Novel discovery of Extended Spectrum β-lactamase (ESBL) Pluralibacter gergoviae in acute urinary tract infection and urolithiasis

2021 ◽  
Vol 156 (Supplement_1) ◽  
pp. S128-S128
Author(s):  
E Coate ◽  
T Merchen ◽  
R Cybulski ◽  
R Collier ◽  
P Mc Gann ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Antibiotic Resistance ◽  
Platelet Rich Plasma ◽  
American Woman ◽  
Antibiotic Resistance Genes ◽  
Illumina Miseq ◽  
Lessons Learned ◽  
Resistant Organism ◽  
Walter Reed Army Institute

Abstract Introduction/Objective This case study describes the diagnosis, treatment, whole genome sequencing (WGS) and antibiotic resistance characterization from the ESBL-producing Pluralibacter gergoviae, a multi-drug resistant organism (MDRO) with a previously-documented presence in foodstuffs and cosmetics. Methods/Case Report A 39-year-old Hispanic American woman was admitted to the emergency department (ED) for fever, suprapubic tenderness, and pyuria. Three days prior to admission, patient underwent elective bilateral lithotripsy for retained nephrolithiasis. Seven days prior to ED admission, patient had an “Orgasm Shot” (O-Shot) which consists of platelet rich plasma that is drawn from the patient and injected into her vulvar area and around her clitoris to increase stimulation potential during orgasm. The patient was started on broad spectrum antibiotics, receiving Vancomycin and Ceftriaxone 1 gram 1 gram IV every 12 hours, intravenously. Urine cultures yielded two organisms, including a lactose fermenting as well as a non-lactose fermenting Gram negative rod. Mass spectrometry-based identification was successful in identifying the non-lactose fermenting colony as Pseudomonas aeruginosa, which also identified from a blood culture collected from the patient upon presentation to the ED. The lactose fermenting colony resulted in no identification by mass spectrometry but was identified using biochemical methods as Pluralibacter gergoviae, a recently-reclassified taxonomy previously identified as Enterobacter gergoviae. The P. gergoviae isolate was submitted to the Multidrug-Resistant Organism Repository (MRSN) at Walter Reed Army Institute of Research (WARIR) for WGS on Illumina Miseq. Sequencing and phenotypic/ genotypic data on isolate confirmed this as an ESBL P. gergoviae organism. Results (if a Case Study enter NA) NA Conclusion Summary data on possible epidemiological associations, antibiotic susceptibility testing, antibiotic resistance genes identified, and information on the antibiotic resistance plasmids will be presented. These findings from the WGS data, antibiotic susceptibilities will provide a lessons-learned for other clinical microbiology labs on how to identify unusual organisms such as P. gergoviae.

Behavior of antibiotics and antibiotic resistance genes in eco-agricultural system: A case study

2016 ◽  
Vol 304 ◽  
pp. 18-25 ◽  
Author(s):  
Weixiao Cheng ◽  
Jianan Li ◽  
Ying Wu ◽  
Like Xu ◽  
Chao Su ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Agricultural System ◽  
System A

scholarly journals Diagnostic Microbiology: Present Status and Future Prospect

2017 ◽  
Vol 2 (2) ◽  
pp. 42-47
Author(s):  
Shahanara Begum ◽  
Md. Abdullah Yusuf ◽  
Bhuiyan Mohammad Mahtab Uddin
Keyword(s):  
Infectious Disease ◽  
Mass Spectrometry ◽  
Antibiotic Resistance ◽  
Historical Perspective ◽  
Future Prospect ◽  
Antibiotic Resistance Genes ◽  
Require Time ◽  
Prior Use ◽  
Diagnostic Microbiology

Diagnostic Microbiology is the tool that makes it possible to identify the exact pathogens of infectious diseases and the most optimal therapy at the level of individual patients. Conventional methods require time to grow the microbes in vitro under specific conditions and not all microbes can easily be cultured. This is followed by biochemical methods for identification which further makes the process lengthy. Transport of the specimens under less than ideal conditions, prior use of antibiotics and small number of organisms are among the factors that render culture-based methods less reliable. Newer methods depend on amplification of nucleic acids followed by use of probes for identification. This mitigates the need for higher microbial load, presence of metabolically active viable organisms and shortens the time. These methods can be used to detect antibiotic resistance genes directly from the specimen and help direct targeted therapy with efficacy. Since these methods will not fulfill all the diagnostic needs, a second approach is being used to shorten the time to identification after the organism has already grown. Mass spectrometry and bioinformatics are the tools making this possible. This review gives a historical perspective on diagnostic microbiology, discusses the pitfalls of current methodology and provides an overview of newer and future methods.Bangladesh Journal of Infectious Disease 2015;2(2):42-47

scholarly journals Plasmid mediated penicillin and tetracycline resistance among Neisseria gonorrhoeae isolates from Kenya

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Mary Wandia Kivata ◽  
Margaret Mbuchi ◽  
Fredrick Eyase ◽  
Wallace Dimbuson Bulimo ◽  
Cecilia Katunge Kyanya ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
Neisseria Gonorrhoeae ◽  
De Novo ◽  
Antibiotic Resistance Genes ◽  
Tetracycline Resistance ◽  
Illumina Miseq ◽  
Miseq Platform ◽  
High Level

Abstract Background Treatment of gonorrhea is complicated by the development of antimicrobial resistance in Neisseria gonorrhoeae (GC) to the antibiotics recommended for treatment. Knowledge on types of plasmids and the antibiotic resistance genes they harbor is useful in monitoring the emergence and spread of bacterial antibiotic resistance. In Kenya, studies on gonococcal antimicrobial resistance are few and data on plasmid mediated drug resistance is limited. The present study characterizes plasmid mediated resistance in N. gonorrhoeae isolates recovered from Kenya between 2013 and 2018. Methods DNA was extracted from 36 sub-cultured GC isolates exhibiting varying drug resistance profiles. Whole genome sequencing was done on Illumina MiSeq platform and reads assembled de-novo using CLC Genomics Workbench. Genome annotation was performed using Rapid Annotation Subsystem Technology. Comparisons in identified antimicrobial resistance determinants were done using Bioedit sequence alignment editor. Results Twenty-four (66.7%) isolates had both β-lactamase (TEM) and TetM encoding plasmids. 8.3% of the isolates lacked both TEM and TetM plasmids and had intermediate to susceptible penicillin and tetracycline MICs. Twenty-six (72%) isolates harbored TEM encoding plasmids. 25 of the TEM plasmids were of African type while one was an Asian type. Of the 36 isolates, 31 (86.1%) had TetM encoding plasmids, 30 of which harbored American TetM, whereas 1 carried a Dutch TetM. All analyzed isolates had non-mosaic penA alleles. All the isolates expressing TetM were tetracycline resistant (MIC> 1 mg/L) and had increased doxycycline MICs (up to 96 mg/L). All the isolates had S10 ribosomal protein V57M amino acid substitution associated with tetracycline resistance. No relation was observed between PenB and MtrR alterations and penicillin and tetracycline MICs. Conclusion High-level gonococcal penicillin and tetracycline resistance in the sampled Kenyan regions was found to be mediated by plasmid borne blaTEM and tetM genes. While the African TEM plasmid, TEM1 and American TetM are the dominant genotypes, Asian TEM plasmid, a new TEM239 and Dutch TetM have emerged in the regions.

scholarly journals Optical maps of plasmids as a proxy for clonal spread of MDR bacteria: a case study of an outbreak in a rural Ethiopian hospital

2020 ◽  
Vol 75 (10) ◽  
pp. 2804-2811
Author(s):  
Yii-Lih Lin ◽  
Tsegaye Sewunet ◽  
Sriram KK ◽  
Christian G Giske ◽  
Fredrik Westerlund
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Large Fraction ◽  
Antibiotic Resistance Genes ◽  
Future Application ◽  
Resistant Bacteria ◽  
Middle Income ◽  
Middle Income Countries ◽  
Clonal Spread

Abstract Objectives MDR bacteria have become a prevailing health threat worldwide. We here aimed to use optical DNA mapping (ODM) as a rapid method to trace nosocomial spread of bacterial clones and gene elements. We believe that this method has the potential to be a tool of pivotal importance for MDR control. Methods Twenty-four Escherichia coli samples of ST410 from three different wards were collected at an Ethiopian hospital and their plasmids were analysed by ODM. Plasmids were specifically digested with Cas9 targeting the antibiotic resistance genes, stained by competitive binding and confined in nanochannels for imaging. The resulting intensity profiles (barcodes) for each plasmid were compared to identify potential clonal spread of resistant bacteria. Results ODM demonstrated that a large fraction of the patients carried bacteria with a plasmid of the same origin, carrying the ESBL gene blaCTX-M-15, suggesting clonal spread. The results correlate perfectly with core genome (cg)MLST data, where bacteria with the same plasmid also had very similar cgMLST profiles. Conclusions ODM is a rapid discriminatory method for identifying plasmids and antibiotic resistance genes. Long-range deletions/insertions, which are challenging for short-read next-generation sequencing, can be easily identified and used to trace bacterial clonal spread. We propose that plasmid typing can be a useful tool to identify clonal spread of MDR bacteria. Furthermore, the simplicity of the method enables possible future application in low- and middle-income countries.

scholarly journals Method for Determining the Profile of Antibiotic Resistance Genes in the Vibrio cholera Strains by RT-PCR

2021 ◽  
pp. 79-86
Author(s):  
A. S. Gladkikh ◽  
I. S. Fedotova ◽  
L. V. Mironova
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antimicrobial Agents ◽  
Experimental Studies ◽  
Antibiotic Resistance Genes ◽  
Illumina Miseq ◽  
Test System ◽  
Diffusion Method ◽  
Disk Diffusion Method ◽  
Integrase Gene

The aim of the work was to design and carry out experimental studies of a set of reagents to identify the spectrum of genes that determine the resistance of the Vibrio cholerae strains to antibacterial drugs.Materials and methods. V. cholerae strains isolated from humans and environmental objects during epidemiological complications and the cholera-free period were included in the study. Sensitivity to antimicrobial drugs was evaluated by the disk diffusion method. Whole genome sequencing was performed on an Illumina MiSeq. The profile of resistance genes was determined based on a comparison with the ResFinder database. The temperature regime, the composition of the reaction mixtures, and the reaction parameters were optimized; the specificity, sensitivity and reproducibility of the constructed prototype test system were measured.Results and discussion. The spectrum of antibiotic resistance and the profile of resistance genes were determined for the studied strains. To develop multiplex PCR, we selected the most common in the V. cholerae populations genes, which are responsible for resistance to tetracycline (tetA), streptomycin (strA), florfenicol/ chloramphenicol (floR) and trimethoprim/sulfamethoxazole (two variants of the dihydrofolate reductase gene: dfrA1 and dhfR), as well as SXT element integrase gene (int). In the reaction, markers were specifically detected in accordance with the genomic resistance profile, which correlates with the phenotypic manifestation of resistance determined by the disco-diffusion method. The sensitivity of the developed panel of primers and probes for V. cholerae strains was 103 –104 CFU/ml. Therefore, taking into account the specificity, rapidity and simplicity of the reaction, the developed system of primers and probes can be successfully applied for a preliminary assessment of the resistance of the V. cholerae strains to antimicrobial agents. 

scholarly journals Core Microbiota Drive the Prevalence of Extracellular Antibiotic Resistome in the Water Compartments

2022 ◽  
Author(s):  
Kai-Feng Yu ◽  
Peng Li ◽  
Yuansheng Huang ◽  
Jun Yang ◽  
Han Li ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Illumina Miseq ◽  
Shannon Index ◽  
Procrustes Analysis ◽  
Extracellular Dna ◽  
Core Microbiota ◽  
The Core ◽  
Water Compartments

Unlike intracellular chromosome, extracellular DNA (eDNA) may accelerate the spreading of antibiotic resistance genes (ARGs) through natural transformation, but one of the core issues regarding to the taxonomic characterization of eDNA in the complex water environments is largely unknown. Hence, Illumina Miseq sequencing was used to identify the genotype of eDNA from wastewater (WW), river water (RW) and stormwater (SW) runoff. High-throughput qPCR targeting 384 genes was implemented to detect extracellular ARGs (eARGs) and mobile genetic elements (eMGEs). We obtained 2,708,291 high quality sequences from 66 eDNA samples. The SW exhibited the significant higher Shannon Index. Subsequently, we identified 34 core bacteria sources of eDNA widely distributed in the three water compartments. Among which, Pseudomonas, Flavobacterium, Limnohabitans, Burkholderiaceae_unclassified, Methylotenera and Acinetobacter were the most prevalent. A total of 302 eARGs and eMGEs were detected, suggesting that eDNA is an important antibiotic resistance reservoir. Among the 127 shared genes of the three groups, 15 core resistance genes were filtered, including IS6100, sul1 NEW, intI1, ISPps1-pseud, aac3-Via, qacH_351 and ISSm2-Xanthob. The Procrustes analysis and Variance Partitioning Analysis (VPA) demonstrated that core bacteria and MGEs were significantly correlated with eARGs. These results suggested that the occurrence and changes of eARGs in the water compartments may be largely attributed to the core microbiota and eMGEs.

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