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BMC veterinary research2025; 21(1); 458; doi: 10.1186/s12917-025-04686-z

Genomic snapshot of Klebsiella spp. isolates from clinically ill animals reveal diverse lineages with limited relatedness to human isolates.

Abstract: Klebsiella spp. is an important human and animal pathogen, and it is commonly found with resistance to clinically important antimicrobials worldwide. The main goals of this study were to determine the prevalence of antimicrobial resistance genes in our study population and to assess the relatedness between Klebsiella spp. isolated from humans and animals. Isolates were collected in 2019 and 2020 from various animal hosts that presented to veterinary hospitals in the U.S. that participate in the FDA's Center for Veterinary Medicine Veterinary Laboratory Investigation and Response Network's antimicrobial resistance monitoring program. Results: We sequenced a total of 204 Klebsiella spp. isolates. A majority of isolates were identified as K. pneumoniae (149/204, 73.0%), followed by K. quasipneumoniae (30/204, 14.7%), K. variicola (15/204, 7.4%), K. aerogenes (5/204, 2.5%), K. oxytoca (4/204, 2.0%), and K. grimontii (1/204, 0.5%). Out of 204 isolates, 138 were recovered from dogs, 25 from horses, 17 from cats, 6 from avian species, 5 from cows and 3 from pigs. The remaining 10 isolates were recovered from a few other mammal species. Klebsiella spp. isolates were very diverse. In silico multilocus sequence typing (MLST), using WGS data, identified a total of 88 known sequence types across all isolates. Seventeen isolates were not assigned an MLST sequence type due to combinations of alleles not previously found in the PubMLST database. 45 of the 204 isolates were assigned to 20 different single nucleotide polymorphism (SNP) clusters in the National Center for Biotechnology Information (NCBI) Pathogen Detection browser, and out of those, four isolates were assigned SNP clusters that also contained human isolates, all from dogs. The closest human isolate was 29 SNPs from a dog isolate. A total of 36 resistance genes were identified. The three most common resistance genes were oqxAB, fosA, and bla. None of the isolates had carbapenem resistance genes, although one isolate from a goat had mcr-8.1, a colistin resistance gene. Conclusions: To our knowledge, this is the largest collection of sequenced Klebsiella from sick animals ever assembled, and the results found limited relatedness between these isolates and those from humans, despite the diversity of sequenced isolates.
© 2025. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.
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Publication Date: 2025-07-11 PubMed ID: 40640834PubMed Central: PMC12247286DOI: 10.1186/s12917-025-04686-zGoogle Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

Genomic analysis of Klebsiella species isolated from clinically ill animals in the U.S. reveals a wide diversity of strains with minimal genetic similarity to human isolates, indicating limited direct transmission between animals and humans.

Study Background and Objectives

  • Klebsiella spp. are significant pathogens affecting both humans and animals, often harboring antimicrobial resistance (AMR) genes.
  • The study aimed to:
    • Determine the prevalence of antimicrobial resistance genes in Klebsiella isolates from clinically ill animals.
    • Assess the genetic relatedness between Klebsiella isolates from animals and humans.

Sample Collection and Methods

  • 204 Klebsiella isolates were collected during 2019-2020 from various animal species presented to U.S. veterinary hospitals under the FDA’s Veterinary Laboratory Investigation and Response Network antimicrobial resistance monitoring program.
  • Animal sources included:
    • Dogs (138 isolates)
    • Horses (25 isolates)
    • Cats (17 isolates)
    • Avian species (6 isolates)
    • Cows (5 isolates)
    • Pigs (3 isolates)
    • Other mammals (10 isolates)
  • Whole genome sequencing (WGS) and in silico multilocus sequence typing (MLST) were performed to analyze genetic diversity and sequence types.
  • National Center for Biotechnology Information (NCBI) Pathogen Detection browser was used to identify single nucleotide polymorphism (SNP) clusters indicating genetic relatedness.

Key Findings: Klebsiella Species and Genetic Diversity

  • Species distribution among 204 isolates:
    • Klebsiella pneumoniae: 149 isolates (73.0%)
    • K. quasipneumoniae: 30 isolates (14.7%)
    • K. variicola: 15 isolates (7.4%)
    • K. aerogenes: 5 isolates (2.5%)
    • K. oxytoca: 4 isolates (2.0%)
    • K. grimontii: 1 isolate (0.5%)
  • MLST analysis revealed:
    • 88 known sequence types among all isolates, indicating high genetic diversity.
    • 17 isolates had novel allele combinations unassigned to known sequence types.

Genetic Relatedness Between Animal and Human Isolates

  • 45 isolates clustered into 20 distinct SNP clusters.
  • Only four isolates (all from dogs) belonged to SNP clusters also containing human isolates.
  • The closest genetic distance between an animal and human isolate was 29 SNPs, suggesting limited direct transmission or recent common ancestry.

Antimicrobial Resistance Genes Identified

  • A total of 36 different resistance genes were detected across isolates.
  • The most prevalent resistance genes included:
    • oqxAB (confers resistance to quinolones)
    • fosA (confers resistance to fosfomycin)
    • bla genes (beta-lactamase enzymes that break down beta-lactam antibiotics)
  • No carbapenem resistance genes were identified in any animal isolates.
  • One isolate from a goat carried mcr-8.1, a gene conferring resistance to colistin, an antibiotic of last resort.

Conclusions and Implications

  • This study represents the largest collection of Klebsiella genomes from sick animals to date.
  • Results demonstrate a highly diverse Klebsiella population in animals with limited overlap and genetic relatedness to human isolates, suggesting that most Klebsiella strains in animals are distinct from those infecting humans.
  • The limited sharing of SNP clusters between animal and human isolates indicates low likelihood of frequent direct transmission.
  • While resistance genes are widespread, the absence of carbapenem resistance and rarity of colistin resistance in animal isolates is notable for public health.
  • These findings provide important baseline genomic data to monitor antimicrobial resistance and potential zoonotic transmission risks involving Klebsiella from animals to humans.

Cite This Article

APA
Martin G, Tyson GH, Guag J, Strain E, Ceric O. (2025). Genomic snapshot of Klebsiella spp. isolates from clinically ill animals reveal diverse lineages with limited relatedness to human isolates. BMC Vet Res, 21(1), 458. https://doi.org/10.1186/s12917-025-04686-z

Publication

BMC veterinary research
ISSN: 1746-6148
NlmUniqueID: 101249759
Country: England
Language: English
Volume: 21
Issue: 1
Pages: 458
PII: 458

Researcher Affiliations

Martin, Gordon
  • Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, USA.
Tyson, Gregory H
  • Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, USA.
Guag, Jake
  • Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, USA.
Strain, Errol
  • Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, USA.
Ceric, Olgica
  • Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, USA. Olgica.Ceric@fda.hhs.gov.
  • Veterinary Laboratory Investigation and Response Network (Vet-LIRN), Center for Veterinary Medicine, United States Food and Drug Administration, 8401 Muirkirk Rd, Laurel, MD, 20708, USA. Olgica.Ceric@fda.hhs.gov.

MeSH Terms

  • Animals
  • Klebsiella / genetics
  • Klebsiella / drug effects
  • Klebsiella / classification
  • Klebsiella / isolation & purification
  • Klebsiella Infections / veterinary
  • Klebsiella Infections / microbiology
  • Humans
  • Anti-Bacterial Agents / pharmacology
  • Dogs
  • Cattle
  • Horses
  • Swine
  • Drug Resistance, Bacterial / genetics
  • Cats
  • Genome, Bacterial
  • Microbial Sensitivity Tests
  • Multilocus Sequence Typing

Conflict of Interest Statement

Declarations. Ethics approval and consent to participate: Not applicable-manuscript does not report on or involve the use of any animal or human data or tissue. Consent for publication: (n/a) Author disclaimer: The views expressed in this article are those of the authors and do not necessarily reflect the official policy of the Department of Health and Human Services, the U.S. Food and Drug Administration or the U.S. Government nor do they endorse either the products or companies mentioned. Competing interests: The authors declare no competing interests.

References

This article includes 76 references
  1. CDC. antibiotic resistance threats in the United States. 2019.
  2. Kahn LH. Antimicrobial resistance: a one health perspective.. Trans R Soc Trop Med Hyg 2017;111(6):255–60.
    pubmed: 29044373
  3. The National Antimicrobial Resistance Monitoring System. https://www.fda.gov/animal-veterinary/antimicrobial-resistance/national-antimicrobial-resistance-monitoring-system
  4. Mader R, Damborg P, Amat J-P, Bengtsson B, Bourély C, Broens EM, Busani L, Crespo-Robledo P, Filippitzi M-E, Fitzgerald W. Building the European antimicrobial resistance surveillance network in veterinary medicine (EARS-Vet).. Eurosurveillance 2021;26(4):2001359.
    pmc: PMC7848785pubmed: 33509339
  5. . Multistate Outbreak of Multidrug-Resistant. Campylobacter Infections Linked to Contact with Pet Store Puppies. .
  6. House TW. National Action Plan for Combating Antibiotic-Resistant Bacteria. Washington, DC; 2015.
  7. Policy OD. NATIONAL ACTION PLAN FOR COMBATING ANTIBIOTIC-RESISTANT. BACTERIA 2020–2025. U.S. Department of Health & Human Services 2020:47.
  8. Ceric O, Tyson GH, Goodman LB, Mitchell PK, Zhang Y, Prarat M, Cui J, Peak L, Scaria J, Antony L. Enhancing the one health initiative by using whole genome sequencing to monitor antimicrobial resistance of animal pathogens: Vet-LIRN collaborative project with veterinary diagnostic laboratories in United States and Canada.. BMC Vet Res 2019;15:130.
    pmc: PMC6501310pubmed: 31060608doi: 10.1186/s12917-019-1864-2google scholar: lookup
  9. Zhang Z, Zhang L, Dai H, Zhang H, Song Y, An Q, Wang J, Xia Z. Multidrug-Resistant Klebsiella pneumoniae complex from clinical dogs and cats in China: molecular characteristics, phylogroups, and Hypervirulence-Associated determinants.. Front Veterinary Sci 2022, 9.
    pmc: PMC8960377pubmed: 35359688
  10. Roberts DE, McClain HM, Hansen DS, Currin P, Howerth EW. An outbreak of Klebsiella pneumoniae infection in dogs with severe enteritis and septicemia.. J Vet Diagn Invest 2000;12(2):168–73.
    pubmed: 10730951
  11. Martin RM, Cao J, Brisse S, Passet V, Wu W, Zhao L, Malani PN, Rao K, Bachman MA. Molecular epidemiology of colonizing and infecting isolates of Klebsiella pneumoniae.. mSphere 2016, 1(5).
    pmc: PMC5071533pubmed: 27777984
  12. Rodrigues C, Passet V, Rakotondrasoa A, Diallo TA, Criscuolo A, Brisse S. Erratum to Description of Klebsiella africanensis sp. nov., Klebsiella variicola subsp. tropicalensis subsp. nov. and Klebsiella variicola subsp. variicola subsp. nov. [Res Microbiol 170 (3) (2019) 165–170].. 2019, 170(6–7):300.
    pubmed: 30817987
  13. Wyres KL, Lam MMC, Holt KE. Population genomics of Klebsiella pneumoniae.. Nat Rev Microbiol 2020;18(6):344–59.
    pubmed: 32055025
  14. . Antimicrobial resistance. global report on surveillance. .
  15. Ko WC, Paterson DL, Sagnimeni AJ, Hansen DS, Von Gottberg A, Mohapatra S, Casellas JM, Goossens H, Mulazimoglu L, Trenholme G. Community-acquired Klebsiella pneumoniae bacteremia: global differences in clinical patterns.. Emerg Infect Dis 2002;8(2):160–6.
    pmc: PMC2732457pubmed: 11897067
  16. . Antimicrobial resistance. .
  17. Garza-Ramos U, Silva-Sánchez J, Catalán-Nájera J, Barrios H, Rodríguez-Medina N, Garza-González E, Cevallos MA, Lozano L. Draft genome sequence of a hypermucoviscous Extended-Spectrum-β-Lactamase-Producing Klebsiella quasipneumoniae subsp. Similipneumoniae clinical isolate. Genome Announc 2016, 4(4).
    pmc: PMC4939778pubmed: 27389261
  18. Rodríguez-Medina N, Barrios-Camacho H, Duran-Bedolla J, Garza-Ramos U. Klebsiella variicola: an emerging pathogen in humans. Emerg Microbes Infect 2019;8(1):973–88.
    pmc: PMC6609320pubmed: 31259664
  19. Giannattasio-Ferraz S, Ene A, Johnson G, Maskeri L, Oliveira AP, Banerjee S, Barbosa-Stancioli EF, Putonti C. Multidrug-Resistant Klebsiella variicola isolated in the urine of healthy bovine heifers, a potential risk as an emerging human pathogen. Appl Environ Microbiol 2022;88(9):e0004422.
    pmc: PMC9088279pubmed: 35416681
  20. Lee D, Oh JY, Sum S, Park HM. Prevalence and antimicrobial resistance of Klebsiella species isolated from clinically ill companion animals. J Vet Sci 2021;22(2):e17.
    pmc: PMC8007443pubmed: 33774933
  21. Aslam B, Chaudhry TH, Arshad MI, Muzammil S, Siddique AB, Yasmeen N, Khurshid M, Amir A, Salman M, Rasool MH. Distribution and genetic diversity of multi-drug-resistant Klebsiella pneumoniae at the human-animal-environment interface in Pakistan. Front Microbiol 2022;13:898248.
    pmc: PMC9486001pubmed: 36147844
  22. Ghenea AE, Cioboată R, Drocaş AI, Țieranu EN, Vasile CM, Moroşanu A, Țieranu CG, Salan AI, Popescu M, Turculeanu A. Prevalence and antimicrobial resistance of Klebsiella strains isolated from a County hospital in Romania. Antibiot (Basel) 2021, 10(7).
    pmc: PMC8300768pubmed: 34356789
  23. Butaye P, Stegger M, Moodley A, Damborg P, Williams A, Halliday-Simmonds I, Guardabassi L. One health genomic study of human and animal Klebsiella pneumoniae isolated at diagnostic laboratories on a small Caribbean Island. Antibiot (Basel) 2021, 11(1).
    pmc: PMC8772961pubmed: 35052919
  24. Castañeda-Barba S, Top EM, Stalder T. Plasmids, a molecular cornerstone of antimicrobial resistance in the one health era. Nat Rev Microbiol 2024;22(1):18–32.
    pmc: PMC12440250pubmed: 37430173
  25. Davis GS, Price LB. Recent research examining links among Klebsiella pneumoniae from food, food animals, and human extraintestinal infections. Curr Environ Health Rep 2016;3(2):128–35.
    pubmed: 27022987
  26. Podder MP, Rogers L, Daley PK, Keefe GP, Whitney HG, Tahlan K. Klebsiella species associated with bovine mastitis in Newfoundland. PLoS ONE 2014;9(9):e106518.
    pmc: PMC4152263pubmed: 25180510
  27. Cheng J, Zhang J, Han B, Barkema HW, Cobo ER, Kastelic JP, Zhou M, Shi Y, Wang J, Yang R. Klebsiella pneumoniae isolated from bovine mastitis is cytopathogenic for bovine mammary epithelial cells. J Dairy Sci 2020;103(4):3493–504.
    pubmed: 32037181
  28. Kikuchi N, Iguchi I, Hiramune T. Capsule types of Klebsiella pneumoniae isolated from the genital tract of mares with metritis, extra-genital sites of healthy mares and the genital tract of stallions. Vet Microbiol 1987;15(3):219–28.
    pubmed: 3324458
  29. Fecteau G, Van Metre DC, Paré J, Smith BP, Higgins R, Holmberg CA, Jang S, Guterbock W. Bacteriological culture of blood from critically ill neonatal calves. Can Vet J 1997;38(2):95–100.
    pmc: PMC1576528pubmed: 9028592
  30. Marques C, Menezes J, Belas A, Aboim C, Cavaco-Silva P, Trigueiro G, Telo Gama L, Pomba C. Klebsiella pneumoniae causing urinary tract infections in companion animals and humans: population structure, antimicrobial resistance and virulence genes. J Antimicrob Chemother 2019;74(3):594–602.
    pubmed: 30535393
  31. Araújo D, Castro J, Matos F, Oliveira R, Ramos C, Almeida C, Silva S. Exploring the prevalence and antibiotic resistance profile of Klebsiella pneumoniae and Klebsiella Oxytoca isolated from clinically ill companion animals from North of Portugal. Res Vet Sci 2023;159:183–8.
    pubmed: 37148737
  32. Harada K, Shimizu T, Mukai Y, Kuwajima K, Sato T, Usui M, Tamura Y, Kimura Y, Miyamoto T, Tsuyuki Y. Phenotypic and molecular characterization of antimicrobial resistance in Klebsiella spp. Isolates from companion animals in Japan: clonal dissemination of Multidrug-Resistant Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae. Front Microbiol 2016;7:1021.
    pmc: PMC4925667pubmed: 27446056
  33. Poirel L, Nordmann P, Ducroz S, Boulouis HJ, Arné P, Millemann Y. Extended-spectrum β-lactamase CTX-M-15-producing Klebsiella pneumoniae of sequence type ST274 in companion animals. Antimicrob Agents Chemother 2013;57(5):2372–5.
    pmc: PMC3632922pubmed: 23422912
  34. Donati V, Feltrin F, Hendriksen RS, Svendsen CA, Cordaro G, García-Fernández A, Lorenzetti S, Lorenzetti R, Battisti A, Franco A. Extended-spectrum-beta-lactamases, AmpC beta-lactamases and plasmid mediated quinolone resistance in Klebsiella spp. From companion animals in Italy. PLoS ONE 2014;9(3):e90564.
    pmc: PMC3942433pubmed: 24595207
  35. Podschun R, Ullmann U. Klebsiella spp. As nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors. Clin Microbiol Rev 1998;11(4):589–603.
    pmc: PMC88898pubmed: 9767057
  36. Hansen DS, Aucken HM, Abiola T, Podschun R. Recommended test panel for differentiation of Klebsiella species on the basis of a trilateral interlaboratory evaluation of 18 biochemical tests. J Clin Microbiol 2004;42(8):3665–9.
    pmc: PMC497635pubmed: 15297514
  37. Hansen DS, Gottschau A, Kolmos HJ. Epidemiology of Klebsiella bacteraemia: a case control study using Escherichia coli bacteraemia as control. J Hosp Infect 1998;38(2):119–32.
    pubmed: 9522290
  38. Watanakunakorn C, Jura J. Klebsiella bacteremia: a review of 196 episodes during a decade (1980–1989). Scand J Infect Dis 1991;23(4):399–405.
    pubmed: 1957125
  39. Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA, Dance D, Jenney A, Connor TR, Hsu LY, Severin J. Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proc Natl Acad Sci U S A 2015;112(27):E3574–3581.
    pmc: PMC4500264pubmed: 26100894
  40. Feng Y, Lu Y, Yao Z, Zong Z. Carbapenem-Resistant hypervirulent Klebsiella pneumoniae of sequence type 36. Antimicrob Agents Chemother 2018, 62(7).
    pmc: PMC6021629pubmed: 29712659
  41. Dong N, Yang X, Chan EW, Zhang R, Chen S. Klebsiella species: taxonomy, hypervirulence and multidrug resistance. EBioMedicine 2022;79:103998.
    pmc: PMC9010751pubmed: 35405387
  42. Mukherjee S, Bhadury P, Mitra S, Naha S, Saha B, Dutta S, Basu S. Hypervirulent Klebsiella pneumoniae causing neonatal bloodstream infections: emergence of NDM-1-Producing hypervirulent ST11-K2 and ST15-K54 strains possessing pLVPK-Associated markers. Microbiol Spectr 2023;11(2):e0412122.
    pmc: PMC10101084pubmed: 36752639
  43. Hala S, Malaikah M, Huang J, Bahitham W, Fallatah O, Zakri S, Antony CP, Alshehri M, Ghazzali RN, Ben-Rached F. The emergence of highly resistant and hypervirulent Klebsiella pneumoniae CC14 clone in a tertiary hospital over 8 years. Genome Med 2024;16(1):58.
    pmc: PMC11025284pubmed: 38637822
  44. Shen Z, Gao Q, Qin J, Liu Y, Li M. Emergence of an NDM-5-Producing hypervirulent Klebsiella pneumoniae sequence type 35 strain with chromosomal integration of an integrative and conjugative element, ICEKp1. Antimicrob Agents Chemother 2019, 64(1).
    pmc: PMC7187603pubmed: 31611359
  45. Qi Y, Wei Z, Ji S, Du X, Shen P, Yu Y. ST11, the dominant clone of KPC-producing Klebsiella pneumoniae in China. J Antimicrob Chemother 2011;66(2):307–12.
    pubmed: 21131324
  46. Gu D, Dong N, Zheng Z, Lin D, Huang M, Wang L, Chan EW, Shu L, Yu J, Zhang R. A fatal outbreak of ST11 carbapenem-resistant hypervirulent Klebsiella pneumoniae in a Chinese hospital: a molecular epidemiological study. Lancet Infect Dis 2018;18(1):37–46.
    pubmed: 28864030
  47. Wohlwend N, Endimiani A, Francey T, Perreten V. Third-generation-cephalosporin-resistant Klebsiella pneumoniae isolates from humans and companion animals in Switzerland: spread of a DHA-producing sequence type 11 clone in a veterinary setting. Antimicrob Agents Chemother 2015;59(5):2949–55.
    pmc: PMC4394820pubmed: 25733505
  48. Li Y, Kumar S, Zhang L, Wu H, Wu H. Characteristics of antibiotic resistance mechanisms and genes of Klebsiella pneumoniae. Open Med (Wars) 2023;18(1):20230707.
    pmc: PMC10183727pubmed: 37197355
  49. Yuan J, Xu X, Guo Q, Zhao X, Ye X, Guo Y, Wang M. Prevalence of the OqxAB gene complex in Klebsiella pneumoniae and Escherichia coli clinical isolates. J Antimicrob Chemother 2012;67(7):1655–9.
    pubmed: 22438434
  50. Yang F, Deng B, Liao W, Wang P, Chen P, Wei J. High rate of multiresistant Klebsiella pneumoniae from human and animal origin. Infect Drug Resist 2019;12:2729–37.
    pmc: PMC6731983pubmed: 31564923
  51. Zhang Z, Zhang L, Dai H, Zhang H, Song Y, An Q, Wang J, Xia Z. Multidrug-Resistant Klebsiella pneumoniae complex from clinical dogs and cats in China: molecular characteristics, phylogroups, and Hypervirulence-Associated determinants. Front Vet Sci 2022;9:816415.
    pmc: PMC8960377pubmed: 35359688
  52. Zhang Z, Lei L, Zhang H, Dai H, Song Y, Li L, Wang Y, Xia Z. Molecular investigation of Klebsiella pneumoniae from clinical companion animals in Beijing, China, 2017–2019. Pathogens 2021, 10(3).
    pmc: PMC7997213pubmed: 33673656
  53. Navon-Venezia S, Kondratyeva K, Carattoli A. Klebsiella pneumoniae: a major worldwide source and shuttle for antibiotic resistance. FEMS Microbiol Rev 2017;41(3):252–75.
    pubmed: 28521338
  54. Ruiz J. Mechanisms of resistance to quinolones: target alterations, decreased accumulation and DNA gyrase protection. J Antimicrob Chemother 2003;51(5):1109–17.
    pubmed: 12697644
  55. El-Sayed Ahmed MAE, Zhong LL, Shen C, Yang Y, Doi Y, Tian GB. Colistin and its role in the era of antibiotic resistance: an extended review (2000–2019). Emerg Microbes Infect 2020;9(1):868–85.
    pmc: PMC7241451pubmed: 32284036
  56. Mondal AH, Khare K, Saxena P, Debnath P, Mukhopadhyay K, Yadav D. A review on colistin resistance: an antibiotic of last resort. Microorganisms 2024, 12(4).
    pmc: PMC11051878pubmed: 38674716
  57. Liu YY, Wang Y, Walsh TR, Yi LX, Zhang R, Spencer J, Doi Y, Tian G, Dong B, Huang X. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a Microbiological and molecular biological study. Lancet Infect Dis 2016;16(2):161–8.
    pubmed: 26603172
  58. Wang X, Wang Y, Zhou Y, Li J, Yin W, Wang S, Zhang S, Shen J, Shen Z, Wang Y. Emergence of a novel mobile colistin resistance gene, mcr-8, in NDM-producing Klebsiella pneumoniae. Emerg Microbes Infect 2018;7(1):122.
    pmc: PMC6030107pubmed: 29970891
  59. Eltai NO, Kelly B, Al-Mana HA, Ibrahim EB, Yassine HM, Al Thani A, Al Maslmani M, Lammens C, Xavier BB, Malhotra-Kumar S. Identification of mcr-8 in Clinical Isolates From Qatar and Evaluation of Their Antimicrobial Profiles. 2020, 11:1954.
    pmc: PMC7476323pubmed: 32983006
  60. Salloum T, Panossian B, Bitar I, Hrabak J, Araj GF, Tokajian S. First report of plasmid-mediated colistin resistance mcr-8.1 gene from a clinical Klebsiella pneumoniae isolate from Lebanon. Antimicrob Resist Infect Control 2020;9(1):94.
    pmc: PMC7318401pubmed: 32586402
  61. Yang C, Han J, Berglund B, Zou H, Gu C, Zhao L, Meng C, Zhang H, Ma X, Li X. Dissemination of Bla (NDM-5) and mcr-8.1 in carbapenem-resistant Klebsiella pneumoniae and Klebsiella quasipneumoniae in an animal breeding area in Eastern China. Front Microbiol 2022;13:1030490.
    pmc: PMC9627307pubmed: 36338046
  62. He T, Wang Y, Sun L, Pang M, Zhang L, Wang R. Occurrence and characterization of blaNDM-5-positive Klebsiella pneumoniae isolates from dairy cows in Jiangsu, China. J Antimicrob Chemother 2017;72(1):90–4.
    pubmed: 27621177
  63. Acman M, Wang R, van Dorp L, Shaw LP, Wang Q, Luhmann N, Yin Y, Sun S, Chen H, Wang H. Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene bla(NDM). Nat Commun 2022;13(1):1131.
    pmc: PMC8894482pubmed: 35241674
  64. GenomeTrakr, Network. https://www.fda.gov/food/whole-genome-sequencing-wgs-program/genometrakr-network
  65. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 2014;30(15):2114–20.
    pmc: PMC4103590pubmed: 24695404
  66. Seemann T. MLST: scan contig files against PubMLST typing schemes. Retrieved Github in; 2016.
  67. Souvorov A, Agarwala R, Lipman DJ. SKESA: strategic k-mer extension for scrupulous assemblies. Genome Biol 2018;19(1):153.
    pmc: PMC6172800pubmed: 30286803
  68. Jolley KA, Maiden MC. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 2010;11:595.
    pmc: PMC3004885pubmed: 21143983
  69. Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 2014;15(3):R46.
    pmc: PMC4053813pubmed: 24580807
  70. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018;9(1):5114.
    pmc: PMC6269478pubmed: 30504855
  71. Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J, Haft DH, Hoffmann M, Pettengill JB, Prasad AB, Tillman GE. AMRFinderPlus and the reference gene catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep 2021;11(1):12728.
    pmc: PMC8208984pubmed: 34135355
  72. Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, Villa L, Møller Aarestrup F, Hasman H. In Silico detection and typing of plasmids using plasmidfinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 2014;58(7):3895–903.
    pmc: PMC4068535pubmed: 24777092
  73. Bharat A, Petkau A, Avery BP, Chen JC, Folster JP, Carson CA, Kearney A, Nadon C, Mabon P, Thiessen J. Correlation between phenotypic and in Silico detection of antimicrobial resistance in Salmonella enterica in Canada using Staramr. Microorganisms 2022, 10(2).
    pmc: PMC8875511pubmed: 35208747
  74. Gardner SN, Slezak T, Hall BG. kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome. Bioinformatics 2015;31(17):2877–8.
    pubmed: 25913206
  75. Tamura K, Stecher G, Kumar S. MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol 2021;38(7):3022–7.
    pmc: PMC8233496pubmed: 33892491
  76. Letunic I, Bork P. Interactive tree of life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 2021;49(W1):W293–6.
    pmc: PMC8265157pubmed: 33885785

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