From Farm to Fork: Persistence of Clinically Relevant Multidrug-Resistant and Copper-Tolerant Klebsiella pneumoniae Long after Colistin Withdrawal in Poultry Production

Mourão, Joana; Ribeiro-Almeida, Marisa; Novais, Carla; Magalhães, Mariana; Rebelo, Andreia; Ribeiro, Sofia; Peixe, Luı́sa; Novais, Ângela; Antunes, Patrı́cia

doi:10.1128/spectrum.01386-23

Cited by 8 publications

(38 citation statements)

References 91 publications

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“…*K. pneumoniae isolates from clonal lineages with <10 allele differences include: 2019-2020 collection -ST1-KL19, ST11-KL105, ST11-KL106, ST11-KL27, ST11-KL111, ST15-KL19, ST15-KL146, ST147-KL64, ST307-KL102, ST392-KL27, ST1537-KL64, and ST6250-KL155 (1); 2022 collection -ST11-KL106, ST11-KL111, ST15-KL19, ST147-KL64, ST280-KL23, ST307-KL102, ST525-KL45, ST1228-KL38, ST2055-KL14, ST1997-KL28, ST4110-KL3. The isolates exhibiting grey shading correspond to the ones already published by(Mourão et al, 2023).…”

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confidence: 70%

“…Spectra were acquired in a Spectrum Two instrument (Perkin-Elmer, USA) under standard conditions (4000-600 cm -1 , 4 cm-1 resolution, and 16 scan co-additions). The region between 1200cm -1 and 900 cm -1 was compared with each other, and with those from two different machine-learning classification models, used to predict K. pneumoniae capsular (KL) types: i) a Random Forest classification model that enables identification of up to 33 KL-types from well-characterized international K. pneumoniae clones from the clinical setting (Novais et al, 2023a); and ii) a Random Forest classification model to allow identification of up to 21 KL-types (eleven in common with the previous model) based on a spectral database of poultry isolates identified in previous studies (Mourão et al, 2023). Isolate relatedness and prediction of KL-types were inferred as described previously (Novais et al, 2023a).…”

Section: Methodsmentioning

confidence: 99%

“…Control strains included Escherichia coli ED8739 carrying the plasmid pRJ1004 with the sil and pco cluster (MICCuSO4=16-20mM) and Enterococcus lactis BM4105RF without acquired copper tolerance genes (MICCuSO4=2-4 mM) (Novais et al, 2023b). All K. pneumoniae isolates were screened for the silA copper tolerance gene using a PCR, given its strong association with the presence of an intact sil operon and a Cu tolerance phenotype (Mourão et al, 2016(Mourão et al, , 2023.…”

Section: Antimicrobial Susceptibility To Coppermentioning

confidence: 99%

“…Most were linked to genomes from human infections in diverse EU countries, including Portugal (ST1997-KL28) (Figure 8). (Mourão et al, 2023). The associated metadata for all isolates was added using iTOL (https://itol.embl.de/).…”

Section: Whole-genome Analysis Of K Pneumoniae Poultry-associated Iso...mentioning

confidence: 99%

“…Our prior study unveiled a significant occurrence of copper tolerance and multidrug resistance among K. pneumoniae strains found in chicken flocks (Mourão et al, 2023). We also identified K. pneumoniae lineages and plasmids carrying sil+pco copper tolerance and variable antibiotic resistance genes, resembling those identified in human clinical isolates worldwide (Mourão et al, 2023). These findings highlight the urgent need to further investigate the factors, drivers, and sources that contribute to the selection and persistence of MDR K. pneumoniae within the poultry production chain.…”

Section: Introductionmentioning

confidence: 97%

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DecodingKlebsiella pneumoniaein Poultry Chain: Unveiling Genetic Landscape, Antibiotic Resistance, and Biocide Tolerance in Non-Clinical Reservoirs

Mourão,

Magalhães,

Ribeiro-Almeida

et al. 2024

Preprint

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The rise of antibiotic resistance in the food chain is influenced by the use of antimicrobial agents, such as antibiotics, metals, and biocides, throughout the entire farm-to-fork continuum. Besides, non-clinical reservoirs potentially contribute to the transmission of critical pathogens such as multidrug-resistant (MDR)Klebsiella pneumoniae. However, limited knowledge exists about the population structure and genomic diversity ofK. pneumoniaecirculating in conventional poultry production. We conducted a comprehensive characterization ofK. pneumoniaeacross the whole chicken production chain (flocks/environment/meat, 2019-2022), exploring factors beyond antibiotics, like copper and quaternary ammonium compounds (QACs). Clonal diversity and adaptive features ofK. pneumoniaewere characterized through cultural, molecular (FT-IR), and whole-genome-sequencing (WGS) approaches. All except one flock were positive forK. pneumoniaewith a significant increase (p < 0.05) from early to pre-slaughter stages, most persisting in chicken meat batches. Colistin-resistantK. pneumoniaerates were low (4%), while most samples carried MDR strains (67%) and copper-tolerant isolates (63%;sil+pcoclusters; MICCuSO4≥16mM), particularly at pre-slaughter. Benzalkonium chloride consistently exhibited activity inK. pneumoniae(MIC/MBC range=4-64mg/L) from diverse and representative strains independently of the presence/absence of genes linked to QACs tolerance. A polyclonalK. pneumoniaepopulation, discriminated by FT-IR and WGS, included various lineages dispersed throughout the chicken’s lifecycle at the farm (ST29-KL124, ST11-KL106, ST15-KL19, ST1228-KL38), until the meat (ST1-KL19, ST11-KL111, ST6405-KL109, and ST6406-CG147-KL111), or over years (ST631-49 KL109, ST6651-KL107, ST6406-CG147-KL111). Notably, some lineages were identical to those from human clinical isolates. WGS also revealed F-type multireplicon plasmids carryingsil+pco(copper) co-located withqacEΔ1±qacF(QACs) and antibiotic resistance genes like those disseminated in humans. In conclusion, chicken farms and their derived meat are significant reservoirs for diverseK. pneumoniaeclones enriched in antibiotic resistance and metal tolerance genes, some exhibiting genetic similarities with human clinical strains. Further research is imperative to unravel the factors influencingK. pneumoniaepersistence and dissemination within poultry production, contributing to improved food safety risk management. This study underscores the significance of understanding the interplay between antimicrobial control strategies and non-clinical sources to effectively address the spread of antimicrobial resistance.

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confidence: 70%

Section: Methodsmentioning

confidence: 99%

Section: Antimicrobial Susceptibility To Coppermentioning

confidence: 99%

Section: Whole-genome Analysis Of K Pneumoniae Poultry-associated Iso...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 97%

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DecodingKlebsiella pneumoniaein Poultry Chain: Unveiling Genetic Landscape, Antibiotic Resistance, and Biocide Tolerance in Non-Clinical Reservoirs

Mourão,

Magalhães,

Ribeiro-Almeida

et al. 2024

Preprint

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Development and validation of a quick, automated, and reproducible ATR FT-IR spectroscopy machine-learning model for Klebsiella pneumoniae typing

Novais,

Gonçalves,

Ribeiro

et al. 2024

J Clin Microbiol

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The reliability of Fourier-transform infrared (FT-IR) spectroscopy for Klebsiella pneumoniae typing and outbreak control has been previously assessed, but issues remain in standardization and reproducibility. We developed and validated a reproducible FT-IR with attenuated total reflectance (ATR) workflow for the identification of K. pneumoniae lineages. We used 293 isolates representing multidrug-resistant K. pneumoniae lineages causing outbreaks worldwide (2002–2021) to train a random forest classification (RF) model based on capsular (KL)-type discrimination. This model was validated with 280 contemporaneous isolates (2021–2022), using wzi sequencing and whole-genome sequencing as references. Repeatability and reproducibility were tested in different culture media and instruments throughout time. Our RF model allowed the classification of 33 capsular (KL)-types and up to 36 clinically relevant K. pneumoniae lineages based on the discrimination of specific KL- and O-type combinations. We obtained high rates of accuracy (89%), sensitivity (88%), and specificity (92%), including from cultures obtained directly from the clinical sample, allowing to obtain typing information the same day bacteria are identified. The workflow was reproducible in different instruments throughout time (>98% correct predictions). Direct colony application, spectral acquisition, and automated KL prediction through Clover MS Data analysis software allow a short time-to-result (5 min/isolate). We demonstrated that FT-IR ATR spectroscopy provides meaningful, reproducible, and accurate information at a very early stage (as soon as bacterial identification) to support infection control and public health surveillance. The high robustness together with automated and flexible workflows for data analysis provide opportunities to consolidate real-time applications at a global level. IMPORTANCE We created and validated an automated and simple workflow for the identification of clinically relevant Klebsiella pneumoniae lineages by FT-IR spectroscopy and machine-learning, a method that can be extremely useful to provide quick and reliable typing information to support real-time decisions of outbreak management and infection control. This method and workflow is of interest to support clinical microbiology diagnostics and to aid public health surveillance.

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Unraveling the Role of Metals and Organic Acids towards Bacterial Antimicrobial Resistance in the Food Chain

Rebelo¹,

Peixe²,

Antunes³

et al. 2023

Preprint

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Antimicrobial resistance (AMR) has a significant global impact on human, animal, and environmental health. Misuse and overuse of antibiotics in clinical and animal production settings are the main drivers behind the emergence of antimicrobial resistant bacteria. However, other compounds with antimicrobial activity may also contribute to this global public health problem. The aim of this comprehensive review is to provide detailed insights into the impact of metals and organic acids on the emergence and spread of AMR in the food chain, for which their role is not fully understood. The review examines the widespread use of organic acids in the food industry as feed additives or disinfectants, the crucial role of copper in animal growth and the harmful effects of mercury and arsenic as pollutants in food-producing environments. Additionally, it explores the antimicrobial mechanisms of metals and organic acids, the tolerance mechanisms developed by bacteria, and the interplay between genes responsible for metal tolerance and AMR. The comprehensive and integrated data presented highlights the need to further explore and understand the role of metals and organic acids as drivers of AMR to develop well-defined strategies effectively mitigating the AMR crisis within the food chain context.

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From Farm to Fork: Persistence of Clinically Relevant Multidrug-Resistant and Copper-Tolerant Klebsiella pneumoniae Long after Colistin Withdrawal in Poultry Production

Abstract: The spread of bacteria resistant to last-resort antibiotics such as colistin throughout the food chain is a serious concern for public health. The poultry sector has responded by restricting colistin use and exploring alternative trace metals/copper feed supplements.

Cited by 8 publications

References 91 publications

DecodingKlebsiella pneumoniaein Poultry Chain: Unveiling Genetic Landscape, Antibiotic Resistance, and Biocide Tolerance in Non-Clinical Reservoirs

DecodingKlebsiella pneumoniaein Poultry Chain: Unveiling Genetic Landscape, Antibiotic Resistance, and Biocide Tolerance in Non-Clinical Reservoirs

Development and validation of a quick, automated, and reproducible ATR FT-IR spectroscopy machine-learning model for Klebsiella pneumoniae typing

Unraveling the Role of Metals and Organic Acids towards Bacterial Antimicrobial Resistance in the Food Chain

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