scholarly journals Complete genomic characterisation of two Escherichia coli lineages responsible for a cluster of carbapenem resistant infections in a Chinese hospital

2017 ◽  
Author(s):  
Zhiyong Zong ◽  
Samuel Fenn ◽  
Christopher Connor ◽  
Yu Feng ◽  
Alan McNally
Keyword(s):  
Escherichia Coli ◽  
Carbapenem Resistance ◽  
Health Crisis ◽  
West China Hospital ◽  
E Coli ◽  
Carbapenem Resistant ◽  
Carbapenemase Gene ◽  
Intergenic Regions ◽  
Resistant Strains ◽  
Drug Resistant Strains

AbstractThe increase in infections as a result of multi-drug resistant strains of Escherichia coli is a global health crisis. The emergence of globally disseminated lineages of E. coli carrying ESBL genes has been well characterised. An increase in strains producing carbapenemase enzymes and mobile colistin resistance is now being reported, but to date there is little genomic characterisation of such strains. Routine screening of patients within an ICU of West China Hospital identified a number of E. coli carrying the blaNDM-5 carbapenemase gene, found to be two distinct clones, E. coli ST167 and ST617. Interrogation of publically available data shows isolation of ESBL and carbapenem resistant strains of both lineages from clinical cases across the world. Further analysis of a large collection of publically available genomes shows that ST167 and ST617 have emerged in distinct patterns from the ST10 clonal complex of E. coli, but share evolutionary events involving switches in LPS genetics, intergenic regions and anaerobic metabolism loci. These may be evolutionary events which underpin the emergence of carbapenem resistance plasmid carriage in E. coli.

scholarly journals Investigation of Carbapenemase Genes in Carbapenem Resistant Enterobacterales Isolates: First KPC Report From Dokuz Eylul University Hospital

2021 ◽  
Author(s):  
Şeyda Şilan Okalin ◽  
Ayşe Nur Sarı Kaygısız ◽  
Mahmut Cem Ergon ◽  
İbrahim Mehmet Ali Öktem
Keyword(s):  
Treatment Options ◽  
Carbapenem Resistance ◽  
Tracheal Aspirate ◽  
University Hospital ◽  
Chain Reaction ◽  
Specific Primers ◽  
E Coli ◽  
Carbapenem Resistant ◽  
Carbapenemase Gene ◽  
Polymerase Chain

Objective: In recent years, increasing carbapenem resistance of Enterobacterales bacteria limits treatment options, considerably. The main mechanism of this resistance is the production of carbapenemase enzymes. The aim of this study is to determine carbapenemase gene types in Enterobacterales isolates from our hospitalized patients and assess the clonal associations of the isolates with KPC gene. Method: A total of 48 clinical Enterobacterales isolates resistant to at least one carbapeneme and received between January 2019 and March 2019 were included in the study. Sample types were consisted of urine, blood, tracheal aspirate, wound and sputum. Of these isolates, three were Escherichia coli while 45 were Klebsiella pneumoniae. Types of carbapenemases were investigated by polymerase chain reaction, using specific primers for VIM, IMP, NDM, KPC and OXA-48 genes. PFGE was performed to determine the clonal associations between blaKPC positive K. pnemoniae isolates. Results: According to the results, blaOXA-48 (n=2) and blaKPC (n=1) were found to be present among E. coli isolates. Regarding 45 K. pneumoniae isolates; only blaOXA-48 and only blaNDM were present in 30 and two isolates, respectively. Seven K. pneumoniae isolates were found positive for both blaOXA-48 and blaNDM. Remaining K. pneumoniae isolates (n=6) harboured only blaKPC. None of the isolates were positive for blaIMP and blaVIM. PFGE analysis showed four isolates had the same pulsotype (A), while two had different pulsotypes (B-C). Conclusion: To our knowledge, this is the first report of KPC gene isolated in Dokuz Eylul University Hospital.

scholarly journals The biotyping ofEscherichia coliisolated from healthy farm animals

1982 ◽  
Vol 88 (3) ◽  
pp. 543-555 ◽  
Author(s):  
M. Hinton ◽  
Vivien Allen ◽  
A. H. Linton
Keyword(s):  
Escherichia Coli ◽  
Farm Animals ◽  
Drug Resistant ◽  
E Coli ◽  
Solid Media ◽  
Resistant Strains ◽  
Drug Resistant Strains

SummaryA total of 2973Escherichia coli, isolated from six different groups of animals, were examined for their ability to ferment adonitol, dulcitol, raffinose, rhamnose and sorbose in solid media. Twenty-nine fermentation patterns were recorded although 2443 (82%) of theE. colibelonged to seven of the 32 possible biotypes. Ninety-six O-serotypes were identified within the 2973E. coli.The number of O-serotypes represented in the 15 most common biotypes ranged from three to 15. Sero types O8 and O9 were found most commonly in the different groups of animals and several biotypes amongst these two O-serotypes were identified in two or more groups of the animals. The ability of theE. colito metabolize aesculin, ornithine, salicin and sucrose was also assessed. These tests proved less reproducible and were not included in the primary biotyping scheme although their use allowed the enumeration of additional biotypes. The application of biotyping to the study of the ecology of drug-resistant strains ofE. coliin five situations is briefly presented.

scholarly journals Emergence of IncHI2 Plasmid-Harboring blaNDM-5 from Porcine Escherichia coli Isolates in Guangdong, China

Pathogens ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 954
Author(s):  
Zhenbao Ma ◽  
Zhenling Zeng ◽  
Jiao Liu ◽  
Chang Liu ◽  
Yu Pan ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Susceptibility Testing ◽  
Carbapenem Resistance ◽  
Guangdong Province ◽  
Whole Genome Sequence ◽  
Molecular Characteristics ◽  
E Coli ◽  
Carbapenem Resistant ◽  
Genetic Feature ◽  
Plasmid Backbone

Carbapenem resistance has posed potential harmful risks to human and animals. The objectives of this study were to understand the prevalence of blaNDM-5 in pigs and investigate the molecular characteristics of NDM-5-producing Escherichia coli isolates in Guangdong province in China. Carbapenem-resistant E. coli isolates were isolated from pigs and obtained using MacConkey plates containing 0.5 mg/L meropenem. Conjugation assay and antimicrobial susceptibility testing were conducted for the isolates and their transconjugants. Whole-genome sequence (WGS) was used to analyze the plasmid genetic feature. A total of five blaNDM-5-carrying E. coli isolates were obtained in the present investigations. They belonged to five ST types. The blaNDM-5 genes were found to be in IncX3 and IncHI2 plasmid. The IncX3 plasmid was 46,161 bp in size and identical to other reports. IncHI2 plasmid was 246,593 bp in size and similar to other IncHI2-ST3 plasmids. It consisted of a typical IncHI2 plasmid backbone region and a multiresistance region (MRR). The blaNDM-5 was closely associated with the IS3000-ISAba125-blaNDM-5-bleMBL-trpF-tat-IS26 unit. We first reported the blaNDM-5-carrying IncHI2 in E. coli isolates recovered from pigs and revealed the molecular characterization. Continued surveillance for the dissemination of blaNDM-5 among food-producing animals is required.

scholarly journals Dissemination of Blandm-5 in Escherichia Coli via the Incx3 Plasmid From Different Regions in China

2021 ◽  
Author(s):  
Xiaofeng Hu ◽  
Lang Yang ◽  
Nian Dong ◽  
Yanfeng Lin ◽  
Ling Zhang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Blot Hybridization ◽  
Carbapenem Resistance ◽  
Southern Blot Hybridization ◽  
Control Measures ◽  
Rrna Gene ◽  
Limited Information ◽  
E Coli ◽  
Carbapenem Resistant ◽  
Antimicrobial Resistance Genes

Abstract Background: Recently, the spread of NDM-5-producing Escherichia coli has become a severe challenge in clinical therapy, which necessitates reliable detection and surveillance methods. However, limited information is available regarding the prevalence and dissemination of the blaNDM-5 gene in Escherichia coli in China. Therefore, we investigated the dissemination of the blaNDM-5 gene in carbapenem-resistant Escherichia coli isolates from different regions in China.Methods: A total of 1,180 carbapenem-resistant enterobacteriaceae strains were obtained from patients admitted to the 20 sentinel hospitals in eight cities. Strains positive for blaNDM-5 were detected using the Vitek 2 compact system, 16S rRNA gene sequencing, PCR, the S1-pulsed-field gel electrophoresis assay, and Southern blot hybridization. The horizontal-transfer capability of the blaNDM gene was assessed by filter mating with a standard E. coli J53 azide-resistant strain as the recipient. Genotyping, susceptibility testing, and whole genome sequencing were performed. Results: Seven strains of blaNDM-5-positive E.coli was detected in 1180 clinical strains from different regions in China. The blaNDM-5-carrying strains showed resistance to multiple tested antibiotics and belonged to two widespread sequence types, ST167 and ST405. Antimicrobial resistance genes including blaCTX-M, blaOXA, blaCMY, and two novel blaTEM variants (blaTEM-230 and blaTEM-231) were also identified. Southern blotting located the blaNDM-5 gene on 46-kb IncX3 plasmids in all isolates, which showed only two single nucleotide differences between EJN003 and the other strains. Conclusions: This study further confirms the increasing occurrence of blaNDM-5-carrying IncX3 plasmids and the dissemination of carbapenem resistance in E. coli isolates via the plasmid from different parts in China, which warrants stringent surveillance and control measures.

scholarly journals Shedding of OXA-181 carbapenemase-producing Escherichia coli from companion animals after hospitalisation in Switzerland: an outbreak in 2018

2019 ◽  
Vol 24 (39) ◽  
Author(s):  
Aurélien Nigg ◽  
Michael Brilhante ◽  
Valentina Dazio ◽  
Mathieu Clément ◽  
Alexandra Collaud ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Prospective Observational Study ◽  
Core Genome ◽  
Ad Hoc ◽  
Companion Animals ◽  
E Coli ◽  
Carbapenem Resistant ◽  
Carbapenemase Gene ◽  
Carbapenem Resistant Enterobacteriaceae

Background Carbapenem-resistant Enterobacteriaceae pose a serious threat to public health worldwide, and the role of companion animals as a reservoir is still unclear. Aims This 4-month prospective observational study evaluated carriage of carbapenem-resistant Enterobacteriaceae at admission and after hospitalisation in a large referral hospital for companion animals in Switzerland. Methods Rectal swabs of dogs and cats expected to be hospitalised for at least 48 h were taken from May to August 2018 and analysed for the presence of carbapenem-resistant Enterobacteriaceae using selective agar plates. Resistant isolates were further characterised analysing whole genome sequences for resistance gene and plasmid identification, and ad hoc core genome multilocus sequence typing. Results This study revealed nosocomial acquisition of Escherichia coli harbouring the carbapenemase gene bla OXA-181, the pAmpC cephalosporinase gene bla CMY-42 as well as quinolone resistance associated with qnrS1 and mutations in the topoisomerases II (GyrA) and IV (ParC). The bla OXA-181 and qnrS1 genes were identified on a 51 kb IncX3 plasmid and bla CMY-42 on a 47 kb IncI1 plasmid. All isolates belonged to sequence type ST410 and were genetically highly related. This E. coli clone was detected in 17 of 100 dogs and four of 34 cats after hospitalisation (21.6%), only one of the tested animals having tested positive at admission (0.75%). Two positive animals were still carriers 4 months after hospital discharge, but were negative after 6 months. Conclusions Companion animals may acquire carbapenemase-producing E. coli during hospitalisation, posing the risk of further dissemination to the animal and human population and to the environment.

scholarly journals Emergence of blaNDM-5-producing Escherichia coli ST410 in Companion Dogs Treated with Meropenem

2020 ◽  
Vol 40 (04) ◽  
pp. 534-536
Author(s):  
JY Oh
Keyword(s):  
Escherichia Coli ◽  
Companion Animals ◽  
Antibiotic Use ◽  
Multidrug Resistant ◽  
Pfge Analysis ◽  
E Coli ◽  
Companion Dogs ◽  
Carbapenem Resistant ◽  
Resistant Phenotype ◽  
Resistant Strains

Carbapenem-resistant Escherichia coli (CRE) with a multidrug resistant phenotype was isolated from four clinically ill dogs treated with meropenem in different local animal hospitals between 2017 and 2019. IncX3-type plasmids of ca. 46 kb in size carrying blaNDM-5 were present in all CRE strains and their transconjugants. High genetic similarity (>90%) by PFGE analysis was observed among the CRE strains, which were identified as ST410.To the best of our knowledge, blaNDM-5-producing E. coli ST410 clones are emerging sporadically in companion dogs treated with meropenem. The spread of Enterobacteriaceae harboring the NDM-5 gene in companion animals can pose a threat to public health; therefore, extensive monitoring in veterinary hospitals using carbapenem and careful antibiotic use are crucial for managing and monitoring these resistant strains

scholarly journals Susceptibility to antibiotics in escherichiae isolated in a multidisciplinary medical centre

2016 ◽  
Vol 65 (4) ◽  
pp. 83-89
Author(s):  
Nadezda S. Kozlova ◽  
Natalia E. Barantsevich ◽  
Elena P. Barantsevich
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Antimicrobial Agents ◽  
E Coli ◽  
Microdilution Method ◽  
Carbapenem Resistant ◽  
Resistant Strains ◽  
High Level

Relevance. Antimicrobial resistance in nosocomial strains currently presents a very important problem.  Aim of the study: Study of antibiotic resistance in Escherichia coli, isolated in a multidisciplinary centre.  Materials and Methods. Susceptibility of 151 E. coli strains to 15 antibiotics was studied by microdilution method. Results. The majority of the studied strains were resistant to antibiotics, including: ampicillin (57.0%), ciprofloxacin and moxifloxacin (42.4% each), III and IV generation cephalosporins (37.1% and 34.4%, respectively) and gentamycin (29.1%). The highest activity against E. coliwas shown for carbapenems (resistance to erthapenem – 2.6%, meropenem – 0.7%), in particular, for imipenem – no strains resistant to this drug were isolated. Resistance to amikacin and phosphomycin was low: 3.3% and 1.3% respectively. Wide diversity of antibiotic resistance spectra was revealed in studied strains, with a high level of multidrug resistance (48.0%). Conclusion. Study of susceptibility to antimicrobial agents in E. coli, isolated in a multidisciplinary centre, showed predominance of resistant strains with a high level of multidrug resistance. The appearance of carbapenem-resistant strains in a multidisciplinary centre presents a rising problem.

scholarly journals Carbapenem resistant Escherichia coli and Pseudomonas aeruginosa in captive blackbucks (Antilope cervicapra) and leopards (Panthera pardus) from India

2021 ◽  
Vol 91 (1) ◽  
pp. 73-80
Author(s):  
Obli R. Vinodh Kumar ◽  
◽  
Bhoj R. Singh ◽  
Mathesh Karikalan ◽  
Shikha Tamta ◽  
...  
Keyword(s):  
Efflux Pump ◽  
Carbapenem Resistance ◽  
Multidrug Resistant ◽  
Beta Lactamases ◽  
E Coli ◽  
Carbapenem Resistant ◽  
Faecal Samples ◽  
Carbapenemase Gene ◽  
Extended Spectrum Beta Lactamases ◽  
Antilope Cervicapra

The study aimed to investigate the occurrence of carbapenem resistant E. coli and P. aeruginosa in apparently healthy, captive blackbucks and leopards of India. Faecal samples of blackbucks (n = 7) and leopards (n = 7) were processed to isolate carbapenem resistant E. coli (CRE) and P. aeruginosa (CRP). Forty (leopards n = 26; blackbuck n = 14) E. coli and two P. aeruginosa (blackbuck n = 2) samples were isolated from the faecal samples (n = 14). Eleven carbapenem resistant isolates were recovered, of which 10 were CRE and one was CRP. The minimum inhibitory concentration (MIC) was determined for meropenem for carbapenem resistant isolates and was between 8 and 64 μg/mL. All the CRE and CRP were phenotypically multidrug resistant, and six CRE were extended-spectrum beta-lactamases (ESBL) producers. On genotypic screening, seven CRE and one CRP were positive for the blaNDM carbapenemase gene. Efflux pump-mediated carbapenem resistance was noticed in four CRE isolates (36.4%, 4/11). Of the six ESBL producing CRE, four isolates carried blaCTX-M-1 genes. The CRE isolates also harbored blaTEM-1, blaAmpC, qnrA, qnrB, qnrS, tetA, tetB and sul1 resistance genes. On Shiga toxin virulence screening, Stx1, Stx2 genes were detected in two and one isolates, respectively. Plasmid typing of CRE revealed that the blaNDM genes were carried on an Incl1 plasmid. The plasmid multilocus sequence typing (pMLST) of the isolates showed the Sequence Type (ST) 297. The occurrence of carbapenem resistance bacteria in captive wildlife should be a major public health priority.

scholarly journals Activity of Cefiderocol, Ceftazidime-Avibactam, and Eravacycline against Carbapenem-Resistant Escherichia coli Isolates from the United States and International Sites in Relation to Clonal Background, Resistance Genes, Coresistance, and Region

2020 ◽  
Vol 64 (10) ◽  
Author(s):  
Brian D. Johnston ◽  
Paul Thuras ◽  
Stephen B. Porter ◽  
Melissa Anacker ◽  
Brittany VonBank ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Carbapenem Resistance ◽  
The United States ◽  
Asia Pacific ◽  
Beta Lactamase ◽  
Content Type ◽  
Beta Lactamases ◽  
E Coli ◽  
Carbapenem Resistant ◽  
Primary Agent

ABSTRACT Emerging carbapenem resistance in Escherichia coli, including sequence type 131 (ST131), the leading cause of extraintestinal E. coli infections globally, threatens therapeutic efficacy. Accordingly, we determined broth microdilution MICs for three distinctive newer agents, i.e., cefiderocol (CFDC), ceftazidime-avibactam (CZA), and eravacycline (ERV), plus 11 comparators, against 343 carbapenem-resistant (CR) clinical E. coli isolates, then compared susceptibility results with bacterial characteristics and region. The collection comprised 203 U.S. isolates (2002 to 2017) and 141 isolates from 17 countries in Europe, Latin America, and the Asia-West Pacific region (2003 to 2017). Isolates were characterized for phylogenetic group, resistance-associated sequence types (STs) and subsets thereof, and relevant beta-lactamase-encoding genes. CFDC, CZA, and ERV exhibited the highest percent susceptible (82% to 98%) after tigecycline (TGC) (99%); avibactam improved CZA's activity over that of CAZ (11% susceptible). Percent susceptible varied by phylogroup and ST for CFDC and CZA (greatest in phylogroups B2, D, and F, and in ST131, ST405, and ST648). Susceptibility also varied by resistance genotype, being higher with the Klebsiella pneumoniae carbapenemase (KPC) for CZA, lower with metallo-beta-lactamases for CFDC and CZA, and higher with the beta-lactamase CTX-M for ERV. Percent susceptible also varied by global region for CZA (lower in Asia-Pacific) and by U.S. region for ERV (lower in the South and Southeast). Although resistance to comparators often predicted reduced susceptibility to a primary agent (especially CFDC and CZA), even among comparator-resistant isolates the primary-agent-susceptible fraction usually exceeded 50%. These findings clarify the likely utility of CFDC, CZA, and ERV against CR E. coli in relation to multiple bacterial characteristics and geographical region.

scholarly journals Activity of Imipenem-Relebactam against Carbapenem-Resistant Escherichia coli Isolates from the United States in Relation to Clonal Background, Resistance Genes, Coresistance, and Region

2020 ◽  
Vol 64 (5) ◽  
Author(s):  
Brian D. Johnston ◽  
Paul Thuras ◽  
Stephen B. Porter ◽  
Melissa Anacker ◽  
Brittany VonBank ◽  
...  
Keyword(s):  
United States ◽  
Escherichia Coli ◽  
Carbapenem Resistance ◽  
The United States ◽  
Resistance Mechanisms ◽  
Beta Lactamase ◽  
Content Type ◽  
E Coli ◽  
Highly Active ◽  
Carbapenem Resistant

ABSTRACT Imipenem-relebactam (I-R) is a recently developed carbapenem–beta-lactamase inhibitor combination agent that can overcome carbapenem resistance, which has now emerged in Escherichia coli, including sequence type 131 (ST131) and its fluoroquinolone-resistant H30R subclone, the leading cause of extraintestinal E. coli infections globally. To clarify the likely utility of I-R for carbapenem-resistant (CR) E. coli infections in the United States, we characterized 203 recent CR clinical E. coli isolates from across the United States (years 2002 to 2017) for phylogroup, clonal group (including ST131, H30R, and the CTX-M-15-associated H30Rx subset within H30R), relevant beta-lactamase genes, and broth microdilution MICs for I-R and 11 comparator agents. Overall, I-R was highly active (89% susceptible), more so than all comparators except tigecycline and colistin (both 99% susceptible). I-R’s activity varied significantly in relation to phylogroup, clonal background, resistance genotype, and region. It was greatest among phylogroup B2, ST131-H30R, H30Rx, Klebsiella pneumoniae carbapenemase (KPC)-positive, and northeast U.S. isolates and lowest among phylogroup C, New Delhi metallo-β-lactamase (NDM)-positive, and southeast U.S. isolates. Relebactam improved imipenem’s activity against CR isolates within each phylogroup—especially groups A, B1, and B2—and particularly against isolates containing KPC. I-R remained substantially active against isolates coresistant to comparator agents, albeit somewhat less so than against the corresponding susceptible isolates. These findings suggest that I-R should be useful for treating most CR E. coli infections in the United States, largely independent of coresistance, although this likely will vary in relation to the local prevalence of specific E. coli lineages and carbapenem resistance mechanisms.

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