Analysis of resistance genes of clinical Pannonibacter phragmitetus strain 31801 by complete genome sequencing

Archives of Microbiology
Desong MingXiao-Tin Chen

Abstract

To clarify the resistance mechanisms of Pannonibacter phragmitetus 31801, isolated from the blood of a liver abscess patient, at the genomic level, we performed whole genomic sequencing using a PacBio RS II single-molecule real-time long-read sequencer. Bioinformatic analysis of the resulting sequence was then carried out to identify any possible resistance genes. Analyses included Basic Local Alignment Search Tool searches against the Antibiotic Resistance Genes Database, ResFinder analysis of the genome sequence, and Resistance Gene Identifier analysis within the Comprehensive Antibiotic Resistance Database. Prophages, clustered regularly interspaced short palindromic repeats (CRISPR), and other putative virulence factors were also identified using PHAST, CRISPRfinder, and the Virulence Factors Database, respectively. The circular chromosome and single plasmid of P. phragmitetus 31801 contained multiple antibiotic resistance genes, including those coding for three different types of β-lactamase [NPS β-lactamase (EC 3.5.2.6), β-lactamase class C, and a metal-dependent hydrolase of β-lactamase superfamily I]. In addition, genes coding for subunits of several multidrug-resistance efflux pumps were identified, including those tar...Continue Reading

References

Feb 1, 1975·Journal of Clinical Pathology·B HolmesH Malnick
May 1, 1990·The Journal of Infection·K P McKinleyR G Masterton
Jan 1, 1986·Antimicrobial Agents and Chemotherapy·D M Livermore, C S Jones
Apr 1, 1993·Journal of Clinical Microbiology·B HolmesM I Daneshvar
Mar 1, 1997·The Journal of Infection·P J Jenks, E J Shaw
Nov 11, 1999·Nucleic Acids Research·A L DelcherS L Salzberg
Dec 3, 1999·Antimicrobial Agents and Chemotherapy·S Westbrock-WadmanC K Stover
Dec 20, 2000·Bioinformatics·K RutherfordB Barrell
Sep 7, 2001·Journal of Bacteriology·N KobayashiA Yamaguchi
Sep 15, 2001·Antimicrobial Agents and Chemotherapy·H Pai, G A Jacoby
Jan 18, 2002·Antimicrobial Agents and Chemotherapy·Xian-Zhi LiKeith Poole
Apr 25, 2003·International Journal of Systematic and Evolutionary Microbiology·Andrea K BorsodiKároly Márialigeti
Jun 28, 2005·Nucleic Acids Research·John Besemer, Mark Borodovsky
Apr 15, 2006·Clinical Microbiology Reviews·Laura J V Piddock
Dec 6, 2006·Antimicrobial Agents and Chemotherapy·Corinna KehrenbergStefan Schwarz
Jan 24, 2007·Bioinformatics·Arthur L DelcherSteven L Salzberg
Dec 19, 2007·Antimicrobial Agents and Chemotherapy·Laurence Damier-PiollePatrice Courvalin
Feb 12, 2008·BMC Genomics·Ramy K AzizOlga Zagnitko
Apr 16, 2008·Nucleic Acids Research·Jason R Grant, Paul Stothard
Apr 30, 2008·Nucleic Acids Research·Ibtissem GrissaChristine Pourcel
Oct 4, 2008·Nucleic Acids Research·Bo Liu, Mihai Pop
Jan 27, 2009·Biochimica Et Biophysica Acta·Klaas M Pos
Jun 30, 2009·Bioinformatics·Victor M MarkowitzNikos C Kyrpides
Aug 11, 2010·Antimicrobial Agents and Chemotherapy·Sébastien CoyneBruno Périchon
Dec 22, 2010·Antimicrobial Agents and Chemotherapy·Sébastien CoyneBruno Périchon
Jun 16, 2011·Nucleic Acids Research·You ZhouDavid S Wishart
Dec 20, 2011·Bioprocess and Biosystems Engineering·Yan ShiYuehun Chen
Jul 12, 2012·The Journal of Antimicrobial Chemotherapy·Ea ZankariMette Voldby Larsen
Sep 4, 2012·Archives of Microbiology·Saumya BandyopadhyaySubrata K Das
Apr 10, 2013·Extremophiles : Life Under Extreme Conditions·Cristian ComanNicolae Dragoş
May 8, 2013·Antimicrobial Agents and Chemotherapy·Andrew G McArthurGerard D Wright
Oct 18, 2013·Molecular Biology and Evolution·Koichiro TamuraSudhir Kumar
Dec 3, 2013·Nucleic Acids Research·Ross OverbeekRick Stevens
Sep 27, 2014·MicrobiologyOpen·Evelyne TurlinCécile Wandersman
Nov 28, 2014·Nucleic Acids Research·Michael Y GalperinEugene V Koonin

❮ Previous
Next ❯

Citations

Jan 17, 2020·International Journal of Environmental Research and Public Health·Alexandra BastaraudRonan Jambou

❮ Previous
Next ❯

Datasets Mentioned

BETA
CP013068
14782
CP013069

Methods Mentioned

BETA
PCR

Software Mentioned

WebMGA
RAST SEED
ResFinder
Glimmer
GCView
BLAST
Artemis
Integrated Microbial Genomes and Microbiomes system
GeneMarkS
ClustalW

Related Concepts

Related Feeds

CRISPR (general)

Clustered regularly interspaced short palindromic repeats (CRISPR) are DNA sequences in the genome that are recognized and cleaved by CRISPR-associated proteins (Cas). CRISPR-Cas system enables the editing of genes to create or correct mutations. Discover the latest research on CRISPR here.

CRISPR for Genome Editing

Genome editing technologies enable the editing of genes to create or correct mutations. Clustered regularly interspaced short palindromic repeats (CRISPR) are DNA sequences in the genome that are recognized and cleaved by CRISPR-associated proteins (Cas). Here is the latest research on the use of CRISPR-Cas system in gene editing.

CRISPR Ribonucleases Deactivation

CRISPR-Cas system enables the editing of genes to create or correct mutations. This feed focuses on mechanisms that underlie deactivation of CRISPR ribonucleases. Here is the latest research.

Aminoglycosides (ASM)

Aminoglycoside is a medicinal and bacteriologic category of traditional Gram-negative antibacterial medications that inhibit protein synthesis and contain as a portion of the molecule an amino-modified glycoside. Discover the latest research on aminoglycoside here.

CRISPRi Screens for Antibiotics

The CRISPR-Cas system is a gene editing technique that can be used for high-throughput genome-wide screens to identify modes of actions of novel antibiotics. Here is the latest research.

Aminoglycosides

Aminoglycoside is a medicinal and bacteriologic category of traditional Gram-negative antibacterial medications that inhibit protein synthesis and contain as a portion of the molecule an amino-modified glycoside. Discover the latest research on aminoglycoside here.