The Intestinal Carriage of Plasmid-Mediated Colistin-Resistant Enterobacteriaceae in Tertiary Care Settings

Background: In order to estimate the prevalence of plasmid borne colistin resistance and to characterize in detail the mcr-positive isolates, we carried out a sentinel testing survey on the intestinal carriage of plasmid-mediated colistin-resistant Enterobacteriaceae in hospitalized patients. Methods: Between June 2018 and September 2019, 1922 faecal samples from hospitalised patients were analysed by selective culture in presence of colistin (3.5 mg/L), and in parallel by direct detection of the mcr-1 to mcr-8 genes by qPCR. The mcr-positive isolates were characterised by whole-genome sequencing. Results: The prevalence of the mcr-1 gene was 0.21% (n = 4/1922); the mcr-2 to 8 genes were not detected. The mcr-1 gene was found to be localised in the IncX4 (n = 3) and IncHI2 (n = 1) plasmid type. One Escherichia coli isolate was susceptible to colistin due to the inactivation of the mcr-1 gene through the insertion of the IS2 element; however, the colistin resistance was inducible by culture in low concentrations of colistin. One human mcr-1 positive E. coli isolate was related genetically to the mcr-1 E. coli isolate derived from turkey meat of Czech origin. Conclusions: mcr-mediated colistin resistance currently poses little threat to patients hospitalised in Czech healthcare settings. The presence of the mcr-1 gene in the human population has a possible link to domestically produced, retail meat.

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A novel report of colistin-resistant Escherichia coli carrying mcr-1 gene from animal and human feacal samples in Nigeria

Pan African Journal of Life Sciences ◽

10.36108/pajols/8102/10(0120) ◽

2018 ◽

Vol 1 (1) ◽

pp. 7-10 ◽

Cited By ~ 1

Author(s):

Olugbenga A. Olowe ◽

Rita A. Olowe ◽

Adeolu S. Oluremi ◽

Olusolabomi J. Adefioye

Keyword(s):

Escherichia Coli ◽

Animal Husbandry ◽

Multiple Drug ◽

Colistin Resistance ◽

Pcr Assay ◽

Southwestern Nigeria ◽

E Coli ◽

Multiple Drug Resistant ◽

Microbiological Methods ◽

Faecal Samples

Background: The mobilized colistin resistance (m cr)-1 gene confers transferable colistin resistance. Reports of mcr-1-positive Escherichia coli (MCRPE) have attracted substantial attention. However, in Nigeria, there is no report of mcr-1 gene resistance. Since colistin is a last resort for multiple drug-resistant isolates, this study therefore report the prevalence of mcr-1 gene among E. coli isolated from human and animal sources. Methods: Out of a total of 280 samples collected from animal and hum an faecal samples from selected farms in Oyo and Osun States, Southwestern Nigeria between July 2015 and June 2016, 60 E. coli were identified using standard microbiological methods. The mcr-1 gene was detected in the isolates by conventional PCR assay. Results: The m cr-1 gene was low and not statistically significant (p≥0.05). It was detected in 5 (8.3%) of 60 E. coli isolates (4= animals; 1= human) Conclusion: This study is the first report of mcr -1 gene from E. coli from human and animal sources in Nigeria. This calls for urgent caution in the use of colistin in animal husbandry.

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Isolation and plasmid characterisation of Salmonella enterica serovar Albany harbouring mcr-5 from retail chicken meat in Japan

FEMS Microbiology Letters ◽

10.1093/femsle/fnaa127 ◽

2020 ◽

Vol 367 (15) ◽

Author(s):

Yuki Wakabayashi ◽

Tsuyoshi Sekizuka ◽

Takahiro Yamaguchi ◽

Akira Fukuda ◽

Masato Suzuki ◽

...

Keyword(s):

Meat Products ◽

Asian Countries ◽

Colistin Resistance ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

E Coli ◽

Retail Meat ◽

Paratyphi B ◽

Retail Chicken Meat ◽

Plasmid Backbone

ABSTRACT The emergence of plasmid-mediated colistin resistance genes (mcr), which is occurring in numerous countries, is a worldwide concern, primarily because colistin is a last-resort antibiotic. Compared to E. coli, prevalence of mcr genes in Salmonella is unclear in Japan. Here we screened for mcr-1–5 genes in our collection of Salmonella strains isolated from retail meat products collected in Japan from 2012 through 2016. We found that Salmonella Albany strain 27A-368 encodes mcr-5 and that mcr genes were undetectable among the remaining 202 isolates. The resistance plasmid p27A-368 was transferred by conjugation to S. Infantis and was stably retained as a transconjugant. Whole-genome sequencing revealed that mcr-5 resided on a 115 kb plasmid (p27A-368). The plasmid backbone of p27A-368 is more similar to that of pCOV27, an ESBL-encoding plasmid recovered from avian pathogenic E. coli, rather than pSE13-SA01718 of S. Paratyphi B that encodes mcr-5. Further, mcr-5 is located on a transposon, and its sequence is similar to that of pSE13-SA01718. A phylogenetic tree based on single nucleotide variants implies a relationship between 27A-368 and S. Albany isolated in Southeast Asian countries.

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Escherichia coli Sequence Type 131 Is a Dominant, Antimicrobial-Resistant Clonal Group Associated with Healthcare and Elderly Hosts

Infection Control and Hospital Epidemiology ◽

10.1086/669865 ◽

2013 ◽

Vol 34 (4) ◽

pp. 361-369 ◽

Cited By ~ 87

Author(s):

Ritu Banerjee ◽

Brian Johnston ◽

Christine Lohse ◽

Stephen B. Porter ◽

Connie Clabots ◽

...

Keyword(s):

Escherichia Coli ◽

Long Term Care ◽

Tertiary Care ◽

Sequence Type ◽

Olmsted County ◽

Term Care ◽

Clonal Group ◽

E Coli ◽

Healthcare Settings

Objective.To determine prevalence, predictors, and outcomes of infection due to Escherichia coli sequence type ST131.Design.Retrospective cohort.Setting.All healthcare settings in Olmsted County, Minnesota (eg, community hospital, tertiary care center, long-term care facilities, and ambulatory clinics).Patients.Ambulatory and hospitalized children and adults with extraintestinal E. coli isolates.Methods.We analyzed 299 consecutive, nonduplicate extraintestinal E. coli isolates submitted to Olmsted County laboratories in February and March 2011. ST131 was identified using single-nucleotide polymorphism polymerase chain reaction and further evaluated through pulsed-field gel electrophoresis. Associated clinical data were abstracted through medical record review.Results.Most isolates were from urine specimens (90%), outpatients (68%), and community-associated infections (61%). ST131 accounted for 27% of isolates overall and for a larger proportion of those isolates resistant to fluoroquinolones (81%), trimethoprim-sulfamethoxazole (42%), gentamicin (79%), and ceftriaxone (50%). The prevalence of ST131 increased with age (accounting for 5% of isolates from those 11–20 years of age, 26% of isolates from those 51–60 years of age, and 50% of isolates from those 91–100 years of age). ST131 accounted for a greater proportion of healthcare-associated isolates (49%) than community-associated isolates (15%) and for fully 76% of E. coli isolates from long-term care facility (LTCF) residents. Multivariable predictors of ST131 carriage included older age, LTCF residence, previous urinary tract infection, high-complexity infection, and previous use of fluoroquinolones, macrolides, and extended-spectrum cephalosporins. With multivariable adjustment, ST131-associated infection outcomes included receipt of more than 1 antibiotic (odds ratio [OR], 2.54 [95% confidence interval (CI), 1.25–5.17]) and persistent or recurrent symptoms (OR, 2.53 [95% CI, 1.08–5.96]). Two globally predominant ST131 pulsotypes accounted for 45% of STB 1 isolates.Conclusions.ST131isa dominant, antimicrobial-resistant clonal group associated with healthcare settings, elderly hosts, and persistent or recurrent symptoms.

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Detection of mcr-1-mediated colistin resistance in E. coli isolate from imported chicken meat from Brazil

Journal of Global Antimicrobial Resistance ◽

10.1016/j.jgar.2019.02.004 ◽

2019 ◽

Vol 16 ◽

pp. 249-250

Author(s):

Naoko Chiba ◽

Koichi Tanimoto ◽

Junzo Hisatsune ◽

Motoyuki Sugai ◽

Keigo Shibayama ◽

...

Keyword(s):

Chicken Meat ◽

Colistin Resistance ◽

Coli Isolate ◽

E Coli

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Detection of MCR-1 Gene in Multiple Drug Resistant Escherichia coli and Klebsiella pneumoniae in Human Clinical Samples from Peshawar, Pakistan

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207323666200914100119 ◽

2020 ◽

Vol 23 ◽

Author(s):

Fareeha Hameed ◽

Muhammad Asif Khan ◽

Hazrat Bilal ◽

Hafsah Muhammad ◽

Tayyab Ur Rehman

Keyword(s):

Sequence Similarity ◽

Tertiary Care ◽

Health Concern ◽

Diffusion Method ◽

Clinical Samples ◽

Multiple Drug ◽

Drug Resistant ◽

Colistin Resistance ◽

E Coli ◽

Multiple Drug Resistant

Background: The presence of plasmid mediated mcr-1 gene in multidrug resistant Gram-negative bacteria poses a serious public health concern in today’s world. Objectives: The present study was aimed to detect the presence of plasmid mediated mcr-1 encoding resistance to colistin in multiple drug resistant (MDR) E. coli and K. pneumoniae isolates. Methods: A total 180 clinical isolates of E. coli (n=120) and K. pneumoniae (n=60) were isolated from different clinical specimens i.e. urine, blood, stool and pus, from diagnostic labs of two major public sector tertiary care hospitals in Peshawar, Pakistan. MDR profile of these isolates was assessed through Kirby-Baur disc diffusion method. All isolates were screened for colistin resistance by dilution methods. Colistin resistant isolates were subjected to PCR for mcr-1 detection and confirmation was done by Sanger sequencing method. Results: Overall 83.3% (100/120) E. coli and 93.3% (56/60) K. pneumoniae were detected as MDR. Colistin resistance was found in 23.3% (28/120) E. coli and 40% (24/60) K. pneumoniae isolates whereas mcr-1 gene was detected in 10 out of 52 colistin resistant isolates including six E. coli and four K. pneumoniae isolates. Minimum inhibitory concentrations (MICs) of colistin in these ten mcr-1 positive isolates ranged from 4µg/ml to 16µg/ml. All mcr-1 positive isolates showed 99% sequence similarity when compared with other present sequences in GenBank. Conclusion: Hence, our study confirms the presence of mcr-1 mediated colistin resistance in the studied area. Therefore, urgently larger scale surveillance studies are recommended to investigate prevalence of mcr-1 mediated colistin resistance and to prevent its further spread in the area.

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Molecular characteristics of antibiotic-resistant Escherichia coli and Klebsiella pneumoniae strains isolated from hospitalized patients in Tehran, Iran

Annals of Clinical Microbiology and Antimicrobials ◽

10.1186/s12941-021-00437-8 ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Javad Yasbolaghi Sharahi ◽

Ali Hashemi ◽

Abdollah Ardebili ◽

Sara Davoudabadi

Keyword(s):

Resistance Genes ◽

Large Scale ◽

Antimicrobial Agents ◽

Tertiary Care ◽

Resistance Mechanisms ◽

Hospitalized Patients ◽

Control Measures ◽

Molecular Characteristics ◽

Colistin Resistance ◽

E Coli

Abstract Background We evaluated the distribution of carbapenem and colistin resistance mechanisms of clinical E. coli and K. pneumoniae isolates from Iran. Methods 165 non-duplicate non-consecutive isolates of K. pneumoniae and E. coli were collected from hospitalized patients admitted to Iran's tertiary care hospitals from September 2016 to August 2018. The isolates were cultured from different clinical specimens, including wound, urine, blood, and tracheal aspirates. Antibiotic susceptibility testing was performed by disc diffusion and microdilution method according to the Clinical and Laboratory Standards Institute (CLSI) guideline. The presence of extended spectrum β-lactamases (ESBLs) genes, carbapenemase genes, as well as fosfomycin resistance genes, and colistin resistance genes was also examined by PCR-sequencing. The ability of biofilm formation was assessed with crystal violet staining method. The expression of colistin resistance genes were measured by quantitative reverse transcription-PCR (RT-qPCR) analysis to evaluate the association between gene upregulation and colistin resistance. Genotyping was performed using the multi-locus sequencing typing (MLST). Results Colistin and tigecycline were the most effective antimicrobial agents with 90.3% and 82.4% susceptibility. Notably, 16 (9.7%) isolates showed resistance to colistin. Overall, 33 (20%), 31 (18.8%), and 95 (57.6%) isolates were categorized as strong, moderate, and weak biofilm-producer, respectively. Additionally, blaTEM, blaSHV, blaCTX-M, blaNDM-1, blaOXA-48-like and blaNDM-6 resistance genes were detected in 98 (59.4%), 54 (32.7%), 77 (46.7%), 3 (1.8%), 17 (10.30%) and 3 (1.8%) isolates, respectively. Inactivation of mgrB gene due to nonsense mutations and insertion of IS elements was observed in 6 colistin resistant isolates. Colistin resistance was found to be linked to upregulation of pmrA-C, pmrK, phoP, and phoQ genes. Three of blaNDM-1 and 3 of blaNDM-6 variants were found to be carried by IncL/M and IncF plasmid, respectively. MLST revealed that blaNDM positive isolates were clonally related and belonged to three distinct clonal complexes, including ST147, ST15 and ST3299. Conclusions The large-scale surveillance and effective infection control measures are also urgently needed to prevent the outbreak of diverse carbapenem- and colistin-resistant isolates in the future.

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A novel method for measuring phenotypic colistin resistance in Escherichia coli populations from chicken flocks

10.1101/2020.10.22.351577 ◽

2020 ◽

Author(s):

Nhung Thi Nguyen ◽

Nguyen Thi Phuong Yen ◽

Nguyen Van Ky Thien ◽

Nguyen Van Cuong ◽

Bach Tuan Kiet ◽

...

Keyword(s):

Escherichia Coli ◽

Production Cycle ◽

Broth Microdilution ◽

Colistin Resistance ◽

E Coli ◽

Microdilution Method ◽

Faecal Samples ◽

Broth Microdilution Method ◽

Field Samples ◽

Over Time

ABSTRACTColistin is extensively used in animal production in many low- and middle-income countries. There is a need to develop methodologies to benchmark and monitor changes in resistance in commensal bacterial populations in farms. We aimed to evaluate the performance of a broth microdilution method based on culturing a pooled Escherichia coli suspension (30-50 organisms) from each sample. In order to confirm the biological basis and sensitivity of the method, we prepared 16 standard suspensions containing variable ratios of colistin-susceptible and mcr-1 encoded colistin-resistant E. coli which were grown in 2mg/L colistin. The optical density (OD600nm) readings over time were used to generate a growth curve, and were adjusted to the values obtained in the absence of colistin. The median limit of detection of the method was 1 colistin-resistant in 104 susceptible colonies [1st - 3rd quartile, 1:102 – 1:105]. We applied this method to 108 pooled faecal samples from 36 chicken flocks in the Mekong Delta (Vietnam) over the production cycle. The correlation between this method and the prevalence of colistin resistance in individual colonies harvested from field samples, determined by the Minimum Inhibitory Concentration (MIC), was established. The overall prevalence of colistin resistance at sample and isolate level was 38.9% and 19.4%, respectively. Increased colistin resistance was associated with recent (2 weeks) use of colistin and other, non-colistin antimicrobials (OR=3.67 and OR=1.84, respectively). Our method is a sensitive and affordable approach to monitor changes in colistin resistance in pooled E. coli populations from faecal samples over time.IMPORTANCEColistin (polymyxin E) is an antimicrobial with poor solubility properties, and therefore broth microdilution is the only appropriate method for testing colistin resistance. However, estimating colistin resistance in commensal mixed Escherichia coli populations is laborious since it requires individual colony isolation, identification and susceptibility testing. We developed a growth-based microdilution method suitable for pooled faecal samples. We validated the method by comparing it with results from individual MIC testing of 909 E. coli isolates. We used the method to investigate phenotypic colistin resistance in 108 pooled faecal samples from 36 healthy chicken flocks, each sampled three times over the production cycle. A higher level of resistance was seen in flocks recently supplemented with colistin in drinking water, although the observed generated resistance was short-lived. Our method is affordable, and may potentially be integrated into surveillance systems aiming at estimating the prevalence of resistance at colony level in flocks/herds. Furthermore, it may also be adapted to other complex biological systems, such as farms and abattoirs.

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Emergence of Carbapenem-Resistant Enterobacteriaceae in a Tertiary Care Hospital in Southern Thailand†

Walailak Journal of Science and Technology (WJST) ◽

10.48048/wjst.2020.10729 ◽

2020 ◽

Vol 17 (10) ◽

pp. 1139-1148

Author(s):

Prerit Upadhyaya ARYAL ◽

Benjamas THAMJARUNGWONG ◽

Kamonnut SINGKHAMANAN ◽

Paramee THONGSUKSAI ◽

Natnicha INGVIYA ◽

...

Keyword(s):

Tertiary Care ◽

Enterobacter Aerogenes ◽

Care Hospital ◽

E Coli ◽

Healthcare Settings ◽

Carbapenem Resistant ◽

Southern Thailand ◽

Disk Diffusion Assay ◽

Susceptibility Profiles ◽

Carbapenem Resistant Enterobacteriaceae

Carbapenem-resistant Enterobacteriaceae (CRE) is emerging as a major problem in healthcare settings globally, including Thailand, due to limited therapeutic options. We reported the detection, antimicrobial susceptibility profiles, and the presence of carbapenemase genes of CRE isolates obtained from Songklanagarind Hospital between July 2012 and June 2015. A total of 273 non-duplicated CRE isolates was recovered from 248 patients. The predominant organism was Klebsiella pneumoniae (183 [67.0 %]), followed by Escherichia coli (38 [13.9 %]). The susceptibility to 13 antibiotics was performed by disk diffusion assay. Most of the CRE isolates remained susceptible to amikacin. Minimum inhibitory concentrations (MIC) of carbapenems were determined by E-test. The MIC50 and MIC90 were varied among genera and species. Multiplex PCRs for the carbapenemase genes blaIMP, blaVIM, blaOXA-48, blaNDM-1, blaKPC, and blaGES were performed. One hundred and seventy-eight out of these 273 CRE isolates (65.2 %) harbored either single or multiple carbapenemase genes. One hundred and fifty nine isolates harbored the blaNDM-1 gene (113 K. pneumoniae, 25 E. coli, 17 E. cloacae, 2 Citrobacter freundii, 1 Enterobacter aerogenes, and 1 Pantoea agglomerans), 7 isolates carried blaIMP (4 K. pneumoniae, 2 C. freundii, and 1 E. cloacae), 7 isolates possessed blaOXA-48 (1 K. pneumoniae, 5 E. coli, and 1 E. aerogenes), whereas 3 and 2 isolates harbored blaNDM-1 and blaIMP (2 K. pneumoniae and 1 E. cloacae) and blaNDM-1 and blaOXA-48 (1 E. coli and 1 E. cloacae), respectively. In conclusion, this study revealed the detection of CRE, with the majority of K. pneumoniae harboring blaNDM-1 in this setting.

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Plasmid-Mediated Colistin Resistance (mcr-1) in Escherichia coli from Non-Imported Fresh Vegetables for Human Consumption in Portugal

Microorganisms ◽

10.3390/microorganisms8030429 ◽

2020 ◽

Vol 8 (3) ◽

pp. 429

Author(s):

Vera Manageiro ◽

Daniela Jones-Dias ◽

Eugénia Ferreira ◽

Manuela Caniça

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance Gene ◽

In Silico Analysis ◽

Upstream Region ◽

Human Consumption ◽

Colistin Resistance ◽

Coli Isolate ◽

E Coli ◽

Fresh Vegetables ◽

Insertion Sequence Is26

In this study, we report the presence of the plasmid-mediated colistin resistance (PMCR)-encoding gene mcr-1 in an Escherichia coli isolate, INSali25, recovered from lettuce produced and marketed in Portugal. Colistin MIC from the vegetable E. coli isolate—determined by microdilution broth method according to EUCAST guidelines—revealed a non-wild-type phenotype of colistin (MIC 16 mg/L). To understand the genetic background of E. coli INSali25, we performed whole genome sequencing. Plasmid sequencing was also performed after plasmid DNA extraction from the transconjugant TcINSali25 (mcr-1). Directed bioinformatics analysis identified the mcr-1 gene in a 39,998 bp length contig, with an upstream region including the antibiotic resistance gene blaTEM-1 in a partial transposon Tn2, truncated by the insertion sequence IS26 and showing >99% identity with previously described mcr-1-harboring IncHI2 plasmids. Further in silico analysis showed the presence of additional genes conferring resistance to β-lactams (blaTEM-1), aminoglycosides (aadA1, aph(4)-Ia, aph(6)-Id, aac(3)-Iv), macrolides (mdf(A)-type), phenicol (floR-type), tetracycline (tetA), and sulphonamides (sul2). INSali25 isolate belonged to the ST1716 lineage and showed the fimH54 and fumC27 alleles. Lettuce is a vegetable that is commonly consumed fresh and not subjected to any cooking process, which may amplify human food safety risks. Moreover, the occurrence of plasmid-mediated colistin resistance in a sample that was not imported and was acquired in a large retail store reinforces the widespread distribution of mcr-1.

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