Applying Nanopore sequencing to a One-Health scenario for colistin resistance transmission among pigs, cows and the farmer

AbstractOne-Health studies applying massive-parallel and single-molecule sequencing are a suitable approximation to try to understand how antibiotic resistances flow between the human-animal-environment scenario. Colistin has been withdrawn in human medicine due to its toxicity, limiting its usage as a last-resort treatment option for multidrug-resistant Gram-negative bacteria. However, it is still used orally to treat Enterobacteriaceae infections in veterinary medicine. Since 2015, colistin resistance appeared to be located in mobile genetic elements, raising the concern of the likelihood of transmission by horizontal gene transfer between animals and humans. In this study, 202 faecal samples were collected in a mixed farm from pigs, calves, and the farmer. PCR for the mcr-1 gene was positive for 18 of the isolates, and Nanopore sequencing allowed us to determine the location of the gene, either on the chromosome or in plasmids. Three types of replicons were found within the positive isolates harbouring the mcr-1: IncX4, IncI2, and IncHI2. Four different genetic contexts probably indicate different stages of gene stabilization, either in the chromosome or plasmid, with ISApl1 as the main insertion element flanking the gene. Moreover, 43 other resistance genes were found in our samples, related to more than six different antibiotic families (e.g. aminoglycosides, lincosamides, beta-lactams, macrolides, trimethoprim, phenicols, and sulphonamides). We found resistance genes against colistin and that six antibiotic families together in at least one of the isolates from human, swine, and bovine. Isolate 15B-22 harboured one plasmid with seven resistance genes related to four families of antibiotics other than polymyxins, meaning that there are more chances to maintain colistin resistance even with the withdrawn of colistin. Nanopore long reads allowed us to assemble the DNA elements within the isolates easily and determine the genetic context of the mcr-1 gene. Furthermore, they allowed us to describe and locate more antimicrobial resistance genes to other antibiotic families and antiseptic compounds.

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

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01193-20 ◽

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.

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Imported One-Day-Old Chicks as Trojan Horses for Multidrug-Resistant Priority Pathogens Harboring mcr-9 , rmtG and Extended-Spectrum β-Lactamase Genes.

Applied and Environmental Microbiology ◽

10.1128/aem.01675-21 ◽

2021 ◽

Author(s):

Nadia Coppola ◽

Nicolás F. Cordeiro ◽

Gustavo Trenchi ◽

Fernanda Esposito ◽

Bruna Fuga ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Resistance Genes ◽

One Health ◽

Production Systems ◽

Animal Health ◽

Critical Issue ◽

Multidrug Resistant ◽

Extended Spectrum ◽

Antimicrobial Resistance Genes ◽

Production Stages

Antimicrobial resistance is a critical issue that is no longer restricted to hospital settings, but also represents a growing problem involving intensive animal production systems. In this study, we have performed a microbiological and molecular investigation of priority pathogens carrying transferable resistance genes to critical antimicrobials in one-day-old chickens imported from Brazil to Uruguay. Bacterial identification was performed by MALDI-TOF mass spectrometry and antibiotic susceptibility was determined by Sensititre. Antimicrobial resistance genes were sought by polymerase chain reaction and clonality was assessed by PFGE. Four multidrug-resistant (MDR) representative strains were sequenced by Illumina and/or Oxford Nanopore Technologies. Twenty-eight MDR isolates identified as Escherichia coli ( n = 14), Enterobacter cloacae ( n = 11) and Klebsiella pneumoniae ( n = 3). While resistance to oxyiminocephalosporins was due to bla CTX-M-2 , bla CTX-M-8 , bla CTX-M-15 , bla CTX-M-55 and bla CMY-2 , plasmid-mediated quinolone resistance was associated with qnrB19 , qnrE1 , and qnrB2 genes. Finally, resistance to aminoglycosides and fosfomycin was due to the presence of 16S rRNA methyltransferase rmtG and fosA -type genes, respectively. Short and long-read genome sequencing of E. cloacae ODC-Eclo3 strain revealed the presence of IncQ/ rmtG (pUR-EC3.1, 7400-pb), IncHI2A/ mcr-9.1 / bla CTX-M-2 [pUR-EC3.2, ST16 (pMLST), 408,436-bp] and IncN2/ qnrB19 / aacC3 / aph(3’’)-Ib (pUR-EC3.3) resistance plasmids. Strikingly, the bla CTX-M-2 gene was carried by a novel Tn 1696 -like composite transposon designated Tn 7337 . In summary, we report that imported one-day-old chicks can act as Trojan horses for the hidden spread of WHO critical priority MDR pathogens harboring mcr-9 , rmtG and extended-spectrum β-lactamase genes in poultry farms, which is a critical issue within a One Health perspective. Importance section Antimicrobial resistance is considered a significant problem for global health, including within the concept of "One Health", therefore, the food chain is a link that connects human and animal health directly. In this work, we searched for microorganisms resistant to antibiotics considered critical for human health in intestinal microbiota of one-day-old baby chicks imported to Uruguay from Brazil. We described antibiotic-resistant genes to antibiotics named as to watch or reserve for the WHO, such as rmtG or mcr9.1 , which confers resistance to all the aminoglycosides and colistin, respectively, among others genes, and their presence in new mobile genetic elements that favor its dissemination. The sustained entry of these microorganisms evades the sanitary measures implemented by the countries and production establishments to reduce the selection of resistant microorganisms. These silently imported resistant microorganisms could explain a considerable part of the antimicrobial resistance problems found in the production stages of the system.

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Antimicrobial Resistance Genes in ESBL-Producing Escherichia coli Isolates from Animals in Greece

Antibiotics ◽

10.3390/antibiotics10040389 ◽

2021 ◽

Vol 10 (4) ◽

pp. 389

Author(s):

Zoi Athanasakopoulou ◽

Martin Reinicke ◽

Celia Diezel ◽

Marina Sofia ◽

Dimitris C. Chatzopoulos ◽

...

Keyword(s):

Escherichia Coli ◽

Multidrug Resistance ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Wild Bird ◽

One Health ◽

Multidrug Resistant ◽

E Coli ◽

Antimicrobial Resistance Genes ◽

Multidrug Resistance Genes

The prevalence of multidrug resistant, extended spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is increasing worldwide. The present study aimed to provide an overview of the multidrug resistance phenotype and genotype of ESBL-producing Escherichia coli (E. coli) isolates of livestock and wild bird origin in Greece. Nineteen phenotypically confirmed ESBL-producing E. coli strains isolated from fecal samples of cattle (n = 7), pigs (n = 11) and a Eurasian magpie that presented resistance to at least one class of non β-lactam antibiotics, were selected and genotypically characterized. A DNA-microarray based assay was used, which allows the detection of various genes associated with antimicrobial resistance. All isolates harbored blaCTX-M-1/15, while blaTEM was co-detected in 13 of them. The AmpC gene blaMIR was additionally detected in one strain. Resistance genes were also reported for aminoglycosides in all 19 isolates, for quinolones in 6, for sulfonamides in 17, for trimethoprim in 14, and for macrolides in 8. The intI1 and/or tnpISEcp1 genes, associated with mobile genetic elements, were identified in all but two isolates. This report describes the first detection of multidrug resistance genes among ESBL-producing E. coli strains retrieved from feces of cattle, pigs, and a wild bird in Greece, underlining their dissemination in diverse ecosystems and emphasizing the need for a One-Health approach when addressing the issue of antimicrobial resistance.

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Serotype distribution, antimicrobial susceptibility, antimicrobial resistance genes and virulence genes of Salmonella isolated from a pig slaughterhouse in Yangzhou, China

AMB Express ◽

10.1186/s13568-019-0936-9 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

Quan Li ◽

Jian Yin ◽

Zheng Li ◽

Zewei Li ◽

Yuanzhao Du ◽

...

Keyword(s):

Public Health ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Antimicrobial Susceptibility ◽

Virulence Genes ◽

Multidrug Resistant ◽

Resistance Rate ◽

Economic Losses ◽

Production Chain ◽

Antimicrobial Resistance Genes

AbstractSalmonella is an important food-borne pathogen associated with public health and high economic losses. To investigate the prevalence and the characteristics of Salmonella in a pig slaughterhouse in Yangzhou, a total of 80 Salmonella isolates were isolated from 459 (17.43%) samples in 2016–2017. S. Derby (35/80, 43.75%) was the most prevalent, followed by S. Rissen (16/80, 20.00%) and S. Newlands (11/80, 13.75%). The highest rates of susceptibility were observed to cefoxitin (80/80, 100.0%) and amikacin (80/80, 100.0%), followed by aztreonam (79/80, 98.75%) and nitrofurantoin (79/80, 98.75%). The highest resistance rate was detected for tetracycline (65/80, 81.25%), followed by ampicillin (60/80, 75.00%), bactrim (55/80, 68.75%), and sulfisoxazole (54/80, 67.50%). Overall, 91.25% (73/80) of the isolates were resistant to at least one antibiotic, while 71.25% (57/80) of the isolate strains were multidrug resistant in the antimicrobial susceptibility tested. In addition, 86.36% (19/22) of the 22 antimicrobial resistance genes in the isolates were identified. Our data indicated that the resistance to certain antimicrobials was significantly associated, in part, with antimicrobial resistance genes. Furthermore, 81.25% (65/80) isolates harbored the virulence gene of mogA, of which 2 Salmonella Typhimurium isolates carried the mogA, spvB and spvC virulence genes at the same time. The results showed that swine products in the slaughterhouse were contaminated with multidrug resistant Salmonella commonly, especially some isolates carry the spv virulence genes. The virulence genes might facilitate the dissemination of the resistance genes to consumers along the production chain, suggesting the importance of controlling Salmonella during slaughter for public health.

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Molecular survey of mcr1 and mcr2 plasmid mediated colistin resistance genes in Escherichia coli isolates of animal origin in Iran

BMC Research Notes ◽

10.1186/s13104-021-05519-6 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Kayhan Ilbeigi ◽

Mahdi Askari Badouei ◽

Hossein Vaezi ◽

Hassan Zaheri ◽

Sina Aghasharif ◽

...

Keyword(s):

Escherichia Coli ◽

Resistance Genes ◽

Companion Animals ◽

Multidrug Resistant ◽

Animal Origin ◽

Colistin Resistance ◽

E Coli ◽

High Level ◽

Farming Industry

Abstract Objectives The emergence of colistin-resistant Enterobacteriaceae from human and animal sources is one of the major public health concerns as colistin is the last-resort antibiotic for treating infections caused by multidrug-resistant Gram-negative bacteria. We aimed to determine the prevalence of the prototype widespread colistin resistance genes (mcr-1 and mcr-2) among commensal and pathogenic Escherichia coli strains isolated from food-producing and companion animals in Iran. Results A total of 607 E. coli isolates which were previously collected from different animal sources between 2008 and 2016 used to uncover the possible presence of plasmid-mediated colistin resistance genes (mcr-1 and mcr-2) by PCR. Overall, our results could not confirm the presence of any mcr-1 or mcr-2 positive E. coli among the studied isolates. It is concluded that despite the important role of food-producing animals in transferring the antibiotic resistance, they were not the main source for carriage of mcr-1 and mcr-2 in Iran until 2016. This study suggests that the other mcr variants (mcr-3 to mcr-9) might be responsible for conferring colistin resistance in animal isolates in Iran. The possible linkage between pig farming industry and high level of mcr carriage in some countries needs to be clarified in future prospective studies.

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Detection of colistin resistance mcr-1 gene in Salmonella enterica serovar Rissen isolated from mussels, Spain, 2012 to 2016

Eurosurveillance ◽

10.2807/1560-7917.es.2019.24.16.1900200 ◽

2019 ◽

Vol 24 (16) ◽

Cited By ~ 5

Author(s):

Antonio Lozano-Leon ◽

Carlos Garcia-Omil ◽

Jacobo Dalama ◽

Rafael Rodriguez-Souto ◽

Jaime Martinez-Urtaza ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Genome Sequencing ◽

Resistance Genes ◽

Salmonella Enterica ◽

Sequence Type ◽

Monitoring Programme ◽

Colistin Resistance ◽

North West ◽

Antimicrobial Resistance Genes

Nineteen Salmonella strains were isolated from 5,907 randomly selected mussel samples during a monitoring programme for the presence of Salmonella in shellfish in Galicia, north-west Spain (2012–16). Serovars, sequence type and antimicrobial resistance genes were determined through genome sequencing. Presence of the mcr-1 gene in one strain belonging to serovar Rissen and ST-469 was identified. The mcr-1 gene had not been isolated previously in environmental Salmonella isolated from mussels in Spain.

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First identification and Limited Dissemination of mcr-1 Colistin Resistance in Salmonella Isolates in Jiaxing

Journal of Food Protection ◽

10.4315/jfp-21-069 ◽

2021 ◽

Author(s):

Ping Li ◽

Li Zhan ◽

Henghui Wang ◽

Wenjie Gao ◽

Lei Gao ◽

...

Keyword(s):

Public Health ◽

Multidrug Resistance ◽

Antimicrobial Resistance ◽

Gastrointestinal Disease ◽

Foodborne Pathogen ◽

Multidrug Resistant ◽

Colistin Resistance ◽

Antimicrobial Resistance Genes ◽

Genetic Features ◽

Multidrug Resistant Strain

Salmonella , a major foodborne pathogen, causes severe gastrointestinal disease in people and animals worldwide. Plasmid-borne mcr-1 , which confers colistin resistance in Salmonella, has significant epidemiological interest for public health safety. Here, we report the first evidence of mcr-1 -mediated colistin resistance in one multidrug-resistant strain，namely 16062 in this study, from 355 Salmonella isolates collected for Jiaxing foodborne pathogen monitoring in Zhejiang Province in 2015–2019. In addition to colistin, 16062 displayed multidrug resistance to various antimicrobials (β-lactams, quinolone, sulfonamide, florfenicol, ampicillin, streptomycin, nalidixic acid, aminoglycoside, and trimethoprim-sulfamethox). The mcr-1 -carrying IncX4 plasmid (p16062-MCR) in this study shares a conserved structure with other mcr -IncX4 plasmids. We found that other antimicrobial-resistance genes ( aac(6')-Ib-cr , aadA1 , aadA2 , aph(3')-Ia , oqxA , oqxB , sul1 , and cmlA1 ) are located on p16062-cmlA, an atypical IncHI2 plasmid, in isolate 16062. This is the first identification of transferable colistin resistance in foodborne Salmonella isolate collected in Jiaxing city, the 5-year monitoring of which revealed limited dissemination. By determining the genetic features of the plasmid vehicle, the characteristics of transferable mcr genes circulating in isolates from Jiaxing are now clearer.

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