scholarly journals Genomic Characterization of A Multidrug-resistant Citrobacter freundii Strain ZT01-0079 Co-Producing blaNDM-1 and blaSHV-12 using MiSeq and MinION

2020 ◽  
Author(s):  
Tingyan Zhang ◽  
Yanfeng Lin ◽  
Zhonghong Li ◽  
Xiong Liu ◽  
Jinhui Li ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Southern Blotting ◽  
Multiple Drug Resistance ◽  
Carbapenem Resistance ◽  
Multidrug Resistant ◽  
Multiple Drug ◽  
Citrobacter Freundii ◽  
Rapid Spread ◽  
Genomic Characterization

Abstract Background: The emergence of multi-drug resistant Citrobacter freundii poses daunting challenges to the treatment of clinical infections. The purpose of this study was to characterize the genome of a C. freundii strain with an IncX3 plasmid encoding both the blaNDM-1 and blaSHV-12 genes.Methods: Strain ZT01-0079 was isolated from a clinical urine sample. The Vitek2 system was used for identification and antimicrobial susceptibility testing. The presence of blaNDM-1 was detected by PCR and sequencing. Conjugation experiments and Southern blotting were performed to determine the transferability of the blaNDM-1- carrying plasmid. Nanopore and Illumina sequencing were performed to better understand the genomic characteristics of the strain.Results: Strain ZT01-0079 was identified as C. freundii, and the coexistence of blaNDM-1 and multiple drug resistance genes was confirmed. Electrophoresis and Southern blotting showed that blaNDM-1 was located on a ~53kb IncX3 plasmid. The NDM-1-encoding plasmid was successfully transferred at a frequency of 1.68×10−3. Both blaNDM-1 and blaSHV-12 were located on the self-transferable IncX3 plasmid.Conclusion: The rapid spread of the IncX3 plasmid highlights the importance of continuous monitoring of the prevalence of NDM-1-encoding Enterobacteriaceae. Mutations of existing carbapenem resistance genes will bring formidable challenges to clinical treatment.

scholarly journals Genomic Characterization of A Multidrug-Resistant Citrobacter Freundii Strain ZT01-0079 Co-Producing blaNDM-1 and blaSHV-12 Using MiSeq and MinION

2020 ◽  
Author(s):  
Tingyan Zhang ◽  
Yanfeng Lin ◽  
Zhonghong Li ◽  
Xiong Liu ◽  
Jinhui Li ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Southern Blotting ◽  
Multiple Drug Resistance ◽  
Carbapenem Resistance ◽  
Multidrug Resistant ◽  
Multiple Drug ◽  
Citrobacter Freundii ◽  
Rapid Spread ◽  
Genomic Characterization

Abstract Background: The emergence of multi-drug resistant Citrobacter freundii poses daunting challenges to the treatment of clinical infections. The purpose of this study was to characterize the genome of a C. freundii strain with an IncX3 plasmid encoding both the blaNDM-1 and blaSHV-12 genes.Methods: Strain ZT01-0079 was isolated from a clinical urine sample. The Vitek2 system was used for identification and antimicrobial susceptibility testing. The presence of blaNDM-1 was detected by PCR and sequencing. Conjugation experiments and Southern blotting were performed to determine the transferability of the blaNDM-1- carrying plasmid. Nanopore and Illumina sequencing were performed to better understand the genomic characteristics of the strain.Results: Strain ZT01-0079 was identified as C. freundii, and the coexistence of blaNDM-1 and multiple drug resistance genes was confirmed. Electrophoresis and Southern blotting showed that blaNDM-1 was located on a ~53kb IncX3 plasmid. The NDM-1-encoding plasmid was successfully transferred at a frequency of 1.68×10−3. Both blaNDM-1 and blaSHV-12 were located on the self-transferable IncX3 plasmid.Conclusion: The rapid spread of the IncX3 plasmid highlights the importance of continuous monitoring of the prevalence of NDM-1-encoding Enterobacteriaceae. Mutations of existing carbapenem resistance genes will bring formidable challenges to clinical treatment.

scholarly journals BKC-2, a New BKC Variant Detected in MCR-9.1-producing Enterobacter hormaechei subsp. xiangfangensis

2020 ◽  
pp. AAC.01193-20
Author(s):  
Willames M. B. S. Martins ◽  
Evelin R. Martins ◽  
Letícia K. de Andrade ◽  
Refath Farzana ◽  
Timothy R. Walsh ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Tertiary Hospital ◽  
Multidrug Resistant ◽  
Colistin Resistance ◽  
Antimicrobial Resistance Genes ◽  
Genomic Characterization ◽  
Enterobacter Hormaechei

We performed the characterization of a multidrug-resistant (MDR) Enterobacter spp. isolate highlighting the genetic aspects of the antimicrobial resistance genes. An Enterobacter spp. isolate (Ec61) was recovered in 2014 from a transtracheal aspirate sample from a patient admitted to a Brazilian tertiary hospital and submitted to further microbiological and genomic characterization. Ec61 was identified as Enterobacter hormaechei subsp. xiangfangensis ST451, showed a MDR profile and the presence of genes codifying new β-lactamase variants, BKC-2 and ACT-84, and the mobile colistin resistance gene mcr-9.1.

scholarly journals Genetyping of Carbapenem-resistant Organisms Isolated from Clinical Isolates Received from Tertiary Care Hospitals of Ahmedabad, Gujarat

2021 ◽  
Vol 15 (3) ◽  
pp. 1689-1696
Author(s):  
Anurag D. Zaveri ◽  
Dilip N. Zaveri ◽  
Lakshmi Bhaskaran
Keyword(s):  
Drug Resistance ◽  
Molecular Characterization ◽  
Multiple Drug Resistance ◽  
Tertiary Care ◽  
Carbapenem Resistance ◽  
Multidrug Resistant ◽  
Resistance Mechanisms ◽  
Clinical Isolates ◽  
Multiple Drug ◽  
Tertiary Care Hospitals

The world is seeing a continuous rise in the levels of antibiotic resistance1. Organisms develop new resistance mechanisms, emerge, and spread the resistance worldwide, making it challenging to treat common infectious diseases. In the current study, clinical isolates received between the years 2017 to 2020 were cultured and the isolated organisms were screened for antibiotic resistance; isolates with multiple drug resistance were further subjected to confirmatory screening through Combined Disc Test (CDT) and Modified Hodge Test (M.H.T.), and molecular characterization to be finally tested for gene expression analysis. Molecular characterization involved screening of genes blaVIM-2, blaKPC-3, blaNDM-1, and blaIMP-11 responsible for imparting carbapenem drug resistance2. From the laboratories of tertiary care hospitals, a total of 1452 clinical isolates were collected and identified. The organisms were subjected to antibiotic susceptibility screening and carbapenem resistance screening. The isolates found positive in the screenings were subjected to molecular characterization for genes, blaVIM-2, blaKPC-3, blaNDM-1, and blaIMP-11, responsible for imparting carbapenem drug resistance. Most of the isolates were resistant variably to aminoglycosides but were found to be resistant to fluoroquinolones and β-lactams group of antibiotics. Carbapenem activity was detected in twelve percent of total isolates and 27 percent among multidrug-resistant isolates. blaNDM-1 gene was found present in 77% isolates, and five organisms among the total number of organisms showed pan drug resistance.

scholarly journals Genomic Characterization of Multidrug-Resistant Escherichia coli BH100 Sub-strains

2021 ◽  
Vol 11 ◽  
Author(s):  
Rodrigo Carvalho ◽  
Flavia Aburjaile ◽  
Marcus Canario ◽  
Andréa M. A. Nascimento ◽  
Edmar Chartone-Souza ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Drug Resistance ◽  
Resistance Genes ◽  
Multidrug Resistant ◽  
Genomic Islands ◽  
Comparative Genomic ◽  
E Coli ◽  
Brazilian Woman ◽  
Genomic Characterization

The rapid emergence of multidrug-resistant (MDR) bacteria is a global health problem. Mobile genetic elements like conjugative plasmids, transposons, and integrons are the major players in spreading resistance genes in uropathogenic Escherichia coli (UPEC) pathotype. The E. coli BH100 strain was isolated from the urinary tract of a Brazilian woman in 1974. This strain presents two plasmids carrying MDR cassettes, pBH100, and pAp, with conjugative and mobilization properties, respectively. However, its transposable elements have not been characterized. In this study, we attempted to unravel the factors involved in the mobilization of virulence and drug-resistance genes by assessing genomic rearrangements in four BH100 sub-strains (BH100 MG2014, BH100 MG2017, BH100L MG2017, and BH100N MG2017). Therefore, the complete genomes of the BH100 sub-strains were achieved through Next Generation Sequencing and submitted to comparative genomic analyses. Our data shows recombination events between the two plasmids in the sub-strain BH100 MG2017 and between pBH100 and the chromosome in BH100L MG2017. In both cases, IS3 and IS21 elements were detected upstream of Tn21 family transposons associated with MDR genes at the recombined region. These results integrated with Genomic island analysis suggest pBH100 might be involved in the spreading of drug resistance through the formation of resistance islands. Regarding pathogenicity, our results reveal that BH100 strain is closely related to UPEC strains and contains many IS3 and IS21-transposase-enriched genomic islands associated with virulence. This study concludes that those IS elements are vital for the evolution and adaptation of BH100 strain.

scholarly journals Housefly (Musca domestica) and Blow Fly (Protophormia terraenovae) as Vectors of Bacteria Carrying Colistin Resistance Genes

2017 ◽  
Vol 84 (1) ◽  
Author(s):  
Jilei Zhang ◽  
Jiawei Wang ◽  
Li Chen ◽  
Afrah Kamal Yassin ◽  
Patrick Kelly ◽  
...  
Keyword(s):  
Musca Domestica ◽  
Resistance Genes ◽  
Multiple Drug Resistance ◽  
Multidrug Resistant ◽  
Ecological Niches ◽  
Multiple Drug ◽  
Colistin Resistance ◽  
Gram Negative ◽  
Content Type ◽  
Initial Identification

ABSTRACT Flies have the capacity to transfer pathogens between different environments, acting as one of the most important vectors of human diseases worldwide. In this study, we trapped flies on a university campus and tested them for mobile resistance genes against colistin, a last-resort antibiotic in human medicine for treating clinical infections caused by multidrug-resistant Gram-negative bacteria. Quantitative PCR assays we developed showed that 34.1% of Musca domestica (86/252) and 51.1% of Protophormia terraenovae (23/45) isolates were positive for the mcr-1 gene, 1.2% of M. domestica (3/252) and 2.2% of P. terraenovae (2.2%, 1/45) isolates were positive for mcr-2, and 5.2% of M. domestica (13/252) and 44.4% of P. terraenovae (20/45) isolates were positive for mcr-3. Overall, 4.8% (9/189) of bacteria isolated from the flies were positive for the mcr-1 gene (Escherichia coli: 8.3%, 4/48; Enterobacter cloacae: 12.5%, 1/8; Providencia alcalifaciens: 11.8%, 2/17; Providencia stuartii: 4.9%, 2/41), while none were positive for mcr-2 and mcr-3. Four mcr-1-positive isolates (two P. stuartii and two P. alcalifaciens) from blow flies trapped near a dumpster had a MIC for colistin above 4 mg/ml. This study reports mcr-1 carriage in Providencia spp. and detection of mcr-2 and mcr-3 after their initial identification in Belgium and China, respectively. This study suggests that flies might contribute significantly to the dissemination of bacteria, carrying these genes into a large variety of ecological niches. Further studies are warranted to explore the roles that flies might play in the spread of colistin resistance genes. IMPORTANCE Antimicrobial resistance is recognized as one of the most serious global threats to human health. An option for treatment of the Gram-negative ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) bacteria with multiple drug resistance was the reintroduction of the older antibiotic colistin. However, a mobile colistin resistance gene (mcr-1) has recently been found to occur widely; very recently, two other colistin resistance genes (mcr-2 and mcr-3) have been identified in Belgium and China, respectively. In this study, we report the presence of colistin resistance genes in flies. This study also reports the carriage of colistin resistance genes in the genus Providencia and detection of mcr-2 and mcr-3 after their initial identification. This study will stimulate more in-depth studies to fully elucidate the transmission mechanisms of the colistin resistance genes and their interaction.

Surgical Site Infections - A Hospital Havoc: Retrospective Study of Surgical Site Infections in Tertiary Health Care Centre in North East India

2018 ◽  
Vol 3 (01) ◽  
Author(s):  
V Singh ◽  
A B Khyriem, W V Lyngdoh ◽  
C J Lyngdoh
Keyword(s):  
Surgical Site Infection ◽  
Multiple Drug Resistance ◽  
Surgical Site Infections ◽  
Multidrug Resistant ◽  
Multiple Drug ◽  
Site Infection ◽  
Retrospective Case ◽  
Acinetobacter Baumanii ◽  
Health Care Centre ◽  
North East

Objectives - Surgical site infections (SSI) has turn out to be a major problem even in hospital with most modern facilities and standard protocols of pre -operative preparation and antibiotic prophylaxis. Objective of this study is to know the prevalence of surgical site infection among the postoperative patients and to identify the relationship between SSI and etiological pathogens along with their antimicrobial susceptibility at North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences (NEIGRIHMS), Shillong. Methods - A retrospective case study conducted at NEIGRIHMS, among patients admitted to the surgical departments during the period between January 1st and December 31st 2016. Swabs from the surgical sites were collected under sterile conditions and standard bacteriological tests were performed for identification and appropriate statistical methods were employed to look for association between SSI and etiological pathogens. Results - Out of the 1284 samples included in the study, 192 samples showed evidence of SSI yielding an infection rate of 14.9%. The most commonly isolated bacteria were: Escherichia coli, Acinetobacter baumanii and Staphylococcus aureus, of the gram negative isolates 6.2% were multidrug resistant of which 19% were carbapenem resistant. Conclusion - SSI with multiple drug resistance strains and polymicrobial etiology reflects therapeutic failure. The outcome of the SSI surveillance in our hospital revealed that in order to decrease the incidence of SSI we would have to: a) incorporate a proper antibiotic stewardship  b) conduct periodic surveillance to keep a check on SSI d) educate medical staffs regarding the prevention of surgical site infection.

INFLUENCE OF GENOTYPIC VARIABILITY OF M. TUBERCULOSIS ON THE COURSE OF TUBERCULOSIS WITH MULTIPLE DRUG RESISTANCE

2020 ◽  
pp. 68-71
Author(s):  
V. S. Krutko ◽  
L. H. Nikolaieva ◽  
T. V. Maistat ◽  
O. A. Oparin ◽  
Anton Viktorovych Rohozhyn
Keyword(s):  
Clinical Laboratory ◽  
Multiple Drug Resistance ◽  
Multidrug Resistant ◽  
Multiple Drug ◽  
Genotypic Variability ◽  
Intensive Phase ◽  
Resistant Tuberculosis ◽  
Multidrug Resistant Tuberculosis ◽  
Promising Area ◽  
Infection Source

Tuberculosis is infectious and socially dependent disease, being now one of the most pressing issues in practical health care. As well the usual types of tuberculosis infection, chemoresistant tuberculosis is spreading rapidly in the world. The WHO estimates that about 500,000 people on the planet are infected with M. tuberculosis, which is resistant to standard anti−tuberculosis drugs. The probability of successful treatment decreases with emergence of new genotypes of M. tuberculosis with total resistance. In the modern epidemiology of tuberculosis, it is important to identify genotypes on certain signs, allowing to address issues such as their origin, identification of the infection source, possible routes and factors of transmission, as well as to reveal cases and spread of resistance to anti−tuberculosis drugs. To evaluate the therapy efficiency of multidrug−resistant tuberculosis patients with revealed genotypic variability during treatment, 10 patients with chemoresistant pulmonary tuberculosis having M. tuberculosis genotypic variability were treated. In these patients, the clinical, laboratory and radiological dynamics of disease in intensive phase of treatment were studied. Analysis of treatment results for patients with chemoresistant tuberculosis with genotypic variability of M. tuberculosis was evaluated by the intoxication syndrome dynamics of, the timing of closure of the decay cavities and cessation of bacterial excretion. The study found that the genotypic variability of M. tuberculosis is characterized by the change of less virulent genotypes of M. tuberculosis to more virulent. Signs of intoxication have been shown to change from less virulent M. tuberculosis genotypes to M. tuberculosis Beijing genotypes. Genotypic variability of mycobacteria in hospital suggests that hospitalization in tuberculosis facilities is a risk of exogenous tuberculosis superinfection. Studying the influence of genotypic variability of M. tuberculosis on the course of multidrug−resistant tuberculosis requires more extensive research, being a very relevant and promising area in phthisiology. Key words: Mycobacterium tuberculosis, genotypic variability, VNTR−genotyping, treatment.

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