Molecular epidemiology of isolates with multiple mcr plasmids from a pig farm in Great Britain: the effects of colistin withdrawal in the short and long term

Duggett, Nicholas; Randall, Luke; Horton, Robert A.; Lemma, Fabrizio; Kirchner, Miranda; Nuñéz-García, Javier; Brena, Camilla; Williamson, Susanna; Teale, Christopher; Anjum, Muna F.

doi:10.1093/jac/dky292

Cited by 43 publications

(42 citation statements)

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“…Plasmids encountered herein contained similar replicons to the ones described in the literature to be potential carriers of colistin resistance, with IncX4 being the most prevalent [50][51][52][53][54][55][56] . In agreement with other studies 51,[57][58][59] , some of the IncX4 plasmids have lost the transposition element ISApl1 involved in the mobilization of the mcr-1 gene suggesting its stabilization within the plasmid. This was also the case for the isolate obtained from the farmer.…”

Section: Discussionsupporting

confidence: 92%

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

Viñes¹,

Cuscó²,

Napp

et al. 2019

Preprint

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One-Health studies applying massive-parallel and single-molecule sequencing are a suitable approximation to try to understand how antibiotic resistances flow between the human-animalenvironment 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 Colistin has been withdrawn in human medicine due to its toxicity, limiting its usage as a last-resort treatment option for multidrug-resistant Gram-negative bacteria.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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Section: Discussionsupporting

confidence: 92%

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

Viñes¹,

Cuscó²,

Napp

et al. 2019

Preprint

View full text Add to dashboard Cite

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“…Based on core genome SNP analysis published elsewhere (Duggett et al . ), isolates RB11 and RB15 are likely to be identical, and isolates RB 2 and RB5 to be very similar.…”

Section: Resultsmentioning

confidence: 99%

“…Details of the plasmids on which the mcr‐1 gene were located are described elsewhere (Duggett et al . ). Interestingly, the newly emerged mcr‐2 plasmid‐mediated colistin resistance gene reported from Belgium has been reported on an IncX4 plasmid (Xavier et al .…”

Section: Discussionmentioning

confidence: 97%

“…), and the results of testing isolates obtained from this farm for these other variants are described elsewhere (Duggett et al . ).…”

Section: Discussionmentioning

confidence: 97%

“…) and those from Duggett et al . () indicate that the mcr‐1 gene present in these multidrug‐resistant E. coli isolates was generally not co‐located on a plasmid with other resistance genes, therefore co‐selection and persistence of the mcr‐1 plasmid would not be expected to occur for most of the mcr‐1 plasmid variants present on this farm. The occurrence of the colistin resistance gene without colocated resistance genes on the same plasmid probably enabled the decline in resistance, as indicated by results from sampling 4, despite continued use of antibiotics other than colistin on the farm.…”

Section: Discussionmentioning

confidence: 97%

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Longitudinal study on the occurrence in pigs of colistin‐resistant Escherichia coli carrying mcr‐1 following the cessation of use of colistin

et al. 2018

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Prevalence of colistin resistance and antibacterial resistance in commensal Escherichia coli from chickens: An assessment of the impact of regulatory intervention in South Africa

Hassan,

Qekwana,

Naidoo

2023

Veterinary Medicine & Sci

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BackgroundAntimicrobial resistance (AMR) is a global health problem largely due to the overuse of antimicrobials. In recognition of this, the World Health Assembly in 2015 agreed on a global action plan to tackle AMR. Following the global emergence of the mcr‐1‐associated colistin resistance gene in the livestock industry in 2016, several countries including South Africa restricted the veterinary use of colistin as the gene threatens the clinical utility of the drug. This study is a follow‐up to the restriction in place in order to evaluate the impact of such policy adoption.ObjectiveTo assess the prevalence of antibacterial resistance (ABR), and the mcr‐1 colistin resistance gene in broiler chicken over a 2‐year period, as a follow‐up to the veterinary ban on colistin use in South Africa.MethodsA total of 520 swab samples were obtained during 2019 (March–April) and 2020 (February–March), from healthy broiler chicken carcasses (n = 20) and chicken droppings in transport crates (n = 20) at various poultry abattoirs (N = 7) in the Gauteng province of South Africa. Escherichia coli organisms were isolated and subjected to a panel of 24 antibacterials using the MicroScan machine. Screening for mcr‐1 colistin resistance gene was undertaken using PCR.ResultFour hundred and thirty‐eight (438) E. coli strains were recovered and none demonstrated phenotypic resistance towards colistin, amikacin, carbapenems, tigecycline and piperacillin/tazobactam. The mcr‐1 gene was not detected in any of the isolates tested. Resistances to the aminoglycosides (0%–9.8%) and fluoroquinolones (0%–18.9%) were generally low. Resistances to ampicillin (32%–39.3%) and trimethoprim/sulphamethoxazole (30.6%–3.6%) were fairly high. A significant (p < 0.05) increase in cephalosporins and cephamycin resistance was noted in the year 2020 (February–March) when compared with the year 2019 (March–April).ConclusionThe absence of mcr‐1 gene and colistin resistance suggests that mitigation strategies adopted were effective and clearly demonstrated the significance of regulatory interventions in reducing resistance to critical drugs. Despite the drawback in regulatory framework such as free farmers access to antimicrobials OTC and a dual registration system in place, there is a general decline in the prevalence of ABR when the present data are compared with the last national veterinary surveillance on AMR (SANVAD 2007). To further drive resistance down, mitigation strategies should focus on strengthening regulatory framework, the withdrawal of OTC dispensing of antimicrobials, capping volumes of antimicrobials, banning growth promoters and investing on routine surveillance/monitoring of AMR and antimicrobial consumption.

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Molecular epidemiology of isolates with multiple mcr plasmids from a pig farm in Great Britain: the effects of colistin withdrawal in the short and long term

Cited by 43 publications

References 23 publications

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

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

Longitudinal study on the occurrence in pigs of colistin‐resistant Escherichia coli carrying mcr‐1 following the cessation of use of colistin

Prevalence of colistin resistance and antibacterial resistance in commensal Escherichia coli from chickens: An assessment of the impact of regulatory intervention in South Africa

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