On the island of Zanzibar people in the community are frequently colonized with the same MDR Enterobacterales found in poultry and retailed chicken meat

2020 ◽  
Vol 75 (9) ◽  
pp. 2432-2441 ◽  
Author(s):  
Thomas Büdel ◽  
Esther Kuenzli ◽  
Edgar I Campos-Madueno ◽  
Ali Haji Mohammed ◽  
Nadir Khatib Hassan ◽  
...  
Keyword(s):  
Core Genome ◽  
Resistance Mechanisms ◽  
Chicken Meat ◽  
Published Data ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
E Coli ◽  
Gut Colonization ◽  
Genome Analyses ◽  
Retail Chicken Meat

Abstract Objectives Intestinal colonization with extended-spectrum cephalosporin-resistant (ESC-R) and colistin-resistant (CST-R) Enterobacterales (Ent) can be driven by contact with colonized animals and/or contamination of the food chain. We studied the ESC-R-Ent and COL-R-Ent colonizing poultry as well as contaminating chicken meat in Zanzibar (Tanzania). Results were compared with recently published data obtained from rectal swabs of people in the community. Methods During June and July 2018, we collected poultry faecal material (n = 62) and retail chicken meat (n = 37) samples. ESC-R and CST-R strains were isolated implementing selective approaches and characterized with different molecular methods, including WGS coupled with core-genome analyses. Results The prevalence of ESC-R-Ent and CST-R-Ent, respectively, were: 88.7% and 48.4% in poultry; and 43.2% and 18.9% in chicken meat. Overall, the following strains and main resistance mechanisms were found in the two settings: 69 ESC-R Escherichia coli (CTX-M-15 subgroup, 75%), 34 ESC-R Klebsiella pneumoniae (CTX-M-9 group, 54.5%), 24 non-ESC-R but CST-R E. coli (mcr-1, 95.8%) and 17 non-ESC-R but CST-R K. pneumoniae (D150G substitution in PhoQ). Several clones (differing by only 0–13 single nucleotide variants) were concomitantly and frequently found in human and non-human settings: mcr-1-carrying E. coli ST46; CTX-M-15-producing E. coli ST361; CTX-M-14-producing K. pneumoniae ST17; and CTX-M-15-producing K. pneumoniae ST1741. Conclusions This is one of the few studies that have assessed the occurrence of identical MDR Enterobacterales in human and non-human settings. The frequent human gut colonization observed in the community might be favoured by the spread of ESC-R-Ent and CST-R-Ent in poultry and chicken meat. Further studies with a One Health approach should be carried out to better investigate this phenomenon.

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

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.

scholarly journals Rapid Increase of CTX-M-Producing Shigella sonnei Isolates in Switzerland Due to Spread of Common Plasmids and International Clones

2020 ◽  
Vol 64 (10) ◽  
Author(s):  
Edgar I. Campos-Madueno ◽  
Odette J. Bernasconi ◽  
Aline I. Moser ◽  
Peter M. Keller ◽  
Francesco Luzzaro ◽  
...  
Keyword(s):  
Core Genome ◽  
The United States ◽  
Sequence Type ◽  
Shigella Sonnei ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Content Type ◽  
Phylogenetic Comparison ◽  
The United Kingdom ◽  
Extended Spectrum

ABSTRACT The Swiss Centre for Antibiotic Resistance (ANRESIS) has recently noted an increase of extended-spectrum cephalosporin-resistant (ESC-R) Shigella sonnei isolates nationwide (3.8% in 2016 versus 37.5% in 2019). To understand this phenomenon, we analyzed 25 representative isolates (of which 14 were ESC-R) collected in Switzerland during 2016 to 2019. Whole-genome sequencing was achieved using both the Illumina and the Nanopore platforms. Both ESC-R and extended-spectrum cephalosporin-susceptible isolates belonged to sequence type 152 (ST152). The ESC-R isolates carried blaCTX-M-3 in IncI1-pST57 (n = 5), blaCTX-M-15 in IncFII (F2:A-:B-) (n = 5), blaCTX-M-15 in IncI1-pST16, and blaCTX-M-27, blaCTX-M-55, or blaCTX-M-134 in other IncFII plasmids (n = 1 each). Plasmids having the same bla and Inc group exhibited high degrees of genetic identity to each other but also to plasmids previously reported in other Enterobacterales. Core-genome analysis showed that there were 4 main clusters, each of which included strains that differed by <58 single nucleotide variants (SNVs) and that consisted of both blaCTX-M-positive and blaCTX-M-negative isolates. Moreover, most isolates belonging to the same cluster shared an identical core-genome sequence type (cgST). For instance, cluster 1 included 4 isolates of cgST113036, of which only 3 harbored the IncI1-pST57 blaCTX-M-3-positive plasmid. The 25 S. sonnei isolates were also subjected to phylogenetic comparison with deposited international strains. As a result, matching isolates (isolates that had the same cgST and that differed by <8 SNVs) have been reported in the United Kingdom, the United States, France, and the Netherlands. Overall, our results suggest that some common S. sonnei clusters can spread between continents and can be imported into other nations after international trips. Such clusters include, in part, isolates that do not possess blaESBL-harboring plasmids, indicating their tendency to acquire them from other Enterobacterales.

scholarly journals Draft Genomic Sequencing of Six Potential Extraintestinal Pathogenic Escherichia coli Isolates from Retail Chicken Meat

2018 ◽  
Vol 6 (21) ◽  
Author(s):  
Aixia Xu ◽  
James R. Johnson ◽  
Shiowshuh Sheen ◽  
David S. Needleman ◽  
Christopher Sommers
Keyword(s):  
Escherichia Coli ◽  
Draft Genome ◽  
Meat Products ◽  
Chicken Meat ◽  
Genome Sequences ◽  
Content Type ◽  
E Coli ◽  
Safety Research ◽  
Pathogenic Escherichia Coli ◽  
Retail Chicken Meat

ABSTRACT Potential extraintestinal pathogenic Escherichia coli strains DP254, WH333, WH398, F356, FEX675, and FEX725 were isolated from retail chicken meat products. Here, we report the draft genome sequences for these six E. coli isolates, which are currently being used in food safety research.

scholarly journals Genomic Epidemiology and Molecular Resistance Mechanisms of Azithromycin-Resistant Neisseria gonorrhoeae in Canada from 1997 to 2014

2016 ◽  
Vol 54 (5) ◽  
pp. 1304-1313 ◽  
Author(s):  
Walter Demczuk ◽  
Irene Martin ◽  
Shelley Peterson ◽  
Amrita Bharat ◽  
Gary Van Domselaar ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Resistance Mechanisms ◽  
23S Rrna ◽  
Phylogenomic Analysis ◽  
Single Nucleotide ◽  
Content Type ◽  
E Coli ◽  
Genomic Epidemiology ◽  
High Level ◽  
Promoter Mutations

The emergence ofNeisseria gonorrhoeaestrains with decreased susceptibility to cephalosporins and azithromycin (AZM) resistance (AZMr) represents a public health threat of untreatable gonorrhea infections. Genomic epidemiology through whole-genome sequencing was used to describe the emergence, dissemination, and spread of AZMrstrains. The genomes of 213 AZMrand 23 AZM-susceptibleN. gonorrhoeaeisolates collected in Canada from 1989 to 2014 were sequenced. Core single nucleotide polymorphism (SNP) phylogenomic analysis resolved 246 isolates into 13 lineages. High-level AZMr(MICs ≥ 256 μg/ml) was found in 5 phylogenetically diverse isolates, all of which possessed the A2059G mutation (Escherichia colinumbering) in all four 23S rRNA alleles. One isolate with high-level AZMrcollected in 2009 concurrently had decreased susceptibility to ceftriaxone (MIC = 0.125 μg/ml). An increase in the number of 23S rRNA alleles with the C2611T mutations (E. colinumbering) conferred low to moderate levels of AZMr(MICs = 2 to 4 and 8 to 32 μg/ml, respectively). Low-level AZMrwas also associated withmtrRpromoter mutations, including the −35A deletion and the presence ofNeisseria meningitidis-like sequences. Geographic and temporal phylogenetic clustering indicates that emergent AZMrstrains arise independently and can then rapidly expand clonally in a region through local sexual networks.

scholarly journals Chromosome-Mediated mcr-3 Variants in Aeromonas veronii from Chicken Meat

2017 ◽  
Vol 61 (11) ◽  
Author(s):  
Zhuoren Ling ◽  
Wenjuan Yin ◽  
Hui Li ◽  
Qidi Zhang ◽  
Xiaoming Wang ◽  
...  
Keyword(s):  
Nucleotide Sequence Identity ◽  
Chicken Meat ◽  
Aeromonas Salmonicida ◽  
Gene Variants ◽  
Colistin Resistance ◽  
Content Type ◽  
E Coli ◽  
Sequence Identity ◽  
Aeromonas Veronii ◽  
Retail Chicken Meat

ABSTRACT Two adjacent colistin resistance gene variants, termed mcr-3.3 and mcr-3-like, were identified in the chromosome of an Aeromonas veronii isolate obtained from retail chicken meat. The variants showed 95.20% and 84.19% nucleotide sequence identity, respectively, to mcr-3 from porcine Escherichia coli. Functional cloning indicated that only mcr-3.3 conferred polymyxin resistance in both E. coli and Aeromonas salmonicida. The mcr-3.3-mcr-3-like segment was also observed in other Aeromonas species, including A. media, A. caviae, and A. hydrophila.

Travellers returning from the island of Zanzibar colonized with MDR Escherichia coli strains: assessing the impact of local people and other sources

2020 ◽  
Author(s):  
Aline I Moser ◽  
Esther Kuenzli ◽  
Thomas Büdel ◽  
Edgar I Campos-Madueno ◽  
Odette J Bernasconi ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Low Income ◽  
Core Genome ◽  
Chicken Meat ◽  
Local People ◽  
Low Income Countries ◽  
Local Sources ◽  
Genome Analyses ◽  
Almost All ◽  
The Impact

Abstract Objectives Many travellers to low-income countries return home colonized at the intestinal level with extended-spectrum cephalosporin-resistant (ESC-R) and/or colistin-resistant (CST-R) Escherichia coli (Ec) strains. However, nothing is known about the local sources responsible for the transmission of these pathogens to the travellers. Methods We compared the ESC-R- and CST-R-Ec strains found in the pre- (n = 23) and post-trip (n = 37) rectal swabs of 37 travellers from Switzerland to Zanzibar with those (i) contemporarily isolated from local people, poultry, retailed chicken meat (n = 31), and (ii) from other sources studied in the recent past (n = 47). WGS and core-genome analyses were implemented. Results Twenty-four travellers returned colonized with ESC-R- (n = 29) and/or CST-R- (n = 8) Ec strains. Almost all ESC-R-Ec were CTX-M-15 producers and belonged to heterogeneous STs/core-genome STs (cgSTs), while mcr-positive strains were not found. Based on the strains’ STs/cgSTs, only 20 subjects were colonized with ESC-R- and/or CST-R-Ec that were not present in their gut before the journey. Single nucleotide variant (SNV) analysis showed that three of these 20 travellers carried ESC-R-Ec (ST3489, ST3580, ST361) identical (0–20 SNVs) to those found in local people, chicken meat, or poultry. Three further subjects carried ESC-R-Ec (ST394, ST648, ST5173) identical or highly related (15–55 SNVs) to those previously reported in local people, fish, or water. Conclusions This is the first known study comparing the ESC-R- and/or CST-R-Ec strains obtained from travellers and local sources using solid molecular methods. We showed that for at least one-third of the returning travellers the acquired antibiotic-resistant Ec had a corresponding strain among resident people, food, animal and/or environmental sources.

scholarly journals Human carriage of cefotaxime-resistant Escherichia coli in North-East India: an analysis of STs and associated resistance mechanisms

2019 ◽  
Author(s):  
Deepjyoti Paul ◽  
Dmitriy Babenko ◽  
Mark A Toleman
Keyword(s):  
Escherichia Coli ◽  
Core Genome ◽  
In Silico Analysis ◽  
Carbapenem Resistance ◽  
Resistance Mechanisms ◽  
E Coli ◽  
North East India ◽  
North East ◽  
The City ◽  
Silico Analysis

Abstract Objectives To determine the prevalence of Escherichia coli STs and associated resistance mechanisms carried by the community in North-East India. Methods E. coli (108) were isolated from sewage collected from 19 sites across the city of Silchar by plating on MacConkey agar with/without selection (50 mg/L cefotaxime). Species identification was confirmed by MALDI-TOF MS for 82 isolates. Common resistance mechanisms were determined by WGS of pooled E. coli isolates. PFGE combined with specific probes determined the presence of common resistance mechanisms in all isolates. Phylotypes, multilocus STs, core-genome multilocus STs, resistance genes and virulence genes were determined by in silico analysis of 38 genomes. Results and conclusions Analysis of isolates collected without selection (n = 33) indicated that cefotaxime resistance in E. coli was 42% (14/33) and estimated meropenem resistance at 9%. The remaining 58% (19/33) were additionally susceptible to ampicillin, trimethoprim, ciprofloxacin and aminoglycosides. The most common ST among the cefotaxime-resistant E. coli was ST167 (29%), followed by ST410 (17%) and ST648 (10%). E. coli ST131 was absent from the collection. Sixty-three isolates were resistant to cefotaxime and harboured blaCTX-M-15 [54% (34/63)] or blaCMY-42 [46% (29/63)], of which 10% (6/63) harboured both genes. Carbapenem resistance was due to blaNDM-5, found in 10/63 cefotaxime-resistant isolates, and/or blaOXA-181, found in 4/63 isolates. NDM-5 was encoded by IncX3 and/or IncFII plasmids and CMY-42 was mostly encoded by IncI plasmids. NDM-5 appears to have replaced NDM-1 in this region and CMY-42 appears to be in the process of replacing CTX-M-15.

scholarly journals Zoonotic Potential of Escherichia coli Isolates from Retail Chicken Meat Products and Eggs

2014 ◽  
Vol 81 (3) ◽  
pp. 1177-1187 ◽  
Author(s):  
Natalie M. Mitchell ◽  
James R. Johnson ◽  
Brian Johnston ◽  
Roy Curtiss ◽  
Melha Mellata
Keyword(s):  
Escherichia Coli ◽  
Meat Products ◽  
Chicken Meat ◽  
Neonatal Meningitis ◽  
Content Type ◽  
Shell Eggs ◽  
E Coli ◽  
Zoonotic Risk ◽  
Retail Chicken Meat ◽  
Meat And Eggs

ABSTRACTChicken products are suspected as a source of extraintestinal pathogenicEscherichia coli(ExPEC), which causes diseases in humans. The zoonotic risk to humans from chicken-sourceE. coliis not fully elucidated. To clarify the zoonotic risk posed by ExPEC in chicken products and to fill existing knowledge gaps regarding ExPEC zoonosis, we evaluated the prevalence of ExPEC on shell eggs and compared virulence-associated phenotypes between ExPEC and non-ExPEC isolates from both chicken meat and eggs. The prevalence of ExPEC among egg-source isolates was low, i.e., 5/108 (4.7%). Based on combined genotypic and phenotypic screening results, multiple human and avian pathotypes were represented among the chicken-source ExPEC isolates, including avian-pathogenicE. coli(APEC), uropathogenicE. coli(UPEC), neonatal meningitisE. coli(NMEC), and sepsis-associatedE. coli(SEPEC), as well as an undefined ExPEC group, which included isolates with fewer virulence factors than the APEC, UPEC, and NMEC isolates. These findings document a substantial prevalence of human-pathogenic ExPEC-associated genes and phenotypes amongE. coliisolates from retail chicken products and identify key virulence traits that could be used for screening.

scholarly journals Population structure and uropathogenic potential of extended-spectrum cephalosporin-resistant Escherichia coli from retail chicken meat

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
May Linn Buberg ◽  
Solveig Sølverød Mo ◽  
Camilla Sekse ◽  
Marianne Sunde ◽  
Yngvild Wasteson ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Monitoring Program ◽  
Chicken Meat ◽  
Pathogenic Potential ◽  
E Coli ◽  
Extended Spectrum ◽  
Antimicrobial Resistance Genes ◽  
Tract Infections ◽  
Retail Chicken Meat

Abstract Background Food-producing animals and their products are considered a source for human acquisition of antimicrobial resistant (AMR) bacteria, and poultry are suggested to be a reservoir for Escherichia coli resistant to extended-spectrum cephalosporins (ESC), a group of antimicrobials used to treat community-onset urinary tract infections in humans. However, the zoonotic potential of ESC-resistant E. coli from poultry and their role as extraintestinal pathogens, including uropathogens, have been debated. The aim of this study was to characterize ESC-resistant E. coli isolated from domestically produced retail chicken meat regarding their population genetic structure, the presence of virulence-associated geno- and phenotypes as well as their carriage of antimicrobial resistance genes, in order to evaluate their uropathogenic potential. Results A collection of 141 ESC-resistant E. coli isolates from retail chicken in the Norwegian monitoring program for antimicrobial resistance in bacteria from food, feed and animals (NORM-VET) in 2012, 2014 and 2016 (n = 141) were whole genome sequenced and analyzed. The 141 isolates, all containing the beta-lactamase encoding gene blaCMY-2, were genetically diverse, grouping into 19 different sequence types (STs), and temporal variations in the distribution of STs were observed. Generally, a limited number of virulence-associated genes were identified in the isolates. Eighteen isolates were selected for further analysis of uropathogen-associated virulence traits including expression of type 1 fimbriae, motility, ability to form biofilm, serum resistance, adhesion- and invasion of eukaryotic cells and colicin production. These isolates demonstrated a high diversity in virulence-associated phenotypes suggesting that the uropathogenicity of ESC-resistant E. coli from chicken meat is correspondingly highly variable. For some isolates, there was a discrepancy between the presence of virulence-associated genes and corresponding expected phenotype, suggesting that mutations or regulatory mechanisms could influence their pathogenic potential. Conclusion Our results indicate that the ESC-resistant E. coli from chicken meat have a low uropathogenic potential to humans, which is important knowledge for improvement of future risk assessments of AMR in the food chains.

scholarly journals Genomic epidemiology of globalKlebsiella pneumoniaecarbapenemase (KPC)-producingEscherichia coli

2017 ◽  
Author(s):  
N Stoesser ◽  
AE Sheppard ◽  
G Peirano ◽  
LW Anson ◽  
L Pankhurst ◽  
...  
Keyword(s):  
Core Genome ◽  
Horizontal Transmission ◽  
Carbapenem Resistance ◽  
Resistance Mechanisms ◽  
E Coli ◽  
Genomic Epidemiology ◽  
Genetic Features ◽  
Human Infections ◽  
Sequence Types ◽  
Animal Reservoirs

ABSTRACTThe dissemination of carbapenem resistance inEscherichia colihas major implications for the management of common human infections.blaKPC,encoding a transmissible carbapenemase (KPC), has historically largely been associated withKlebsiella pneumoniae,a predominant plasmid (pKpQIL), and a specific transposable element (Tn4401,~10kb). Here we characterize the genetic features of the emergence ofblaKPCin globalE. coli,2008-2013, using both long-and short-read whole genome sequencing.Amongst 43/45 successfully sequencedblaKPC-E. colistrains, we identified high strain (n=21 sequence types, 18% of annotated genes in the core genome); plasmid (≥9 replicon types); andblaKPC-associated, mobile genetic element (MGE) diversity (50% not within complete Tn4401elements). We also found evidence of interspecies, regional and international plasmid spread. In several casesblaKPCwas found on high copy number, small Col-like plasmids, previously associated with horizontal transmission of resistance genes in the absence of antimicrobial selection pressures.E. coliis a common human pathogen, but also a commensal in a multiple environmental and animal reservoirs, and easily transmissible. The association ofblaKPCwith a range of MGEs previously linked to the successful spread of widely endemic resistance mechanisms (e.g.blaTEM,blaCTX-M) suggests that it is likely to become similarly prevalent.

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