Emergence of Stutzerimonas nitrititolerans co-carrying carbapenem and tigecycline resistance genes from geese feces in China

Arifiani Media; Muhammad Shoaib; Wenhui Zhang; Tianyang Hao; Asim Munir; Patrick Butaye; Kai Peng; Zhiqiang Wang; Ruichao Li

doi:10.1016/j.emcon.2026.100699

Emergence of Stutzerimonas nitrititolerans co-carrying carbapenem and tigecycline resistance genes from geese feces in China

Arifiani Media
, Muhammad Shoaib
, Wenhui Zhang
, Tianyang Hao
, Asim Munir
, Patrick Butaye
, Kai Peng
, Zhiqiang Wang^*
, Ruichao Li^*

^*Corresponding author for this work

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

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Abstract

The evolutionary trajectories of antimicrobial resistance in environmental bacteria remain poorly understood. Here, we investigated the chromosomal architecture and evolutionary context of meropenem and tigecycline resistance in Stutzerimonas nitrititolerans from geese feces in Yangzhou, China. From 60 samples, we isolated five multidrug-resistant strains exhibiting meropenem resistance (MICs 8-32 μg/mL) and reduced tigecycline susceptibility (MICs 1-4 μg/mL). Hybrid sequencing revealed chromosomal assemblies of 4.17-4.36 Mb with no plasmids detection and identified two resistance hotspots, including a mobile element-rich island carrying tmexC2D2-toprJ2 flanked by Tn3-family transposases, class 1 integrons, and phage integrases; and a conserved locus containing bla_PST-2 accumulating insertion sequences (IS66, ISPpu14) and recombination-related gene (xerC). Comparative genomics against 99 public genomes revealed complete tmexCD-toprJ clusters are rare (9.6%, 10/104), with co-occurrence alongside bla_PST in only 8.7% of strains (9/104), five being our geese isolates. Core-genome phylogeny and pairwise SNP distances (233-23,043 SNPs) indicated that, except for the closely related F61-1/F61-3 isolates, the other geese isolates were genetically heterogeneous, suggesting that similar resistance-associated architectures occurred across distinct genomic backgrounds rather than through expansion of a single clone. These findings provide a farm-level genomic snapshot of livestock-associated S. nitrititolerans carrying chromosomal resistance-associated determinants with mobile genetic element signatures. The co-occurrence of tmexC2D2-toprJ2 and bla_PST-2, despite the rarity of complete tmexCD-toprJ clusters across the available species dataset, supports further surveillance of S. nitrititolerans in livestock-associated environments within a One Health framework. © 2026 The Authors. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co. Ltd. This is an open access article under the CC BY-NC-ND license. http://creativecommons.org/licenses/by-nc-nd/4.0/

Original language	English
Article number	100699
Journal	Emerging Contaminants
Volume	12
Issue number	3
Online published	7 Jun 2026
DOIs	https://doi.org/10.1016/j.emcon.2026.100699
Publication status	Published - Sept 2026

Funding

This work was supported by the National Key Research and Development Program of China (2025ZD01901203), the Outstanding Youth Foundation of Jiangsu Province of China (BK20231524), the 111 Project D18007, the National Key Laboratory of Veterinary Public Health and Safety Open Project Fund (2024SKLVPHS04) and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).

Research Keywords

Antimicrobial resistance
blaPST
Geese feces
One health
Stutzerimonas nitrititolerans
tmexCD-toprJ

Publisher's Copyright Statement

This full text is made available under CC-BY-NC-ND 4.0. https://creativecommons.org/licenses/by-nc-nd/4.0/

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title = "Emergence of Stutzerimonas nitrititolerans co-carrying carbapenem and tigecycline resistance genes from geese feces in China",

abstract = "The evolutionary trajectories of antimicrobial resistance in environmental bacteria remain poorly understood. Here, we investigated the chromosomal architecture and evolutionary context of meropenem and tigecycline resistance in Stutzerimonas nitrititolerans from geese feces in Yangzhou, China. From 60 samples, we isolated five multidrug-resistant strains exhibiting meropenem resistance (MICs 8-32 μg/mL) and reduced tigecycline susceptibility (MICs 1-4 μg/mL). Hybrid sequencing revealed chromosomal assemblies of 4.17-4.36 Mb with no plasmids detection and identified two resistance hotspots, including a mobile element-rich island carrying tmexC2D2-toprJ2 flanked by Tn3-family transposases, class 1 integrons, and phage integrases; and a conserved locus containing blaPST-2 accumulating insertion sequences (IS66, ISPpu14) and recombination-related gene (xerC). Comparative genomics against 99 public genomes revealed complete tmexCD-toprJ clusters are rare (9.6\%, 10/104), with co-occurrence alongside blaPST in only 8.7\% of strains (9/104), five being our geese isolates. Core-genome phylogeny and pairwise SNP distances (233-23,043 SNPs) indicated that, except for the closely related F61-1/F61-3 isolates, the other geese isolates were genetically heterogeneous, suggesting that similar resistance-associated architectures occurred across distinct genomic backgrounds rather than through expansion of a single clone. These findings provide a farm-level genomic snapshot of livestock-associated S. nitrititolerans carrying chromosomal resistance-associated determinants with mobile genetic element signatures. The co-occurrence of tmexC2D2-toprJ2 and blaPST-2, despite the rarity of complete tmexCD-toprJ clusters across the available species dataset, supports further surveillance of S. nitrititolerans in livestock-associated environments within a One Health framework. {\textcopyright} 2026 The Authors. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co. Ltd. This is an open access article under the CC BY-NC-ND license. http://creativecommons.org/licenses/by-nc-nd/4.0/",

keywords = "Antimicrobial resistance, blaPST, Geese feces, One health, Stutzerimonas nitrititolerans, tmexCD-toprJ",

author = "Arifiani Media and Muhammad Shoaib and Wenhui Zhang and Tianyang Hao and Asim Munir and Patrick Butaye and Kai Peng and Zhiqiang Wang and Ruichao Li",

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T1 - Emergence of Stutzerimonas nitrititolerans co-carrying carbapenem and tigecycline resistance genes from geese feces in China

AU - Media, Arifiani

AU - Shoaib, Muhammad

AU - Zhang, Wenhui

AU - Hao, Tianyang

AU - Munir, Asim

AU - Butaye, Patrick

AU - Peng, Kai

AU - Wang, Zhiqiang

AU - Li, Ruichao

PY - 2026/9

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N2 - The evolutionary trajectories of antimicrobial resistance in environmental bacteria remain poorly understood. Here, we investigated the chromosomal architecture and evolutionary context of meropenem and tigecycline resistance in Stutzerimonas nitrititolerans from geese feces in Yangzhou, China. From 60 samples, we isolated five multidrug-resistant strains exhibiting meropenem resistance (MICs 8-32 μg/mL) and reduced tigecycline susceptibility (MICs 1-4 μg/mL). Hybrid sequencing revealed chromosomal assemblies of 4.17-4.36 Mb with no plasmids detection and identified two resistance hotspots, including a mobile element-rich island carrying tmexC2D2-toprJ2 flanked by Tn3-family transposases, class 1 integrons, and phage integrases; and a conserved locus containing blaPST-2 accumulating insertion sequences (IS66, ISPpu14) and recombination-related gene (xerC). Comparative genomics against 99 public genomes revealed complete tmexCD-toprJ clusters are rare (9.6%, 10/104), with co-occurrence alongside blaPST in only 8.7% of strains (9/104), five being our geese isolates. Core-genome phylogeny and pairwise SNP distances (233-23,043 SNPs) indicated that, except for the closely related F61-1/F61-3 isolates, the other geese isolates were genetically heterogeneous, suggesting that similar resistance-associated architectures occurred across distinct genomic backgrounds rather than through expansion of a single clone. These findings provide a farm-level genomic snapshot of livestock-associated S. nitrititolerans carrying chromosomal resistance-associated determinants with mobile genetic element signatures. The co-occurrence of tmexC2D2-toprJ2 and blaPST-2, despite the rarity of complete tmexCD-toprJ clusters across the available species dataset, supports further surveillance of S. nitrititolerans in livestock-associated environments within a One Health framework. © 2026 The Authors. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co. Ltd. This is an open access article under the CC BY-NC-ND license. http://creativecommons.org/licenses/by-nc-nd/4.0/

AB - The evolutionary trajectories of antimicrobial resistance in environmental bacteria remain poorly understood. Here, we investigated the chromosomal architecture and evolutionary context of meropenem and tigecycline resistance in Stutzerimonas nitrititolerans from geese feces in Yangzhou, China. From 60 samples, we isolated five multidrug-resistant strains exhibiting meropenem resistance (MICs 8-32 μg/mL) and reduced tigecycline susceptibility (MICs 1-4 μg/mL). Hybrid sequencing revealed chromosomal assemblies of 4.17-4.36 Mb with no plasmids detection and identified two resistance hotspots, including a mobile element-rich island carrying tmexC2D2-toprJ2 flanked by Tn3-family transposases, class 1 integrons, and phage integrases; and a conserved locus containing blaPST-2 accumulating insertion sequences (IS66, ISPpu14) and recombination-related gene (xerC). Comparative genomics against 99 public genomes revealed complete tmexCD-toprJ clusters are rare (9.6%, 10/104), with co-occurrence alongside blaPST in only 8.7% of strains (9/104), five being our geese isolates. Core-genome phylogeny and pairwise SNP distances (233-23,043 SNPs) indicated that, except for the closely related F61-1/F61-3 isolates, the other geese isolates were genetically heterogeneous, suggesting that similar resistance-associated architectures occurred across distinct genomic backgrounds rather than through expansion of a single clone. These findings provide a farm-level genomic snapshot of livestock-associated S. nitrititolerans carrying chromosomal resistance-associated determinants with mobile genetic element signatures. The co-occurrence of tmexC2D2-toprJ2 and blaPST-2, despite the rarity of complete tmexCD-toprJ clusters across the available species dataset, supports further surveillance of S. nitrititolerans in livestock-associated environments within a One Health framework. © 2026 The Authors. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co. Ltd. This is an open access article under the CC BY-NC-ND license. http://creativecommons.org/licenses/by-nc-nd/4.0/

KW - Antimicrobial resistance

KW - blaPST

KW - Geese feces

KW - One health

KW - Stutzerimonas nitrititolerans

KW - tmexCD-toprJ

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UR - https://www.scopus.com/pages/publications/105043629458#tab=impact

U2 - 10.1016/j.emcon.2026.100699

DO - 10.1016/j.emcon.2026.100699

M3 - RGC 21 - Publication in refereed journal

SN - 2405-6650

VL - 12

JO - Emerging Contaminants

JF - Emerging Contaminants

IS - 3

M1 - 100699

ER -

Emergence of Stutzerimonas nitrititolerans co-carrying carbapenem and tigecycline resistance genes from geese feces in China

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