3, 3, 24, 38, 36, 39, 8, 793, 44]
Authors: 8
Total Words: 11449
Unqiue Words: 4192

2.001 Mikeys
#2. Core components of endosomal mRNA transport are evolutionarily conserved in fungi
Jessica Mueller, Thomas Pohlmann, Michael Feldbruegge
Active movement of mRNAs by sophisticated transport machineries determines precise spatiotemporal expression of encoded proteins. A prominent example discovered in fungi is microtubule-dependent transport via endosomes. This mode of transport was thought to be only operational in the basidiomycete Ustilago maydis. Here, we report that distinct core components are evolutionarily conserved in fungal species of distantly related phyla like Mucoromycota. Interestingly, orthologues of the key RNA-binding protein Rrm4 from the higher basidiomycete Coprinopsis cinerea and the mucoromycete Rhizophagus irregularis shuttle on endosomes in hyphae of U. maydis. Thus, endosomal mRNA transport appears to be more wide-spread than initially anticipated.
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RNApreprints: Müller, Pohlmann, et al: Core components of endosomal mRNA transport are evolutionarily conserved in fungi https://t.co/rXlI42VfQ5
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Sample Sizes : None.
Authors: 3
Total Words: 3085
Unqiue Words: 1156

1.998 Mikeys
#3. The cyclic nitroxide antioxidant 4-methoxy-TEMPO decreases mycobacterial burden in vivo through host and bacterial targets
Harrison D Black, Wenbo Xu, Elinor Hortle, Sonia I Robertson, Warwick J Britton, Amandeep Kaur, Elizabeth J New, Paul K Witting, Belal Chami, Stefan Oehlers
Tuberculosis is a chronic inflammatory disease caused by persistent infection with Mycobacterium tuberculosis. The rise of antibiotic resistant strains necessitates the design of novel treatments. Recent evidence shows that not only is M. tuberculosis highly resistant to oxidative killing, it also co-opts host oxidant production to induce phagocyte death facilitating bacterial dissemination. We have targeted this redox environment with the cyclic nitroxide derivative 4-methoxy-TEMPO (MetT) in the zebrafish-M. marinum infection model. MetT inhibited the production of mitochondrial ROS and decreased infection-induced cell death to aid containment of infection. We identify a second mechanism of action whereby stress conditions, including hypoxia, found in the infection microenvironment appear to sensitise M. marinum to killing by MetT both in vitro and in vivo. Together, our study demonstrates MetT inhibited the growth and dissemination of M. marinum through host and bacterial targets.
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Sample Sizes : None.
Authors: 10
Total Words: 7736
Unqiue Words: 2554

1.998 Mikeys
#4. Rapid, seamless generation of recombinant poxviruses using host-range and visual selection
Sameera Vipat, Greg Brennan, Sherry L. Haller, Stefan Rothenburg
Vaccinia virus (VACV) was instrumental in eradicating variola virus (VARV), the causative agent of smallpox, from nature. Since this first use as a vaccine, VACV has been developed as a vector for therapeutic vaccines and as an oncolytic virus. These applications take advantage of VACVs easily manipulated genetics and broad host range as an outstanding platform to generate recombinant therapeutics. Several methods have been developed to generate recombinant VACV, including marker selection methods and transient dominant selection. Here, we present a refinement of a host-range selection method coupled with visual identification. Our method takes advantage of selective pressure generated by the host antiviral protein kinase R (PKR) coupled with a fluorescent fusion gene expressing mCherry-tagged E3L, one of two VACV PKR antagonists. This method permits rapid, seamless generation of rVACV in a variety of cell types.
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asbhattac: RT @biorxiv_micrbio: Rapid, seamless generation of recombinant poxviruses using host-range and visual selection https://t.co/KIjQzko52k #b…
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Authors: 4
Total Words: 3277
Unqiue Words: 1105

1.998 Mikeys
#5. Evolutionary dynamics of carbapenem-resistant Acinetobacter baumannii circulating in Chilean hospitals
Andres Opazo-Capurro, Iván San Martín, Mario Quezada-Aguiluz, Felipe Morales, Mariana Domínguez-Yévenes, Celia Lima, Fernanda Esposito, Louise Teixeira Cerdeira, Helia M. Bello-Toledo, Nilton Lincopan, Gerardo Enrique González-Rocha
We analyze the evolutionary dynamics of ninety carbapenem-resistant Acinetobacter baumannii (CRAB) isolates collected between 1990 and 2015 in Chile. CRAB were identified at first in an isolate collected in 2005, which harbored the IS Aba1 - bla OXA-69 arrangement. Later, OXA-58- and OXA-23-producing A. baumannii strains emerged in 2007 and 2009, respectively. This phenomenon was associated with variations in the epidemiology of OXA-type carbapenemases, linked to nosocomial lineages belonging to ST109 (CC1), ST162 (CC79), ST15 (CC15) and ST318 (CC15).
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biorxivpreprint: Evolutionary dynamics of carbapenem-resistant Acinetobacter baumannii circulating in Chilean hospitals https://t.co/SKnuaBQDDk #bioRxiv
biorxiv_micrbio: Evolutionary dynamics of carbapenem-resistant Acinetobacter baumannii circulating in Chilean hospitals https://t.co/JZbOJ1Q5pn #biorxiv_micrbio
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Sample Sizes : [3, 5]
Authors: 11
Total Words: 3560
Unqiue Words: 1627

1.996 Mikeys
#6. Comparative genomics and phylogeny of sequenced IncHI plasmids
Senen Alvarez
Conjugative plasmids from the IncHI incompatibility group are relevant vectors for multidrug resistance. In this study, a comparison of the similarities and differences in the 44 publicly available sequences of IncHI plasmids from Enterobacteriaceae (1961-2013), revealed extensive conservation of their coding sequences. However, each genome had accessory regions with features of degradation or resistance to antibacterial agents. This article elucidates the IncHI1, IncHI2 and IncHI3 subgroup plasmids from the evolutive line based on multiple drug-resistant modules, explains the origin of the IncHI1 pAKU1-like composite transposon lineage, typifies the subgroup IncHI3, which is distantly related to IncHI1 and IncHI2 in phylogenetic analyses, confirms the relations within the transfer regions of H-group plasmids, and points to the divergence time of evolution with phylogenetic trees. Homology between subgroups, as measured by the molecular clock test, indicated that the contemporary IncHI1 and IncHI2 transfer region lineages diverged...
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Sample Sizes : None.
Authors: 1
Total Words: 14416
Unqiue Words: 3703

1.995 Mikeys
#7. Oxidative pathways of deoxyribose and deoxyribonate catabolism
Morgan N. Price, Jayashree Ray, Anthony T. Iavarone, Hans K. Carlson, Elizabeth M. Ryan, Rex R. Malmstrom, Adam P. Arkin, Adam M. Deutschbauer
Using genome-wide mutant fitness assays in diverse bacteria, we identified novel oxidative pathways for the catabolism of 2-deoxy-D-ribose and 2-deoxy-D-ribonate. We propose that deoxyribose is oxidized to deoxyribonate, oxidized to ketodeoxyribonate, and cleaved to acetyl-CoA and glyceryl-CoA. We have genetic evidence for this pathway in three genera of bacteria, and we confirmed the oxidation of deoxyribose to ketodeoxyribonate in vitro. In Pseudomonas simiae , the expression of enzymes in the pathway is induced by deoxyribose or deoxyribonate, while in Paraburkholderia bryophila and in Burkholderia phytofirmans , the pathway proceeds in parallel with the known deoxyribose 5-phosphate aldolase pathway. We identified another oxidative pathway for the catabolism of deoxyribonate, with acyl-CoA intermediates, in Klebsiella michiganensis . Of these four bacteria, only P. simiae relies entirely on an oxidative pathway to consume deoxyribose. The deoxyribose dehydrogenase of P. simiae is either non-specific or evolved recently, as...
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Sample Sizes : None.
Authors: 8
Total Words: 11745
Unqiue Words: 3283

1.985 Mikeys
#8. Biliary microbiota and bile acids composition in cholelithiasis
Vyacheslav Alexeyevich Petrov, María A. Fernández-Peralbo, Rico Derks, Elena M. Knyazeva, Nikolay V. Merzlikin, Alexey E. Sazonov, Oleg A. Mayboroda, Irina V. Saltykova
Background A functional interplay between BAs and microbial composition in gut is a well-documented phenomenon. In bile this phenomenon is far less studied and with this report we describe the interactions between the BAs and microbiota in this complex biological matrix. Methodology Thirty-seven gallstone disease patients of which twenty-one with Opisthorchis felineus infection were enrolled in the study. The bile samples were obtained during laparoscopic cholecystectomy for gallstone disease operative treatment. Common bile acids composition were measured by LC-MS/MS using a column in reverse phase. For all patients gallbladder microbiota was previously analyzed with 16S rRNA gene sequencing on Illumina MiSeq platform. The associations between bile acids composition and microbiota were analysed. Principal findings Bile acids signature and O. felineus infection status exerts influence on beta-diversity of bile microbial community. Direct correlations were found between taurocholic acid, taurochenodeoxycholic acid concentrations...
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Sample Sizes : None.
Authors: 8
Total Words: 4745
Unqiue Words: 1720

0.0 Mikeys
#9. Intravenous colistin use for infections due to multidrug-resistant gram-negative bacilli in critically ill paediatric patients: a systematic review and meta-analysis
Spyridon A Karageorgos, Hamid Bassiri, George Siakallis, Michael Miligkos, Constantinos Tsioutis
Background: Data are limited regarding the clinical effectiveness and safety of intravenous colistin for treatment of infections by multidrug-resistant gram-negative bacilli (MDR-GNB) in the paediatric intensive care unit (PICU). Methods: Systematic review of intravenous colistin use in critically ill paediatric patients with MDR-GNB infection in PubMed, Scopus and Embase (through January 31st, 2018). Results: Out of 1,181 citations, 7 studies were included on the use of intravenous colistin for 405 patients in PICU. Majority of patients were diagnosed with lower respiratory tract infections, with Acinetobacter baumannii being the predominant pathogen. Colistin dosages ranged between 2.6-18 mg/kg/day, with none but one case reporting a loading dose. Emergence of colistin-resistance during treatment was reported in two cases. Nephrotoxicity and neurotoxicity were reported in 6.1% and 0.5% respectively, but concomitant medications and severe underlying illness limited our ability to definitively associate use of colistin with...
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Sample Sizes : None.
Authors: 5
Total Words: 7166
Unqiue Words: 2791

0.0 Mikeys
#10. DETECTION OF Wolbachia IN FIELD-COLLECTED MOSQUITO VECTOR, Aedes aegypti
Thaddeus Carvajal, Kazuki Hashimoto, Reza Kurniawan Harnandika, Divina Amalin, Kozo Watanabe
It was the impression from past literature that Wolbachia is not naturally found in Ae. aegypti. However, there are have been reports that recently reveals the presence of this endosymbiont in this mosquito vector. With this, our study presents additional support of Wolbachia infection in Ae. aegypti by screening field-collected adult mosquitoes using Wolbachia-specific 16S rDNA and its surface protein (wsp) makers under optimized PCR conditions. From a total of 672 Ae. aegpyti adult mosquito samples collected in Metropolitan Manila, Philippines, 113 (16.8%) and 89 (13.2%) individual mosquito samples were determined to be Wolbachia infected using the wsp and 16S rDNA markers, respectively. The Ae. aegpyti wsp sample sequences were similar or identical to five known Wolbachia strains belonging to supergroups A or B while majority of 16S rDNA sample sequences were similar to strains belonging to supergroup B. Overall, 80 (11.90%) individual mosquito samples revealed to show positive amplifications in both markers and 69.0% showed...
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biorxivpreprint: DETECTION OF Wolbachia IN FIELD-COLLECTED MOSQUITO VECTOR, Aedes aegypti https://t.co/OXY8QYGlS4 #bioRxiv
biorxiv_micrbio: DETECTION OF Wolbachia IN FIELD-COLLECTED MOSQUITO VECTOR, Aedes aegypti https://t.co/zRR0ztfdDw #biorxiv_micrbio
LlewellynGreen: I was just telling people otherwise last week… DETECTION OF Wolbachia IN FIELD-COLLECTED MOSQUITO VECTOR, Aedes aegypti https://t.co/MjoThiGQ1F Could have a big impact if true; some additional phenotypic confirmation might also be nice #365papers
thelonevirologi: DETECTION OF Wolbachia IN FIELD-COLLECTED MOSQUITO VECTOR, Aedes aegypti https://t.co/EVWeY2qh0f
JohannaOhm: DETECTION OF Wolbachia IN FIELD-COLLECTED MOSQUITO VECTOR, Aedes aegypti https://t.co/5q6BnL5yHA
john_jxw: RT @biorxivpreprint: DETECTION OF Wolbachia IN FIELD-COLLECTED MOSQUITO VECTOR, Aedes aegypti https://t.co/OXY8QYGlS4 #bioRxiv
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Sample Sizes : None.
Authors: 5
Total Words: 9012
Unqiue Words: 3198

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