Detection of themcr-1Colistin Resistance Gene in Carbapenem-Resistant Enterobacteriaceae from Different Hospitals in China

ABSTRACTThe spread of the plasmid-mediated colistin resistance gene,mcr-1, into carbapenem-resistantEnterobacteriaceae(CRE) clinical isolates poses a significant threat to global health. Here we report the identification of threemcr-1-harboring carbapenem-resistantEscherichia colistrains, collected from three patients in two provinces in China. Our results show thatmcr-1-harboring CRE strains have started to spread in different hospitals in China. In addition, this report presents the first description of chromosomal integration ofmcr-1into a carbapenem-resistantE. colistrain.

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Emergence of Colistin Resistance Gene mcr-1 in Cronobacter sakazakii Producing NDM-9 and in Escherichia coli from the Same Animal

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01444-16 ◽

2016 ◽

Vol 61 (2) ◽

Cited By ~ 29

Author(s):

Bao-Tao Liu ◽

Feng-Jing Song ◽

Ming Zou ◽

Zhi-Hui Hao ◽

Hu Shan

Keyword(s):

Escherichia Coli ◽

Resistance Gene ◽

Resistance Genes ◽

Cronobacter Sakazakii ◽

Colistin Resistance ◽

Content Type ◽

E Coli ◽

Carbapenem Resistant

ABSTRACT We report the presence of mcr-1 in Escherichia coli and carbapenem-resistant Cronobacter sakazakii from the same diseased chicken. The mcr-1 gene linked with ISApl1 was located on two different IncI2 plasmids, including one multidrug plasmid in E. coli, whereas fosA3-bla NDM-9 was on an IncB/O plasmid in C. sakazakii. The development of the fosA3-bla NDM-9 resistance region was mediated by IS26. The colocation of mcr-1 or bla NDM-9 with other resistance genes will accelerate the dissemination of the two genes.

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Occurrence and Genomic Characterization of Two MCR-1-Producing Escherichia coli Isolates from the Same Mink Farmer

mSphere ◽

10.1128/msphere.00602-19 ◽

2019 ◽

Vol 4 (6) ◽

Cited By ~ 1

Author(s):

Beiwen Zheng ◽

Hao Xu ◽

Chen Huang ◽

Xiao Yu ◽

Lihua Guo ◽

...

Keyword(s):

Escherichia Coli ◽

Resistance Gene ◽

Animal Health ◽

Molecular Characteristics ◽

Colistin Resistance ◽

Public Health Importance ◽

Content Type ◽

E Coli ◽

Human Interface ◽

Healthy Humans

ABSTRACT The spread of colistin resistance gene mcr-1 at the animal-human interface remains largely unknown. This work aimed to investigate the molecular characteristics of two extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli strains with mcr-1, i.e., strains H8 and H9, isolated from the same mink farmer. In this study, five mcr-positive E. coli strains were isolated from the mink farm. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) identified two genetically unrelated MCR-1 producers (H8 and H9) from the same farmer and two clonally related MCR-1-positive isolates (M5 and M6) from two different mink samples. Additionally, a mcr-1 variant, designated mcr-1.12, was identified in isolate M4. MIC determination revealed that all of the MCR-producing strains exhibited multiresistant phenotypes but showed susceptibility to imipenem, meropenem, amikacin, and tigecycline. Replicon typing showed that mcr-1 was associated with IncHI2 plasmids in 4 cases, while the gene was located on an IncI2 plasmid in 1 case. PacBio sequencing and plasmid analysis confirmed that the mcr-1 gene was located on an ∼204-kb IncHI2 plasmid in H8 and was carried by an ∼61-kb IncI2 plasmid in H9. To our knowledge, this work represents the first report of the occurrence of MCR-producing isolates from mink. Moreover, our report also describes the coexistence of two different MCR-1 producers in the same farmer. It highlights that fur farms can be reservoirs of mcr-1 genes. The identification of mcr-carrying plasmids on a fur farm is of potential public health importance, as it suggests that mcr is widespread in the animal husbandry industry. IMPORTANCE Colistin resistance is a real threat for both human and animal health. The mobile colistin resistance gene mcr has contributed to the persistence and transmission of colistin resistance at the interfaces of animals, humans, and ecosystems. Although mcr genes have usually been recovered from food animals, patients, and healthy humans, transmission of mcr genes at the animal-human interface remains largely unknown. This was the first study to isolate and characterize MCR-producing isolates from mink, as well as to report the coexistence of two different MCR-1 producers in the same farmer. The characterization and analysis of two MCR-1-producing E. coli isolates may have important implications for comprehension of the transmission dynamics of these bacteria. We emphasize the importance of improved multisectorial surveillance of colistin-resistant E. coli in this region.

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ISKpn40-Mediated Mobilization of the Colistin Resistance Gene mcr-3.11 in Escherichia coli

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00851-20 ◽

2020 ◽

Vol 64 (10) ◽

Author(s):

Yu-Zhang He ◽

Teng-Fei Long ◽

Cai-Ping Chen ◽

Bing He ◽

Xing-Ping Li ◽

...

Keyword(s):

Escherichia Coli ◽

Resistance Gene ◽

Wild Type ◽

Colistin Resistance ◽

Content Type ◽

First Report ◽

E Coli ◽

Target Sites

ABSTRACT The mobile colistin resistance gene mcr-3 has globally disseminated since it was first reported in 2017 in Escherichia coli. In vitro mobilization assays in this study demonstrate the functionality of the composite transposon structure ISKpn40-mcr-3.11-dgkA-ISKpn40 in wild-type and recA− E. coli strains. These transpositions generated 4-bp duplications at the target sites. This is the first report demonstrating the mobility of the mcr-3.11 gene by transposition.

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Various Sequence Types of Escherichia coli Isolates Coharboring blaNDM-5 and mcr-1 Genes from a Commercial Swine Farm in China

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02167-16 ◽

2016 ◽

Vol 61 (3) ◽

Cited By ~ 33

Author(s):

Ling-Han Kong ◽

Chang-Wei Lei ◽

Su-Zhen Ma ◽

Wei Jiang ◽

Bi-Hui Liu ◽

...

Keyword(s):

Escherichia Coli ◽

Resistance Gene ◽

Genome Sequencing ◽

Carbapenem Resistance ◽

Whole Genome ◽

Swine Farm ◽

Colistin Resistance ◽

Content Type ◽

E Coli ◽

Sequence Types

ABSTRACT Sixteen different sequence types (STs) of Escherichia coli isolates from a commercial swine farm in China were confirmed to coharbor the carbapenem resistance gene bla NDM-5 and the colistin resistance gene mcr-1. Whole-genome sequencing revealed that bla NDM-5 and mcr-1 were located on a 46-kb IncX3 plasmid and a 32-kb IncX4 plasmid, respectively. The two plasmids can transfer together with a low fitness cost, which might explain the presence of various STs of E. coli coharboring bla NDM-5 and mcr-1.

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First Report of the mcr-1 colistin Resistance Gene Identified in Escherichia coli Isolated from a Clinical Sample in Naples in 2020

10.21203/rs.3.rs-135159/v1 ◽

2020 ◽

Author(s):

BIAGIO SANTELLA ◽

CARLA ZANNELLA ◽

CHIARA DEL VECCHIO ◽

ANNALISA CHIANESE ◽

VERONICA FOLLIERO ◽

...

Keyword(s):

Escherichia Coli ◽

Resistance Gene ◽

Clinical Sample ◽

Resistance Mechanism ◽

Multidrug Resistant ◽

Health Concern ◽

Colistin Resistance ◽

Gram Negative ◽

E Coli ◽

Carbapenem Resistant

Abstract Background: The emergence of a novel plasmid-mediated colistin resistance mechanism, encoded by the mcr-1 gene, represents a major public health concern. The mechanism of resistance to colistin, mediated by plasmids, is a serious problem, both for its ability to be transferred to other species, and for infections caused by carbapenem-resistant Gram-negative, in which colistin is used as an antimicrobial drug of last line for the treatment of these infections. The present study highlights the first isolation and genetic evaluation of detecting plasmid-mediated resistance to colistin in a multidrug-resistant (MDR) Escherichia coli (E. coli) isolated from a clinical sample in the metropolitan city of Naples, Italy. Results: Colistin-resistant E. coli isolate was identified in August 2020 from the blood culture of a male patient with multiple comorbidities. The minimum inhibitory concentration (MIC) of colistin was 8 mg/L. In addition to colistin, the isolate was resistant to third-generation cephalosporins (cefotaxime and ceftazidime), penicillin (amoxicillin and piperacillin), aminoglycosides (gentamicin and tobramycin), and fluoroquinolones (ciprofloxacin and levofloxacin). However, it showed susceptibility to carbapenems (ertapenem, imipenem, and meropenem), tetracyclines (tigecycline), and piperacillin-tazobactam. The results of the PCR confirmed the presence of the mcr-1 resistance gene. Conclusion: This study confirms the presence of resistance to colistin mediated by the mcr-1 gene in a clinical isolate of E. coli. Although resistance to colistin caused by the mcr-1 gene is not common in our region, it should not be ignored. Therefore, further surveillance studies are recommended to monitor the spread of plasmid-mediated colistin resistance genes in Gram-negative MDR bacteria.

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Colistin Resistance in Carbapenem-Resistant Klebsiella pneumoniae Mediated by Chromosomal Integration of Plasmid DNA

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00404-17 ◽

2017 ◽

Vol 61 (8) ◽

Cited By ~ 2

Author(s):

Astrid V. Cienfuegos-Gallet ◽

Liang Chen ◽

Barry N. Kreiswirth ◽

J. Natalia Jiménez

Keyword(s):

Klebsiella Pneumoniae ◽

Plasmid Dna ◽

Clonal Expansion ◽

Genetic Alterations ◽

Sequence Type ◽

Chromosomal Integration ◽

Colistin Resistance ◽

Content Type ◽

Carbapenem Resistant ◽

Single Locus Variant

ABSTRACT Here we describe the spread of colistin resistance in clinical isolates of carbapenem-resistant Klebsiella pneumoniae in Medellín, Colombia. Among 32 isolates collected between 2012 and 2014, 24 showed genetic alterations in mgrB. Nineteen isolates belonged to sequence type 512 (ST512) (or its single locus variant [SLV]) and harbored an 8.1-kb hsdMSR insertion corresponding to ISKpn25, indicating a clonal expansion of the resistant strain. The insertion region showed 100% identity to several plasmids, suggesting that the colistin resistance is mediated by chromosomal integration of plasmid DNA.

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Single Clinical Isolates from Acute Uncomplicated Urinary Tract Infections Are Representative of Dominant In Situ Populations

mBio ◽

10.1128/mbio.01064-13 ◽

2014 ◽

Vol 5 (2) ◽

Cited By ~ 18

Author(s):

Dana Willner ◽

Serene Low ◽

Jason A. Steen ◽

Narelle George ◽

Graeme R. Nimmo ◽

...

Keyword(s):

Escherichia Coli ◽

Urinary Tract ◽

Urinary Tract Infections ◽

Clinical Isolates ◽

Content Type ◽

E Coli ◽

Strain Diversity ◽

Amplicon Pyrosequencing ◽

Culture Independent ◽

Tract Infections

ABSTRACTUrinary tract infections (UTIs) are one of the most commonly acquired bacterial infections in humans, and uropathogenicEscherichia colistrains are responsible for over 80% of all cases. The standard method for identification of uropathogens in clinical laboratories is cultivation, primarily using solid growth media under aerobic conditions, coupled with morphological and biochemical tests of typically a single isolate colony. However, these methods detect only culturable microorganisms, and characterization is phenotypic in nature. Here, we explored the genotypic identity of communities in acute uncomplicated UTIs from 50 individuals by using culture-independent amplicon pyrosequencing and whole-genome and metagenomic shotgun sequencing. Genus-level characterization of the UTI communities was achieved using the 16S rRNA gene (V8 region). Overall UTI community richness was very low in comparison to other human microbiomes. We strain-typedEscherichia-dominated UTIs using amplicon pyrosequencing of the fimbrial adhesin gene,fimH. There were nine highly abundantfimHtypes, and each UTI sample was dominated by a single type. Molecular analysis of the corresponding clinical isolates revealed that in the majority of cases the isolate was representative of the dominant taxon in the community at both the genus and the strain level. Shotgun sequencing was performed on a subset of eightE. coliurine UTI and isolate pairs. The majority of UTI microbial metagenomic sequences mapped to isolate genomes, confirming the results obtained using phylogenetic markers. We conclude that for the majority of acute uncomplicatedE. coli-mediated UTIs, single cultured isolates are diagnostic of the infection.IMPORTANCEIn clinical practice, the diagnosis and treatment of acute uncomplicated urinary tract infection (UTI) are based on analysis of a single bacterial isolate cultured from urine, and it is assumed that this isolate represents the dominant UTI pathogen. However, these methods detect only culturable bacteria, and the existence of multiple pathogens as well as strain diversity within a single infection is not examined. Here, we explored bacteria present in acute uncomplicated UTIs using culture-independent sequence-based methods.Escherichia coliwas the most common organism identified, and analysis ofE. colidominant UTI samples and their paired clinical isolates revealed that in the majority of infections the cultured isolate was representative of the dominant taxon at both the genus and the strain level. Our data demonstrate that in most cases single cultured isolates are diagnostic of UTI and are consistent with the notion of bottlenecks that limit strain diversity during UTI pathogenesis.

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Amdinocillin (Mecillinam) Resistance Mutations in Clinical Isolates and Laboratory-Selected Mutants of Escherichia coli

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.04819-14 ◽

2015 ◽

Vol 59 (3) ◽

pp. 1718-1727 ◽

Cited By ~ 58

Author(s):

Elisabeth Thulin ◽

Martin Sundqvist ◽

Dan I. Andersson

Keyword(s):

Escherichia Coli ◽

Clinical Isolates ◽

Cysteine Biosynthesis ◽

Resistance Mutations ◽

Content Type ◽

E Coli ◽

Major Mechanism ◽

Laboratory Selection ◽

Lactam Antibiotic ◽

Tract Infections

ABSTRACTAmdinocillin (mecillinam) is a β-lactam antibiotic that is used mainly for the treatment of uncomplicated urinary tract infections. The objectives of this study were to identify mutations that confer amdinocillin resistance on laboratory-isolated mutants and clinical isolates ofEscherichia coliand to determine why amdinocillin resistance remains rare clinically even though resistance is easily selected in the laboratory. Under laboratory selection, frequencies of mutation to amdinocillin resistance varied from 8 × 10−8to 2 × 10−5per cell, depending on the concentration of amdinocillin used during selection. Several genes have been demonstrated to give amdinocillin resistance, but here eight novel genes previously unknown to be involved in amdinocillin resistance were identified. These genes encode functions involved in the respiratory chain, the ribosome, cysteine biosynthesis, tRNA synthesis, and pyrophosphate metabolism. The clinical isolates exhibited significantly greater fitness than the laboratory-isolated mutants and a different mutation spectrum. ThecysBgene was mutated (inactivated) in all of the clinical isolates, in contrast to the laboratory-isolated mutants, where mainly other types of more costly mutations were found. Our results suggest that the frequency of mutation to amdinocillin resistance is high because of the large mutational target (at least 38 genes). However, the majority of these resistant mutants have a low growth rate, reducing the probability that they are stably maintained in the bladder. Inactivation of thecysBgene and a resulting loss of cysteine biosynthesis are the major mechanism of amdinocillin resistance in clinical isolates ofE. coli.

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Detection of antimicrobial resistance genes of carbapenem-resistant Enterobacteriaceae in Escherichia coli isolated from the water supply of smallholder dairy farms in Saraburi and Maha Sarakham, Thailand

International Journal of One Health ◽

10.14202/ijoh.2020.1-5 ◽

2020 ◽

Vol 6 (1) ◽

pp. 1-5

Author(s):

Natapol Pumipuntu ◽

Sangkom Pumipuntu

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Water Samples ◽

Dairy Farms ◽

Drug Resistant ◽

E Coli ◽

Carbapenem Resistant ◽

Carbapenem Resistant Enterobacteriaceae ◽

Smallholder Dairy Farms

Background and Aim: The problem of antimicrobial resistance of bacteria in both humans and animals is an important public health concern globally, which is likely to increase, including in Thailand, where carbapenem-resistant Enterobacteriaceae (CRE), such as Escherichia coli, are of particular concern. They are pathogens found in the gastrointestinal tract of humans and other animals as well as in the environment. They may cause opportunistic infection and are often resistant to antibiotics in various fields especially in animal husbandry, such as pets or livestock farms. This study aimed to investigate the occurrence of carbapenem-resistant E. coli from water samples of smallholder dairy farms in Saraburi and Maha Sarakham, Thailand. Materials and Methods: Sixty-four water samples were collected from 32 dairy farms in Kaeng Khoi district, Muak Lek district, and Wang Muang district of Saraburi Province, and Kantharawichai district and Mueang district of Maha Sarakham Province, Thailand. All samples were cultured and isolated for E. coli by biochemical tests. All E. coli isolates were tested for drug susceptibility using imipenem, meropenem, and drug resistance genes of carbapenemases such as blaNDM, blaIMP, and blaOXA48 of drug-resistant E. coli isolates detected by polymerase chain reaction (PCR) technique. Results: A total of 182 E. coli isolates were found (140 and 42 isolates from Saraburi and Maha Sarakham, respectively). Drug sensitivity tests found that two isolates of E. coli from water in Kaeng Khoi were resistant to imipenem; therefore, the incidence of E. coli resistance to carbapenem was 1.43% of Saraburi Province. On the other hand, there was no incidence of drug-resistant E. coli in Maha Sarakham. In addition, the detection of the drug-resistant gene of E. coli in both isolates by PCR showed the expression of blaNDM. Conclusion: This study reports E. coli resistance to antimicrobial drugs on livestock farms. It can be considered to be the first report of E. coli CRE detection in a dairy farm at Saraburi, which should be the subject of further extended study.

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The global distribution and spread of the mobilized colistin resistance gene mcr-1

10.1101/220921 ◽

2017 ◽

Author(s):

Ruobing Wang ◽

Lucy van Dorp ◽

Liam Shaw ◽

Phelim Bradley ◽

Qi Wang ◽

...

Keyword(s):

Resistance Gene ◽

Antibiotic Resistance Genes ◽

Global Distribution ◽

Colistin Resistance ◽

Posterior Density ◽

Carbapenem Resistant ◽

Significant Public Health ◽

Monitoring And Surveillance ◽

Multiple Levels ◽

Carbapenem Resistant Enterobacteriaceae

AbstractColistin represents one of the very few available drugs for treating infections caused by carbapenem resistant Enterobacteriaceae (CRE). As such, the recent plasmid-mediated spread of the mobilized colistin resistance gene mcr-1 poses a significant public health threat requiring global monitoring and surveillance. In this work, we characterize the global distribution of mcr-1 using a dataset of 457 mcr-1 positive sequenced isolates consisting of currently publicly available mcr-1 carrying sequences combined with an additional 110 newly sequenced mcr-1 positive isolates from China. We find mcr-1 in a diversity of plasmid backgrounds but identify an immediate background common to all mcr-1 sequences. Our analyses establish that all mcr-1 elements in circulation descend from the same initial mobilization of mcr-1 by an ISApl1 transposon in the mid 2000s (2002-2008; 95% higher posterior density), followed by a dramatic demographic expansion, which led to its current global distribution. Our results provide the first systematic phylogenetic analysis of the origin and spread of mcr-1, and emphasize the importance of understanding the movement of mobile elements carrying antibiotic resistance genes across multiple levels of genomic organization.

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