Deciphering the resistome of the widespreadP. aeruginosaST175 international high-risk clone through whole genome sequencing

Whole genome sequencing (WGS) was used for the characterization of the, frequently extensively-drug resistant (XDR),P. aeruginosahigh-risk clone ST175. A total of eighteen ST175 isolates recovered from 8 different Spanish hospitals were analyzed; four isolates from four different French hospitals were included for comparison. The typical resistance profile of ST175 included penicillins, cephalosporins, monobactams, carbapenems, aminoglycosides, and fluoroquinolones. In the phylogenetic analysis, the four French isolates clustered together with the two isolates from one of the Spanish regions. Sequence variation was analyzed for 146 chromosomal genes related to antimicrobial resistance and horizontally-acquired genes were explored using online databases. The resistome of ST175 was mainly determined by mutational events, with resistance traits common to all or nearly all of the strains, including specificampRmutations leading toampCoverexpression, specific mutations inoprDconferring carbapenem resistance or amexZmutation leading to MexXY overexpression. All isolates additionally harbored anaadBgene conferring gentamicin and tobramycin resistance. Several other resistance traits were specific to certain geographic areas such as a streptomycin resistanceaadA13gene detected in all four isolates from France and in the 2 isolates from the Cantabria region or aglpTmutation conferring fosfomycin resistance detected in all but these six isolates. Finally, several unique resistance mutations were detected in single isolates; particularly interesting among them were those in genes encoding PBPs (PBP1A, PBP3 and PBP4). Thus, these results provide valuable information for understanding the genetic basis of resistance and the dynamics of dissemination and evolution of high-risk clones.

Download Full-text

Molecular characterization of rectal isolates of carbapenemase-negative carbapenem-resistant enterobacterales obtained from ICU patients in Kuwait by whole-genome sequencing

Journal of Medical Microbiology ◽

10.1099/jmm.0.001409 ◽

2021 ◽

Vol 70 (9) ◽

Author(s):

Amani Al Fadhli ◽

Wafaa Jamal ◽

Vincent O. Rotimi

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Carbapenem Resistance ◽

Efflux Pumps ◽

Multidrug Resistant ◽

Whole Genome ◽

Genetic Characteristics ◽

Carbapenem Resistant ◽

Genes Encoding ◽

Amoxicillin Clavulanic Acid

Introduction. Carbapenem-resistant enterobacterales (CRE) are listed among the most urgent antibiotic resistance threats. Hypothesis. Previous studies on the mechanisms of CRE in Kuwait have focused on carbapenemases. There have been no studies on non-carbapenemase-producing CRE in Kuwait. Aim/Gap Statement. The aim of this study was to investigate the genetic characteristics of non-carbapenemase-producing carbapenem-resistant enterobacterales (NCPE) isolates using whole-genome sequencing (WGS). Methodology. Fourteen confirmed NCPE isolates that were negative for genes encoding carbapenemase production by polymerase chain reaction (PCR) assays using rectal swabs from intensive care unit patients were characterized using phenotypic, PCR and WGS methods. Susceptibility testing was performed via Etest and clonality via multi-locus sequence typing (MLST). Results. All of the isolates were resistant to ertapenem; 78.6 % were resistant to imipenem, meropenem and trimethoprim–sulfamethoxazole. Resistance to the other antibiotics was variable, ranging from 28.5 (colistin) through 50 (tigecycline) and 64.3 (amikacin) up to 85.7 % against both amoxicillin–clavulanic acid and ciprofloxacin. WGS detected several resistance genes mediating the production of β-lactamases, genes encoding an outer-membrane porin permeability mutation resulting in reduced susceptibility to β-lactams, including carbapenems, and genes for multidrug-resistant (MDR) efflux pumps. The isolates also possessed global activator protein MarA, which mediated reduced permeability to β-lactams. The existence of β-lactamase genes, overexpression of MDR efflux pumps and reduced permeability mediated by the porin genes were responsible for carbapenem resistance. Conclusions. This finding reflects the superior detection capabilities offered by WGS analysis, which can be used to complement traditional methods and overcome their limited resolution in clinical settings.

Download Full-text

Phenotype prediction and characterization of 25 pharmacogenes in Thais from whole genome sequencing for clinical implementation

Scientific Reports ◽

10.1038/s41598-020-76085-3 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

John Mauleekoonphairoj ◽

Monpat Chamnanphon ◽

Apichai Khongphatthanayothin ◽

Boosamas Sutjaporn ◽

Pharawee Wandee ◽

...

Keyword(s):

High Risk ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Structural Variation ◽

Whole Genome ◽

Clinical Implementation ◽

Thai Population ◽

Phenotype Prediction ◽

Specific Variation

Abstract Publicly available pharmacogenomics (PGx) databases enable translation of genotype data into clinically actionable information. As variation within pharmacogenes is population-specific, this study investigated the spectrum of 25 clinically relevant pharmacogenes in the Thai population (n = 291) from whole genome sequencing. The bioinformatics tool Stargazer was used for phenotype prediction, through assignment of alleles and detection of structural variation. Known and unreported potentially deleterious PGx variants were identified. Over 25% of Thais carried a high-risk diplotype in CYP3A5, CYP2C19, CYP2D6, NAT2, SLCO1B1, and UGT1A1. CYP2D6 structural variants accounted for 83.8% of all high-risk diplotypes. Of 39 known PGx variants identified, six variants associated with adverse drug reactions were common. Allele frequencies of CYP3A5*3 (rs776746), CYP2B6*6 (rs2279343), and NAT2 (rs1041983) were significantly higher in Thais than East-Asian and global populations. 121 unreported variants had potential to exert clinical impact, majority were rare and population-specific, with 60.3% of variants absent from gnomAD database. This study demonstrates the population-specific variation in clinically relevant pharmacogenes, the importance of CYP2D6 structural variation detection in the Thai population, and potential of unreported variants in explaining drug response. These findings are essential in development of dosing guidelines, PGx testing, clinical trials, and drugs.

Download Full-text

Characterization of an Enterobacter cloacae Strain Producing both KPC and NDM Carbapenemases by Whole-Genome Sequencing

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01275-15 ◽

2015 ◽

Vol 59 (10) ◽

pp. 6625-6628 ◽

Cited By ~ 27

Author(s):

Wenjing Wu ◽

Yu Feng ◽

Alessandra Carattoli ◽

Zhiyong Zong

Keyword(s):

Whole Genome Sequencing ◽

Bloodstream Infection ◽

Genome Sequencing ◽

Carbapenem Resistance ◽

Enterobacter Cloacae ◽

Whole Genome ◽

Content Type ◽

Carbapenem Resistant

ABSTRACTA carbapenem-resistantEnterobacter cloacaestrain, WCHECl-14653, causing a fatal bloodstream infection, was characterized by genome sequencing and conjugation experiments. The strain carried two carbapenemase genes,blaNDM-1andblaKPC-2, on separate IncF plasmids. The coexistence ofblaNDM-1andblaKPC-2conferred slightly higher-level carbapenem resistance compared with that ofblaNDM-1orblaKPC-2alone, and the coexistence of two IncF plasmids may generate new platforms for spreading carbapenemase genes.

Download Full-text

Faculty Opinions recommendation of Characterization of uterine leiomyomas by whole-genome sequencing.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718021966.793479049 ◽

2013 ◽

Author(s):

Hiroshi Ishikawa

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Uterine Leiomyomas ◽

Whole Genome

Download Full-text

Characterization of Shiga Toxin‐Producing Escherichia coli Isolated From Cattle and Sheep in Xinjiang Province, China, Using Whole‐Genome Sequencing

Transboundary and Emerging Diseases ◽

10.1111/tbed.13999 ◽

2021 ◽

Author(s):

Yingyu Liu ◽

Huoming Li ◽

Xuhua Chen ◽

Panpan Tong ◽

Yan Zhang ◽

...

Keyword(s):

Escherichia Coli ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Shiga Toxin ◽

Whole Genome ◽

Cattle And Sheep

Download Full-text

SureSelect targeted enrichment, a new cost effective method for the whole genome sequencing of Candidatus Liberibacter asiaticus

Scientific Reports ◽

10.1038/s41598-019-55144-4 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

Weili Cai ◽

Schyler Nunziata ◽

John Rascoe ◽

Michael J. Stulberg

Keyword(s):

Whole Genome Sequencing ◽

Molecular Characterization ◽

Genome Sequencing ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Coverage ◽

Metagenomic Sample ◽

Liberibacter Asiaticus

AbstractHuanglongbing (HLB) is a worldwide deadly citrus disease caused by the phloem-limited bacteria ‘Candidatus Liberibacter asiaticus’ (CLas) vectored by Asian citrus psyllids. In order to effectively manage this disease, it is crucial to understand the relationship among the bacterial isolates from different geographical locations. Whole genome sequencing approaches will provide more precise molecular characterization of the diversity among populations. Due to the lack of in vitro culture, obtaining the whole genome sequence of CLas is still a challenge, especially for medium to low titer samples. Hundreds of millions of sequencing reads are needed to get good coverage of CLas from an HLB positive citrus sample. In order to overcome this limitation, we present here a new method, Agilent SureSelect XT HS target enrichment, which can specifically enrich CLas from a metagenomic sample while greatly reducing cost and increasing whole genome coverage of the pathogen. In this study, the CLas genome was successfully sequenced with 99.3% genome coverage and over 72X sequencing coverage from low titer tissue samples (equivalent to 28.52 Cq using Li 16 S qPCR). More importantly, this method also effectively captures regions of diversity in the CLas genome, which provides precise molecular characterization of different strains.

Download Full-text

Transmission of Multidrug/Rifampicin-Resistant Mycobacterium Tuberculosis in Chongqing, China: A Retrospective Observational Study Using Whole-Genome Sequencing

10.21203/rs.3.rs-717466/v1 ◽

2021 ◽

Author(s):

Bing Zhao ◽

Chunfa Liu ◽

Jiale Fan ◽

Aijing Ma ◽

Wencong He ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Resistance Mutations ◽

Treatment Information ◽

Recent Transmission ◽

Drugs Analysis ◽

Lineage 2 ◽

And Cluster Analysis

Abstract Background: Multidrug/rifampicin-resistant tuberculosis (MDR/RR-TB) is a global barrel for ‘Stop TB plan’. China has the second highest MDR/RR-TB burden in whole world wide. Understanding the transmission dynamic is facilitated for disease control. Methods: Whole genome sequencing (WGS) data from patients of Chongqing tuberculosis control institute were used for phylogenetic classifications, resistance predictions, and cluster analysis as indicator for recent transmission (RT). Factors associated with MDR/RR-TB were defined by a logistic regression model. Results: A total of 223 cases of MDR/RR-TB were recorded between Jan 1, 2018 and Dec 31, 2020, and 200 cases obtained relevant treatment information. The patients who are older than 55 year old were more likely to suffering from death. 178 MDR/RR strains were obtained WGS data, 152 were classified as lineage 2 strains. 80 (44.9%, 80 of 178) strains were in 20 genomic clusters that differed by 12 or fewer single nucleotide polymorphisms (SNPs), indicating RT. Patients who were infected with lineage 2 strains is a significant factor driving the epidemic towards MDR/RR-TB. Resistance mutations of first-line tuberculosis drugs analysis found that 79 (98.8%) of all 80 strains defined as RT have same mutations among each clusters totally. 55% (44 of 80) of the MDR/RR-TB strains accumulated additional drug resistance mutations along the transmission chain, especially fluoroquinolones (FQs) (63.6%, 28 of 44). Conclusions: The age is the most significant factor that causes death of MDR/RR-TB patients. RT of MDR/RR strains is not only drove the MDR/RR-TB epidemic, but also accumulated more serious resistance along the transmission chains.

Download Full-text

Serotype Diversity and Antimicrobial Resistance amongSalmonella entericaIsolates from Patients at an Equine Referral Hospital

Applied and Environmental Microbiology ◽

10.1128/aem.02829-17 ◽

2018 ◽

Vol 84 (13) ◽

pp. e02829-17 ◽

Cited By ~ 3

Author(s):

I. M. Leon ◽

S. D. Lawhon ◽

K. N. Norman ◽

D. S. Threadgill ◽

N. Ohta ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Salmonella Enterica ◽

Referral Hospital ◽

Whole Genome ◽

Content Type ◽

Genes Encoding ◽

Life Threatening ◽

Common Serotypes

ABSTRACTAlthoughSalmonella entericacan produce life-threatening colitis in horses, certain serotypes are more commonly associated with clinical disease. Our aim was to evaluate the proportional morbidity attributed to different serotypes, as well as the phenotypic and genotypic antimicrobial resistance (AMR) ofSalmonellaisolates from patients at an equine referral hospital in the southern United States. A total of 255Salmonellaisolates was obtained from clinical samples of patients admitted to the hospital between 2007 and 2015. Phenotypic resistance to 14 antibiotics surveilled by the U.S. National Antimicrobial Resistance Monitoring System was determined using a commercially available panel. Whole-genome sequencing was used to identify serotypes and genotypic AMR. The most common serotypes wereSalmonella entericaserotype Newport (18%),Salmonella entericaserotype Anatum (15.2%), andSalmonella entericaserotype Braenderup (11.8%). Most (n= 219) of the isolates were pansusceptible, while 25 were multidrug resistant (≥3 antimicrobial classes). Genes encoding beta-lactam resistance, such asblaCMY-2,blaSHV-12,blaCTX-M-27, andblaTEM-1B, were detected. TheqnrB2 andaac(6′)-Ib-crgenes were present in isolates with reduced susceptibility to ciprofloxacin. Genes encoding resistance to gentamicin (aph(3′)-Ia,aac(6′)-IIc), streptomycin (strA andstrB), sulfonamides (sul1), trimethoprim (dfrA), phenicols (catA), tetracyclines [tet(A) andtet(E)], and macrolides [ere(A)] were also identified. The main predicted incompatibility plasmid type was I1 (10%). Core genome-based analyses revealed phylogenetic associations between isolates of common serotypes. The presence of AMRSalmonellain equine patients increases the risk of unsuccessful treatment and causes concern for potential zoonotic transmission to attending veterinary personnel, animal caretakers, and horse owners. Understanding the epidemiology ofSalmonellain horses admitted to referral hospitals is important for the prevention, control, and treatment of salmonellosis.IMPORTANCEIn horses, salmonellosis is a leading cause of life-threatening colitis. At veterinary teaching hospitals, nosocomial outbreaks can increase the risk of zoonotic transmission, lead to restrictions on admissions, impact hospital reputation, and interrupt educational activities. The antimicrobials most often used in horses are included in the 5th revision of the World Health Organization's list of critically important antimicrobials for human medicine. Recent studies have demonstrated a trend of increasing bacterial resistance to drugs commonly used to treatSalmonellainfections. In this study, we identify temporal trends in the distribution ofSalmonellaserotypes and their mechanisms of antimicrobial resistance; furthermore, we are able to determine the likely origin of several temporal clusters of infection by using whole-genome sequencing. These data can be used to focus strategies to better contain the dissemination and enhance the mitigation ofSalmonellainfections and to provide evidence-based policies and guidelines to steward antimicrobial use in veterinary medicine.

Download Full-text

First isolation and characterization of Brucella suis from yak

Genome ◽

10.1139/gen-2019-0101 ◽

2020 ◽

Vol 63 (8) ◽

pp. 397-405

Author(s):

Xiaowen Yang ◽

Ning Wang ◽

Xiaofang Cao ◽

Pengfei Bie ◽

Zhifeng Xing ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Health And Safety ◽

Host Cells ◽

Whole Genome ◽

Genetic Characteristics ◽

Qinghai Province ◽

Isolation And Characterization ◽

Smooth Strain

Brucella spp., facultative intracellular pathogens that can persistently colonize animal host cells and cause zoonosis, affect public health and safety. A Brucella strain was isolated from yak in Qinghai Province. To detect whether this isolate could cause an outbreak of brucellosis and to reveal its genetic characteristics, several typing and whole-genome sequencing methods were applied to identify its species and genetic characteristics. Phylogenetic analysis based on MLVA and whole-genome sequencing revealed the genetic characteristics of the isolated strain. The results showed that the isolated strain is a B. suis biovar 1 smooth strain, and this isolate was named B. suis QH05. The results of comparative genomics and MLVA showed that B. suis QH05 is not a vaccine strain. Comparison with other B. suis strains isolated from humans and animals indicated that B. suis QH05 may be linked to specific animal and human sources. In conclusion, B. suis QH05 does not belong to the Brucella epidemic species in China, and as the first isolation of B. suis from yak, this strain expands the host range of B. suis.

Download Full-text