scholarly journals Identification of the novel tigecycline resistance gene tet(X6) and its variants in Myroides, Acinetobacter and Proteus of food animal origin

2020 ◽  
Vol 75 (6) ◽  
pp. 1428-1431 ◽  
Author(s):  
Dejun Liu ◽  
Weishuai Zhai ◽  
Huangwei Song ◽  
Yulin Fu ◽  
Stefan Schwarz ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Binding Capacity ◽  
Homology Modelling ◽  
Bacterial Species ◽  
Animal Origin ◽  
The Novel ◽  
Food Animal ◽  
Genomic Environment ◽  
Pig Farm ◽  
Acinetobacter Spp

Abstract Objectives To report a novel tigecycline resistance gene, tet(X6), and its variants in four bacterial species isolated from chickens and pigs in China. Methods WGS was conducted to identify the suspected resistance genes in the tigecycline-resistant Myroides phaeus 18QD1AZ29W. Functional cloning, homology modelling and molecular docking were performed to compare the function with other Tet(X) variants. Retrospective screening for tet(X6) was conducted for 80 isolates in our WGS data collection, and all genomic environments of tet(X6)-positive isolates were analysed. Results The tigecycline-resistant M. phaeus 18QD1AZ29W isolated from a pig farm in Shandong in 2018 was positive for tet(X2) and a novel tet(X) gene, designated tet(X6). Tet(X6) could increase the MICs of all tested tetracyclines/glycylcyclines for Escherichia coli only 2- to 4-fold, which was possibly due to a lower tetracycline binding capacity of Tet(X6) compared with that of other Tet(X) variants. Retrospective screening showed that seven other isolates (7/80, 8.8%), comprising four Proteus spp. and three Acinetobacter spp. from chickens and pigs in Shandong and Guangdong, were positive for three different variants of tet(X6). The analysis of the genomic environment revealed that two tet(X6)-positive isolates from M. phaeus and Proteus cibarius, respectively, contained ISCR2, which may play a role in tet(X6) transmission. Conclusions This study identified a novel type of tigecycline resistance gene, tet(X6), in Myroides, Acinetobacter and Proteus from chickens and swine. Tet(X6) conferred lower tetracycline/glycylcycline MICs than other Tet(X) variants, and ISCR2 may play a role in the transmission of tet(X6).

scholarly journals Detection of the plasmid-encoded fosfomycin resistance gene fosA3 in Escherichia coli of food-animal origin

2012 ◽  
Vol 68 (4) ◽  
pp. 766-770 ◽  
Author(s):  
J. Hou ◽  
X. Yang ◽  
Z. Zeng ◽  
L. Lv ◽  
T. Yang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Resistance Gene ◽  
Animal Origin ◽  
Food Animal ◽  
Fosfomycin Resistance

scholarly journals Nearly Identical Plasmids Encoding VIM-1 and Mercury Resistance in Enterobacteriaceae from North-Eastern Germany

2021 ◽  
Vol 9 (7) ◽  
pp. 1345
Author(s):  
Stefan E. Heiden ◽  
Katharina Sydow ◽  
Stephan Schaefer ◽  
Ingo Klempien ◽  
Veronika Balau ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Bacterial Species ◽  
Genomic Analysis ◽  
Public Health Problem ◽  
Multidrug Resistant ◽  
Mercury Resistance ◽  
Major Public Health Problem ◽  
Eastern Germany ◽  
North Eastern ◽  
Resistance Plasmids

The emergence of carbapenemase-producing Enterobacteriaceae limits therapeutic options and presents a major public health problem. Resistances to carbapenems are mostly conveyed by metallo-beta-lactamases (MBL) including VIM, which are often encoded on resistance plasmids. We characterized four VIM-positive isolates that were obtained as part of a routine diagnostic screening from two laboratories in north-eastern Germany between June and August 2020. Whole-genome sequencing was performed to address (a) phylogenetic properties, (b) plasmid content, and (c) resistance gene carriage. In addition, we performed phenotypic antibiotic and mercury resistance analyses. The genomic analysis revealed three different bacterial species including C. freundii, E. coli and K. oxytoca with four different sequence types. All isolates were geno- and phenotypically multidrug-resistant (MDR) and the phenotypic profile was explained by the underlying resistance gene content. Three isolates of four carried nearly identical VIM-1-resistance plasmids, which in addition encoded a mercury resistance operon and showed some similarity to two publicly available plasmid sequences from sources other than the two laboratories above. Our results highlight the circulation of a nearly identical IncN-type VIM-1-resistance plasmid in different Enterobacteriaceae in north-eastern Germany.

scholarly journals Comparative genomics suggests a taxonomic revision of the Staphylococcus cohnii species complex

2021 ◽  
Author(s):  
Anna Lavecchia ◽  
Matteo Chiara ◽  
Caterina De Virgilio ◽  
Caterina Manzari ◽  
Carlo Pazzani ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Species Complex ◽  
Large Scale ◽  
Genomic Sequence ◽  
Bacterial Species ◽  
Taxonomic Revision ◽  
Distinct Species ◽  
The Novel ◽  
Staphylococcus Cohnii ◽  
Taxonomic Assignments

Abstract Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences—including a novel SC isolate—revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.

scholarly journals Detection of the staphylococcal multiresistance gene cfr in Proteus vulgaris of food animal origin

2011 ◽  
Vol 66 (11) ◽  
pp. 2521-2526 ◽  
Author(s):  
Y. Wang ◽  
Y. Wang ◽  
C.-M. Wu ◽  
S. Schwarz ◽  
Z. Shen ◽  
...  
Keyword(s):  
Animal Origin ◽  
Proteus Vulgaris ◽  
Food Animal

Genetic mapping of the novel Turnip mosaic virus resistance gene TuRB03 in Brassica napus

2003 ◽  
Vol 107 (7) ◽  
pp. 1169-1173 ◽  
Author(s):  
S. L. Hughes ◽  
P. J. Hunter ◽  
A. G. Sharpe ◽  
M. J. Kearsey ◽  
D. J. Lydiate ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Genetic Mapping ◽  
Mosaic Virus ◽  
Resistance Gene ◽  
Virus Resistance ◽  
Turnip Mosaic Virus ◽  
The Novel ◽  
Virus Resistance Gene

scholarly journals Genotyping of evolving prokaryotic populations

2016 ◽  
Author(s):  
Markus Zojer ◽  
Lisa N Schuster ◽  
Frederik Schulz ◽  
Alexander Pfundner ◽  
Matthias Horn ◽  
...  
Keyword(s):  
Experimental Evolution ◽  
Bacterial Species ◽  
Clinical Diagnostics ◽  
Structural Variations ◽  
Natural Habitats ◽  
Reliable Prediction ◽  
Low Frequencies ◽  
Bacterial Populations ◽  
Sequencing Errors ◽  
Genomic Environment

Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments, clinical diagnostics and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with the currently used short sequencing reads. Recent advances in NGS technologies improved the speed and coverage and thus allowed for deep sequencing of bacterial populations. This facilitates the quantitative assessment of genomic heterogeneity, including low frequent alleles or haplotypes. However, false positive variant predictions due to sequencing errors and mapping artifacts of short reads need to be prevented. We therefore created VarCap, a workflow for the reliable prediction of different types of variants even at low frequencies. In order to predict SNPs, indels and structural variations, we evaluated the sensitivity and accuracy of different software tools using synthetic read data. The results suggested that the best sensitivity could be reached by a combination of different tools. We identified possible reasons for false predictions and used this knowledge to improve the accuracy by post-filtering the predicted variants according to properties such as frequency, coverage, genomic environment/localization and co-localization with other variants. This resulted in the reliable prediction of variants above a minimum relative abundance of 2%. VarCap is designed for being routinely used within experimental evolution experiments or for clinical diagnostics. The detected variants are reported as frequencies within a vcf file and as a graphical overview of the distribution of the different variant/allele/haplotype frequencies. The source code of VarCap is available at https://github.com/ma2o/VarCap. In order to provide this workflow to a broad community, we implemeted VarCap on a Galaxy webserver (Afgan et al. 2016) , which is accessible at http://galaxy.csb.univie.ac.at.

scholarly journals Evaluating Flinders Technology Associates card for transporting bacterial isolates and retrieval of bacterial DNA after various storage conditions

2020 ◽  
Vol 13 (10) ◽  
pp. 2243-2251
Author(s):  
Azhar G. Shalaby ◽  
Neveen R. Bakry ◽  
Abeer A. E. Mohamed ◽  
Ashraf A. Khalil
Keyword(s):  
Nucleic Acid ◽  
Bacterial Species ◽  
Storage Conditions ◽  
Animal Origin ◽  
Cell Detection ◽  
Bacterial Cells ◽  
Gram Positive ◽  
Bacterial Dna ◽  
Gram Negative ◽  
Fta Cards

Background and Aim: Flinders Technology Associates (FTA) cards simplify sample storage, transport, and extraction by reducing cost and time for diagnosis. This study evaluated the FTA suitability for safe transport and storage of Gram-positive and Gram-negative bacterial cells of animal origin on its liquid culture form and from organ impression smears (tissues) under the same routine condition of microbiological laboratory along with detecting their nucleic acid over different storage conditions. Materials and Methods: Increase in bacterial count from 104 to 107 (colony-forming units/mL) of 78 isolates representing seven bacterial species was applied onto cards. FTA cards were grouped and inoculated by these bacteria and then stored at different conditions of 24-27°C, 4°C, and –20°C for 24 h, for 2 weeks, for 1 and 3 month storage, respectively. Bacteriological examination was done, after which bacterial DNA was identified using specific primers for each bacterial type and detected by polymerase chain reaction (PCR). Results: The total percentage of recovered bacteria from FTA cards was 66.7% at 24-27–C for 24 h, the detection limit was 100% in Gram-positive species, while it was 57.4% in Gram-negative ones. Regarding viable cell detection from organ impression smears, it was successful under the previous conditions. No live bacterial cells were observed by bacteriological isolation rather than only at 24-27°C for 24 h storage. All bacterial DNA were sufficiently confirmed by the PCR technique at different conditions. Conclusion: Overall, the FTA card method was observed to be a valid tool for nucleic acid purification for bacteria of animal origin in the form of culture or organ smears regardless of its Gram type and is used for a short time only 24 h for storage and transport of live bacteria specifically Gram-positive type. Moreover, the bacterial nucleic acid was intact after storage in –20°C for 3 months and was PCR amplifiable.

scholarly journals Synonymous lysine codon usage modification in a mobile antibiotic resistance gene similarly alters protein production in bacterial species with divergent lysine codon usage biases because it removes a duplicate AAA lysine codon

2018 ◽  
Author(s):  
Mohammed Alorabi ◽  
Aisha M. AlAmri ◽  
Yuiko Takebayashi ◽  
Kate J. Heesom ◽  
Matthew B. Avison
Keyword(s):  
Antibiotic Resistance ◽  
Codon Usage ◽  
Resistance Gene ◽  
Codon Bias ◽  
Protein Production ◽  
Bacterial Species ◽  
Antibiotic Resistance Gene ◽  
Site Directed Mutagenesis ◽  
Acinetobacter Baumanii ◽  
Highly Expressed Genes

AbstractThe mobile antibiotic resistance gene blaIMP-1 is clinically important and has a synonymous AAA:AAG lysine codon usage bias of 73:27. This bias is like that seen in experimentally determined highly expressed genes in Escherichia coli and Acinetobacter baumanii, but quite different from that seen in Pseudomonas aeruginosa (26:74 AAA:AAG). Here we show that, paradoxically, shifting the AAA:AAG lysine codon bias to 8:92 in blaIMP-1 expressed from a natural promoter results in significantly more IMP-1 production in all three species. Sequential site directed mutagenesis revealed that increased IMP-1 production occurs following removal of an AAA,AAA double lysine codon and that otherwise, lysine codon usage had no observable impact on IMP-1 production. We conclude that ribosomal slippage at this poly-adenosine region reduces efficient translation of IMP-1 and that punctuating the region with guanine reduces ribosomal slippage and increases IMP-1 production.

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