scholarly journals Occurrence and Molecular Characterization of Abundant tet(X) Variants Among Diverse Bacterial Species of Chicken Origin in Jiangsu, China

2021 ◽  
Vol 12 ◽  
Author(s):  
Yingshan Li ◽  
Kai Peng ◽  
Yi Yin ◽  
Xinran Sun ◽  
Wenhui Zhang ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Bioinformatics Analysis ◽  
Bacterial Species ◽  
Whole Genome ◽  
Poultry Farms ◽  
High Level ◽  
Level Resistance

Many novel tigecycline-inactivating enzymes encoded by tet(X) variants from different bacteria were discovered since the plasmid-mediated tet(X3) and tet(X4) genes conferring high-level resistance to tigecycline in Enterobacterales and Acinetobacter were reported. However, there have been no comprehensive studies of the prevalence of different tet(X) variants in poultry farms. In this study, we collected 45 chicken fecal samples, isolated tet(X)-positive strains, and performed antimicrobial susceptibility testing, conjugation assay, whole-genome sequencing, and bioinformatics analysis. A total of 15 tet(X)-bearing strains were isolated from 13 samples. Species identification and tet(X) subtyping analysis found that the 15 strains belonged to eight different species and harbored four different tet(X) variants. Genomic investigation showed that transmission of tet(X) variants was associated with various mobile genetic elements, and tet(X4) was the most prevalent variant transferred by conjugative plasmids. Meanwhile, we characterized a plasmid co-harboring tet(X6) and blaOXA–58 in Acinetobacter baumannii. In summary, we demonstrated that different tet(X) variants were widely disseminated in the chicken farming environment and dominated by tet(X4). This finding expands the understanding of the prevalence of tet(X) among different animal sources, and it was advocated to reduce the usage of antibiotics to limit the emergence and transmission of novel tet(X) variants in the poultry industry.

scholarly journals KPC-53, a KPC-3 Variant of Clinical Origin Associated with Reduced Susceptibility to Ceftazidime-Avibactam

2020 ◽  
Vol 65 (1) ◽  
pp. e01429-20
Author(s):  
Vincenzo Di Pilato ◽  
Noemi Aiezza ◽  
Valentina Viaggi ◽  
Alberto Antonelli ◽  
Luigi Principe ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Clinical Isolate ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Mechanisms Of Resistance ◽  
Content Type ◽  
High Level ◽  
Level Resistance

ABSTRACTThis study reports on the characterization of a Klebsiella pneumoniae clinical isolate showing high-level resistance to ceftazidime-avibactam associated with the production of KPC-53, a KPC-3 variant exhibiting a Leu167Glu168 duplication in the Ω-loop and a loss of carbapenemase activity. Whole-genome sequencing (WGS) revealed the presence of two copies of blaKPC-53, located on a pKpQIL-like plasmid and on a plasmid prophage of the Siphoviridae family, respectively. The present findings provide new insights into the mechanisms of resistance to ceftazidime-avibactam.

scholarly journals Expanding U.S. Laboratory Capacity for Neisseria gonorrhoeae Antimicrobial Susceptibility Testing and Whole-Genome Sequencing through the CDC's Antibiotic Resistance Laboratory Network

2020 ◽  
Vol 58 (4) ◽  
Author(s):  
Ellen N. Kersh ◽  
Cau D. Pham ◽  
John R. Papp ◽  
Robert Myers ◽  
Richard Steece ◽  
...  
Keyword(s):  
Public Health ◽  
Antibiotic Resistance ◽  
Neisseria Gonorrhoeae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Whole Genome ◽  
Content Type ◽  
Laboratory Capacity

ABSTRACT U.S. gonorrhea rates are rising, and antibiotic-resistant Neisseria gonorrhoeae (AR-Ng) is an urgent public health threat. Since implementation of nucleic acid amplification tests for N. gonorrhoeae identification, the capacity for culturing N. gonorrhoeae in the United States has declined, along with the ability to perform culture-based antimicrobial susceptibility testing (AST). Yet AST is critical for detecting and monitoring AR-Ng. In 2016, the CDC established the Antibiotic Resistance Laboratory Network (AR Lab Network) to shore up the national capacity for detecting several resistance threats including N. gonorrhoeae. AR-Ng testing, a subactivity of the CDC’s AR Lab Network, is performed in a tiered network of approximately 35 local laboratories, four regional laboratories (state public health laboratories in Maryland, Tennessee, Texas, and Washington), and the CDC’s national reference laboratory. Local laboratories receive specimens from approximately 60 clinics associated with the Gonococcal Isolate Surveillance Project (GISP), enhanced GISP (eGISP), and the program Strengthening the U.S. Response to Resistant Gonorrhea (SURRG). They isolate and ship up to 20,000 isolates to regional laboratories for culture-based agar dilution AST with seven antibiotics and for whole-genome sequencing of up to 5,000 isolates. The CDC further examines concerning isolates and monitors genetic AR markers. During 2017 and 2018, the network tested 8,214 and 8,628 N. gonorrhoeae isolates, respectively, and the CDC received 531 and 646 concerning isolates and 605 and 3,159 sequences, respectively. In summary, the AR Lab Network supported the laboratory capacity for N. gonorrhoeae AST and associated genetic marker detection, expanding preexisting notification and analysis systems for resistance detection. Continued, robust AST and genomic capacity can help inform national public health monitoring and intervention.

scholarly journals Sparfloxacin Resistance in Clinical Isolates ofStreptococcus pneumoniae: Involvement of Multiple Mutations in gyrA and parC Genes

1998 ◽  
Vol 42 (9) ◽  
pp. 2193-2196 ◽  
Author(s):  
Hideki Taba ◽  
Nobuchika Kusano
Keyword(s):  
Streptococcus Pneumoniae ◽  
Amino Acid ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Clinical Isolates ◽  
Amino Acid Substitutions ◽  
Sequencing Analysis ◽  
High Level ◽  
Additional Nucleotide ◽  
Level Resistance

ABSTRACT Antimicrobial susceptibility testing revealed among 150 clinical isolates of Streptococcus pneumoniae 4 pneumococcal isolates with resistance to fluoroquinolones (MIC of ciprofloxacin, ≥32 μg/ml; MIC of sparfloxacin, ≥16 μg/ml). Gene amplification and sequencing analysis of gyrA andparC revealed nucleotide changes leading to amino acid substitutions in both GyrA and ParC of all four fluoroquinolone-resistant isolates. In the case of strains 182 and 674 for which sparfloxacin MICs were 16 and 64 μg/ml, respectively, nucleotide changes were detected at codon 81 in gyrA and codon 79 in parC; these changes led to an Ser→Phe substitution in GyrA and an Ser→Phe substitution in ParC. Strains 354 and 252, for which sparfloxacin MICs were 128 μg/ml, revealed multiple mutations in both gyrA and parC. These strains exhibited nucleotide changes at codon 85 leading to a Glu→Lys substitution in GyrA, in addition to Ser-79→Tyr and Lys-137→Asn substitutions in ParC. Moreover, strain 252 showed additional nucleotide changes at codon 93, which led to a Trp→Arg substitution in GyrA. These results suggest that sparfloxacin resistance could be due to the multiple mutations in GyrA and ParC. However, it is possible that other yet unidentified mutations may also be involved in the high-level resistance to fluoroquinolones in S. pneumoniae.

scholarly journals Characterization of Pseudomonas aeruginosa isolates from patients with endophthalmitis using conventional microbiologic techniques and whole genome sequencing

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Jesse D. Sengillo ◽  
Jacob Duker ◽  
Maribel Hernandez ◽  
Jorge Maestre ◽  
Daniela Reyes-Capo ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Antibiotic Susceptibility ◽  
Virulence Genes ◽  
Susceptibility Testing ◽  
Secretion System ◽  
Whole Genome ◽  
Drug Resistant

Abstract Purpose To demonstrate antibiotic susceptibility and genomic virulence factor profiles of Pseudomonas aeruginosa isolates from patients with culture-confirmed endophthalmitis. Methods Clinical isolates from patients diagnosed with pseudomonas endophthalmitis were included. Laboratory antibiotic susceptibility testing and whole genome sequencing was performed on all isolates. Results In the current study, 8 patients had vitreous culture-confirmed endophthalmitis due to P. aeruginosa. All isolates were multi-drug resistant but sensitive to ceftazidime and each fluoroquinolone tested. Whole genome sequencing revealed a total of 179 unique genes. The most common type of virulence genes included those involved in adherence and the secretion system. Seven of 8 (88%) isolates were of the cytoinvasive phenotype (exoST) and no isolates contained exoU. Conclusions P. aeruginosa associated endophthalmitis is often multi-drug resistant and demonstrates a variety of virulence factors with those involved in adherence and the secretion system being the most common.

scholarly journals Arthrobacter woluwensis Bacteremia: A Clinical and Genomic Report

Pathogens ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 443
Author(s):  
Shu-Yuan Li ◽  
Chin-Chuan Kao ◽  
Yu-Cheng Hu ◽  
Chung-Hsu Lai ◽  
Yi-Ping Jiang ◽  
...  
Keyword(s):  
Case Report ◽  
Whole Genome Sequencing ◽  
Clinical Isolate ◽  
Genome Sequencing ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Immunocompromised Host ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Commercial Kits

Arthrobacter woluwensis is a Gram-positive, aerobic Actinobacteria that is widely distributed in the environment worldwide. Little is known about A. woluwensis infection and it is commonly mis-identified by culturing with commercial kits. To date, only six cases of bacteremia caused by A. woluwensis have been reported in the literature. Herein, we report a case of Arthrobacter woluwensis bacteremia in an immunocompromised host. In this case report, the results of antimicrobial susceptibility testing showed that this clinical isolate of A. woluwensis is sensitive to vancomycin, teicoplanin, but resistant to penicillin, cephalosporin and ciprofloxacin. Additionally, whole genome sequencing analysis identified common subunits of the urease system.

scholarly journals A study of the correlation between phenotypic antimicrobial susceptibility testing methods and the associated genotypes determined by whole genome sequencing for a collection of Escherichia coli of bovine origin

2021 ◽  
Author(s):  
Thomas J. Maunsell ◽  
Scott Nguyen ◽  
Farid El Garach ◽  
Christine Miossec ◽  
Emmanuel Cuinet ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Disk Diffusion ◽  
Whole Genome ◽  
Antimicrobial Compounds ◽  
Perfect Agreement ◽  
Positive Predicted Value

Antimicrobial resistance (AMR) has increased at an alarming pace in the recent years. Molecular-based methods such as whole genome sequencing (WGS) offer a potential alternative to the conventional labour-intensive methods traditionally used to characterise AMR phenotypes. The aim of this study was to investigate whether WGS could be used as a predictor of AMR in Escherichia coli isolates of bovine origin. Genomes of 143 E. coli cultured from cattle presenting with diarrhoea or mastitis were sequenced on an Illumina MiSeq platform. AMR genes were identified using the ResFinder and AMRFinder databases. Antimicrobial susceptibility testing by disk diffusion was performed on a panel of 10 antibiotics, covering 7 antimicrobial classes. Minimum inhibitory concentration (MIC) measurements were made using the Sensititre plate with 6 antibiotics, covering 5 antimicrobial classes. Correlation between genotype and phenotype was assessed statistically by means of a two-by-two table analysis and Cohen's kappa (κ) test. The overall κ correlation between WGS and disk diffusion was 0.81, indicating a near perfect agreement, and the average positive predicted value was 77.4 %. Correlation for individual antimicrobial compounds varied, with five yielding near perfect agreement (κ = 0.81-1.00; amoxicillin, florfenicol, gentamicin, tetracycline and trimethoprim-sulfamethoxazole), one showing substantial agreement (κ = 0.65; nalidixic acid), and four showing moderate agreement (κ = 0.41-0.60). The overall κ correlation between WGS and MIC was 0.55 indicating moderate agreement, and the average positive predicted value was 68.6 %. Three antibiotics yielded near perfect agreement (gentamicin, tetracycline and trimethoprim-sulfamethoxazole) and a further three showed fair agreement (κ = 0.21-0.40). WGS is a useful tool that can be used for the prediction of AMR phenotypes, and correlates well with disk diffusion results. MIC measurements may be necessary for antimicrobial compounds with a high proportion of intermediately resistant isolates recorded, such as cephalothin.

scholarly journals Antimicrobial Susceptibilities of Group B Streptococci Isolated from Patients with Invasive Disease: 10-Year Perspective

2001 ◽  
Vol 45 (12) ◽  
pp. 3623-3624 ◽  
Author(s):  
David R. Murdoch ◽  
L. Barth Reller
Keyword(s):  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Invasive Disease ◽  
Antimicrobial Susceptibility Testing ◽  
Streptococcal Infections ◽  
Group B Streptococci ◽  
Treatment And Prevention ◽  
Group B ◽  
High Level ◽  
Level Resistance

ABSTRACT Antimicrobial susceptibility testing of 192 group B streptococcal isolates from patients with invasive disease demonstrated that 31 (16%) were resistant to erythromycin and 17 (9%) were resistant to clindamycin. One isolate demonstrated high-level resistance to streptomycin, but none was highly resistant to gentamicin. Erythromycin and clindamycin are no longer reliable empirical alternatives to penicillin for the treatment and prevention of group B streptococcal infections.

scholarly journals Phenotypic and Molecular Characterization of Mycobacterium tuberculosis Isolates Resistant to both Isoniazid and Ethambutol

2005 ◽  
Vol 49 (6) ◽  
pp. 2218-2225 ◽  
Author(s):  
Linda M. Parsons ◽  
Max Salfinger ◽  
Anne Clobridge ◽  
Jillian Dormandy ◽  
Lisa Mirabello ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Susceptibility Testing ◽  
Rapid Screening ◽  
The Past ◽  
Resistant Strains ◽  
The Common ◽  
Susceptibility Tests ◽  
High Level ◽  
Level Resistance

ABSTRACT In performing radiometric susceptibility testing on over 2,000 patient isolates of Mycobacterium tuberculosis during the past 6 years, we found that resistance to 7.5 μg/ml ethambutol (EMB) occurred only in isolates that are also resistant to 0.4 μg/ml isoniazid (INH). Using 157 selected isolates in the present study, we performed radiometric and agar proportion susceptibility tests and DNA sequencing of genetic regions associated with resistance to these two drugs. The goal was to study the occurrence of the common mutations associated with resistance to each drug and also to determine whether any particular INH-resistance-associated mutation occurred more often in combination with any particular EMB-resistance-associated mutation. In an analysis of 128 isolates resistant to 0.4 μg/ml INH, we found that a mutation at katG Ser315 was more common in isolates also resistant to 7.5 μg/ml EMB (61 of 67 = 91.0%) than in isolates either susceptible to EMB or resistant to 2.5 μg/ml EMB (39 of 60 = 65.0%). These observations suggest that INH-resistant strains with a mutation at katG Ser315 are more likely to acquire resistance to 7.5 μg/ml EMB than are isolates with INH-resistance-associated mutations at other sites. In addition, we found that 64 of 67 (95.5%) isolates resistant to 7.5 μg/ml EMB contained a mutation in either codon 306 or codon 406 of embB. Met306Val was the most common embB mutation, present in 52 (77.6%) of the 67 isolates. Most occurrences of this mutation (49 of 52 = 94.2%) were found in isolates that also contained the katG Ser315Thr mutation. Finally, sequencing this region of embB appears to be sufficiently sensitive for use as a rapid screening tool for detection of high-level resistance to EMB.

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