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Background <p>Mobilized colistin resistance (<i>mcr</i>) gene has emerged as a major driver of colistin resistance. Therefore, this study aimed to determine the distribution of <i>mcr</i>-variants and <i>mcr</i>-carrying genomes deposited in the NCBI database by sample collection periods and across continents, countries, genera, species, and ecosystems.</p> Methods <p>In this database mining study, the keyword “<i>mcr</i>” was used to identify all <i>mcr</i>-carrying genomes deposited in the NCBI Pathogen Detection database until June 07, 2025, 12h15 GMT. A purely descriptive approach was used in this study, and percentages were calculated by dividing the number of an event by the total number of events (percentage = n/Nx100).</p> Results <p>Of the 2422739 whole genomes registered in the NCBI database, 18785 (0.78%) carried complete <i>mcr</i> variant sequences. Seventy-seven <i>mcr</i> subvariants were detected, including mostly <i>mcr-1.1</i> (9431/18785; 50%), and <i>mcr-9.1</i> (5971/18785; 32%). <i>Mcr</i>-<i>9.1</i> was the most frequently detected subvariant in several genera, including <i>Serratia</i> spp. (17/17; 100%), <i>Cronobacter</i> spp. (155/160; 97%), and <i>Pluralibacter</i> spp. (19/20; 95%), whereas <i>mcr</i>-<i>1.1</i> was the most commonly detected subvariant in <i>Escherichia</i> and <i>Shigella</i> spp. (8235/9678; 85%). Regarding geographical distribution, <i>mcr-1.1</i> was the most observed subvariant in Asia (6759/9033; 75%) and Europe (1886/4680; 40%), whereas <i>mcr-9.1</i> was the most identified in America (2982/4017; 74%) and Oceania (546/771; 71%). In Africa, <i>mcr-10.1</i> (52/160; 33%), and <i>mcr-1.1</i> (50/160; 31%) were the most frequent subvariants. <i>Mcr</i>-carrying genomes deposited in the NCBI database were distributed across ecosystems, including humans (<i>n</i> = 8185), animals (<i>n</i> = 4521), the environment (<i>n</i> = 468), and food (<i>n</i> = 48). The sample collection years for <i>mcr</i>-carrying bacteria ranged from 1953 to 2025, and the distribution of <i>mcr</i>-carrying genomes was as follows: 1953–1990 (<i>n</i> = 49), 1991–1999 (<i>n</i> = 47), 2000–2009 (<i>n</i> = 704), 2010–2019 (<i>n</i> = 12810), and 2020–2025 (<i>n</i> = 4297). Another key finding was that 705 of the 18785 <i>mcr</i>-carrying genomes deposited in the NCBI database (3.8%) harbored multiple <i>mcr</i> genes, including 693 and 12 genomes co-carrying two and three <i>mcr</i> genes, respectively.</p> Conclusion <p><i>Mcr</i>-carrying bacteria represent a significant One Health concern because of their major role in colistin resistance and potential for global dissemination. Key actions, such as global surveillance, One Health monitoring, and appropriate stewardship, should be taken to preserve the efficacy of colistin for decades.</p>

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Global distribution of mcr-carrying bacteria: an analysis of genomic data

  • 期刊论文

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  • 发表日期：

    2026年5月1日

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  • Komla Mawunyo Dossouvi,
  • Fábio Parra Sellera,
  • Ephraim Ehidiamen Ibadin,
  • Tchilabalo Bouyo,
  • David Kanzin,
  • Bissoume Sambe Ba,
  • Sika Dossim,
  • Amr El Kelish,
  • Makhtar Camara

摘要

Background

Mobilized colistin resistance (mcr) gene has emerged as a major driver of colistin resistance. Therefore, this study aimed to determine the distribution of mcr-variants and mcr-carrying genomes deposited in the NCBI database by sample collection periods and across continents, countries, genera, species, and ecosystems.

Methods

In this database mining study, the keyword “mcr” was used to identify all mcr-carrying genomes deposited in the NCBI Pathogen Detection database until June 07, 2025, 12h15 GMT. A purely descriptive approach was used in this study, and percentages were calculated by dividing the number of an event by the total number of events (percentage = n/Nx100).

Results

Of the 2422739 whole genomes registered in the NCBI database, 18785 (0.78%) carried complete mcr variant sequences. Seventy-seven mcr subvariants were detected, including mostly mcr-1.1 (9431/18785; 50%), and mcr-9.1 (5971/18785; 32%). Mcr-9.1 was the most frequently detected subvariant in several genera, including Serratia spp. (17/17; 100%), Cronobacter spp. (155/160; 97%), and Pluralibacter spp. (19/20; 95%), whereas mcr-1.1 was the most commonly detected subvariant in Escherichia and Shigella spp. (8235/9678; 85%). Regarding geographical distribution, mcr-1.1 was the most observed subvariant in Asia (6759/9033; 75%) and Europe (1886/4680; 40%), whereas mcr-9.1 was the most identified in America (2982/4017; 74%) and Oceania (546/771; 71%). In Africa, mcr-10.1 (52/160; 33%), and mcr-1.1 (50/160; 31%) were the most frequent subvariants. Mcr-carrying genomes deposited in the NCBI database were distributed across ecosystems, including humans (n = 8185), animals (n = 4521), the environment (n = 468), and food (n = 48). The sample collection years for mcr-carrying bacteria ranged from 1953 to 2025, and the distribution of mcr-carrying genomes was as follows: 1953–1990 (n = 49), 1991–1999 (n = 47), 2000–2009 (n = 704), 2010–2019 (n = 12810), and 2020–2025 (n = 4297). Another key finding was that 705 of the 18785 mcr-carrying genomes deposited in the NCBI database (3.8%) harbored multiple mcr genes, including 693 and 12 genomes co-carrying two and three mcr genes, respectively.

Conclusion

Mcr-carrying bacteria represent a significant One Health concern because of their major role in colistin resistance and potential for global dissemination. Key actions, such as global surveillance, One Health monitoring, and appropriate stewardship, should be taken to preserve the efficacy of colistin for decades.