Skip to main content

Prevalence and dissemination of mcr-9.1-producing non-typhoidal Salmonella strains from diarrhea patients throughout China during 2010–2020


The emergence of mobilized colistin resistance (mcr) genes has raised significant concerns as they pose a public health issue. The prevalence of mcr genes, particularly the newly discovered mcr-9 gene, in non-typhoidal Salmonella (NTS) isolates remains unclear. We characterized mcr-9.1-producing NTS isolates from China. Among 7,106 NTS isolates from diarrhea cases in 32 provinces during 2010–2020, 11 mcr-9.1-producing isolates were identified and were all not resistant to colistin. Five isolates belonged to Salmonella Thompson and sequence type (ST) 26, two belonged to Salmonella Typhimurium and ST34, two belonged to Salmonella Typhimurium and ST36, and two belonged to Salmonella 1,4,[5],12:i:- and ST34. Plasmids harboring mcr-9.1 tended to possess the IncHI2 backbone and were ~ 300 kb long. All mcr-9.1 genes shared the same flanking sequence, rcnR-rcnA-pcoS-IS903-mcr-9.1-wbuC. According to the NCBI data, we found that NTS serves as the primary host of mcr-9.1, although the prevalence of specific serotypes differed between domestic and international settings. Notably, most data came from developed countries, such as the USA. mcr-9.1 tended to be transferred as a gene cassette or to be mobilized by a conjugational plasmid in multiple bacteria across humans, animals, and the environment. Furthermore, mcr-9.1 frequently co-existed and was co-transferred with various genes encoding resistance to first-line drugs, reducing the effectiveness of available therapeutic options. In summary, although mcr-9 does not mediate colistin resistance, it can silently spread with some genes encoding resistance to first-line drugs, and therefore warrants research attention.


In the context of antimicrobial resistance gene (ARG) dissemination, the concept of “One Health” which underlines the interconnectivity of human, animal, and ecosystem health, becomes paramount. This concept recognizes the crucial role that multidrug-resistant (MDR) bacteria and ARGs play within this interconnected framework. Non-typhoidal Salmonella (NTS) are gram-negative pathogenic bacteria of the family Enterobacteriaceae, genus Salmonella, species Salmonella enterica and Salmonella enterica subsp. enterica. According to the surface structures expressed on the bacterial surface, including lipopolysaccharide, the flagella, and capsular polysaccharides, Salmonella enterica subsp. enterica has been classified into more than 2,600 serovars [1]. Serovars Typhi and Paratyphi, known as typhoidal serovars, can only infect humans and cause severe systemic disease. Most NTS serovars, including Enteritidis, Typhimurium, 1,4,[5],12:i:-, and Thompson, have a broad host range and cause self-limiting gastroenteritis in humans and animals [2, 3].

The MDR phenotype in NTS was initially identified in the UK in the early 1980s in isolates demonstrating resistance to ampicillin, chloramphenicol, streptomycin, sulfonamides, and tetracycline. Subsequently, reports of resistance to fluoroquinolones (qnrB, 24.43%, 1,736/7,106) emerged shortly after their introduction. By the mid-1980s, it had become evident that NTS possessed resistance to extended-spectrum cephalosporins, typically mediated by extended-spectrum ß-lactamases (ESBLs) (blaCTX-M, 14.93%, 1,061/7,106) or AmpC-type beta-lactamases (blaCMY-2, 1.97%, 140/7,106) (unpublished data). In recent years, increasing numbers of reports have noted the emergence of extensively drug-resistant NTS isolates, with strains exhibiting MDR phenotypes [4]. These findings underscore the escalating global public health challenge of antimicrobial resistance.

ß-lactams (conferred by blaCTX-M, blaTEM gene, and so on [5]), aminoglycosides (conferred by the aac(6’)-Iaa gene), and fluoroquinolones (conferred by qnr, aac(6’)-Ib-cr, qepA [6], and oqxAB [7]) are frequently used to treat NTS infection in humans and animals [8]. However, the misuse and abuse of antibiotics have led to the development and spread of MDR NTS. The majority of NTS infections are associated with food-producing animals and contaminated vegetables, fruits, and other plant products [9]. The above ARGs co-exist on transferable plasmids and can be transmitted from animal-derived foods to humans [10, 11].

The first plasmid-mediated colistin resistance gene mcr-1 was identified in late 2015 [12]. In 2019, a new mcr gene, mcr-9.1, was identified in an MDR Salmonella Typhimurium strain isolated in 2010 from a patient’s stool sample in the USA [13]. Unlike mcr-1, mcr-9.1 seems to only reduce sensitivity to colistin, rather than conferring resistance to colistin. Therefore, it is conceivable that the mcr-9.1 gene may circulate silently. However, the clinical use of colistin may trigger high mcr-9.1 expression, resulting in resistance and accelerating its transmission and dissemination [14]. The mcr-9.1 gene was widely disseminated among Enterobacteriaceae strains isolated from human, animal, food, and environmental samples from 21 countries spanning six continents, including but not limited to South Africa [15], the USA [16], Brazil [17], South Korea [8], Italy [18], and China [19]. The sources of isolation have expanded from patients to healthy individuals, livestock, animal-derived foods, pets, and the environment [20]. Furthermore, bacterial hosts are no longer limited to NTS, but also include Escherichia coli, Enterobacter cloacae complex [21, 22], Morganella morganii, Enterobacter hormaechei [23], Cronobacter sakazakii [24], and Enterobacter kobei [20]. These findings underscore the wide dissemination and potential risks associated with mcr-9.1.

We investigated the prevalence and dissemination of mcr-9.1-producing NTS strains in Chinese hospitals over a decade to paint a comprehensive picture of the distribution and transmission of mcr-9.1 in China.


Identification and characterization of mcr-9.1-producing isolates

Among the 7,106 NTS isolates in this study, 11 isolates carried mcr-9.1, five of which were isolated in 2017, three in 2018, and one in 2015, 2016, and 2019, respectively. These isolates were collected from different provinces across China, including Sichuan, Jiangsu, Anhui, Henan, Jilin, Shandong, Guangdong, Zhejiang, Fujian, and Heilongjiang. Despite the diversity in isolation years and geographic locations, all 11 strains harbored the mcr-9.1 gene, indicating its widespread presence within NTS populations across China. To profile the resistance of the mcr-9.1-positive isolates in this study, Antimicrobial susceptibility test (AST) were conducted on the 11 isolates. All isolates (11/11, 100%) were resistant to ampicillin, cefotaxime, and ceftazidime, and 90.9% (10/11) were resistant to tetracycline. Several isolates were resistant to amikacin (18.2%, 2/11), ciprofloxacin (27.3%, 3/11), gentamicin (54.5%, 6/11), florfenicol (36.4%, 4/11), chloramphenicol (63.6%, 7/11) and aztreonam (18.2%, 2/11); however, all isolates were susceptible to colistin (MICs ≤ 1 \(\upmu\)g/ml) (Additional file 1). Molecular typing of these isolates showed a diverse distribution, with 5/11 belonging to Salmonella Thompson and sequence type (ST) 26, 2/11 being Salmonella Typhimurium with ST34, 2/11 being Salmonella Typhimurium with ST36, and 2/11 being Salmonella 1,4, [5],12:i:- with ST34. Further exploration into the associated ARGs revealed a range of 5 to 25 ARGs per isolate, with an average of 12.6 ARGs (Additional file 2). This suggests a significant level of antibiotic resistance within these strains.

Analysis of mcr-9.1-producing plasmids and the genetic environment of mcr-9.1 genes

We chose long and short read sequencing illustrated that the mcr-9.1 genes of eight isolates located in plasmids. Four out of eight were located on IncHI2A/IncHI2 plasmids, three on IncHI2A/IncHI2/IncQ1 plasmids, and one on IcHI2A/IncHI2/IncY plasmids. Notably, the latter two types of hybrid plasmids were identified as carriers of mcr-9.1 for the first time. Genetic environment analysis revealed that all mcr-9.1 genes in this study share a common flanking sequence, rcnR-rcnA-pcoS-IS903-mcr-9.1-wbuC, implying possible horizontal transfer of this resistance determinant.

To characterize mcr-9.1-encoding plasmids, we examined 142 mcr-9.1-positive plasmids, including 134 mcr-9.1-encoding plasmids downloaded from the RefSeq database on January 19, 2022 and the eight mcr-9.1-encoding plasmids obtained from hybrid assemblies in our study. Plasmid length was not related to the bacterial host species (Fig. 1A). Upon examining the relationship between the number of ARGs and incompatibility (Inc) groups, we found that the number of ARGs ranged between 7 and 17, and the number of Inc ranged between 0 and 3 (Fig. 1B). Additionally, mcr-9.1-encoding plasmids predominantly incorporated two Incs. The IncHI2/IncHI2A plasmid was the most widespread, accounting for 117 out of 142 instances. This information could be vital for future studies and strategies aiming at combating antibiotic resistance.

Fig. 1
figure 1

Plasmids harboring mcr-9.1 found in this study and the NCBI database. A Relationship between plasmid length and genus. B Relationship between the number of antimicrobial resistance genes and replicon types. C Clustering tree of 117 IncHI2/IncHI2A plasmids based on Mash distance

To further characterize the backbones and profiles of the 117 IncHI2/IncHI2A plasmids, a clustering tree based on Mash distance was constructed, and their bacterial hosts and lengths were analyzed. The results revealed a rich sequence diversity among the IncHI2/IncHI2A plasmids. Plasmid length varied quite significantly, from 50,622 bp to 477,340 bp, with an average of 298,141 bp. Enterobacter was the most common host (73 out of 117), followed by Salmonella (21 out of 117) (Fig. 1C). This distribution of bacterial hosts adds another layer of complexity to our understanding of these plasmids.

To outline the genetic environment of the mcr-9.1 gene and understand the mechanism of spread, we used the flanking sequence of mcr-9.1 in pZJ-S162 (upstream: 100,000 bp, downstream: ending) as a query sequence in the NCBI BLASTn tool. The most similar plasmid identified was p628. Using p628 as a reference sequence and the plasmids in our study as queries, we performed a series of alignments and visualized them using BLAST Ring Image Generator (BRIG) (Fig. 2) (Version 0.95). p628 exhibited a high degree of sequence identity with pHL-19S4. Interestingly, the gene cassette rcnR-rcnA-pcoS-IS903-mcr-9.1-wbuC was present in all plasmids in this study [20]. A conjugation transfer test confirmed that the backbone plasmid can indeed be transferred from Salmonella to recipient bacteria, also, the transformants were all not resistant to colistin (MICs ≤ 0.5 \(\upmu\)g/ml) (Additional file 3). This ability to transfer plasmids plays a crucial role in the spread of resistance genes.

Fig. 2
figure 2

Alignment of mcr-9.1-encoding plasmids in this study

Co-existence and co-transfer of mcr-9.1 with other resistance genes

The co-existence and co-transfer of mcr-9.1 with clinically relevant resistance genes such as ESBL [11] and PMQR genes, and occasionally, blaKPC, blaNDM-1 [25], and tmexCD2-toprJ2 [23], have been closely examined in previous studies. We systematically analyzed plasmids carrying mcr-9.1 in the NCBI database. By examining the correlation between the replicon type of the plasmid and the mcr-9.1 gene, we found that all plasmids carrying mcr-9.1 contain the IncHI2 type plasmid backbone. It has been reported that IncHI2 plasmids serve as the transmission vector for various antibiotic-resistance genes [26], including those encoding resistance against β-lactams, quinolones, and aminoglycosides. Further analysis of the correlations among resistance genes revealed that mcr-9.1 was the most strongly correlated with tetracycline resistance genes, such as tet(D), followed by quinolone (qnrA1), sulfonamide (sul1), trimethoprim (dfrA19), macrolide (mph(A)), ESBLs (blaTEM-1B, blaCTX-M, blaSHV-12), phenicol (catA2), and aminoglycoside (aac(6’)-IIc) (Fig. 3).

Fig. 3
figure 3

Coexistence of antimicrobial resistance genes (ARGs) and plasmid Inc-types. Red boxes and circles indicate the coexistence of ARGs, plasmid Inc-types, or ARGs and plasmid Inc-types. The coexistence of ARGs and plasmid Inc-types is summarized in the bottom left corner

Global prevalence and epidemiological traits of mcr-9.1-encoding assemblies

A total of 2,623 mcr-9.1-encoding assemblies were retrieved from the NCBI pathogen database as of September 18, 2022. Figure 4A shows the prevalence and distribution of these assemblies across countries. The USA accounted for most assemblies (1,382), followed by the UK with 304 assemblies, Australia with 277 assemblies, and China with 205 assemblies. Most assemblies were reported from economically developed regions.

Fig. 4
figure 4

Epidemic features of isolates harboring the mcr-9.1 gene. A Geographical distribution of isolates harboring mcr-9.1 in this study and the NCBI database. B Sankey diagram combining the isolating year, isolating country, genus of bacteria host, and sources of isolation. Numbers of isolates are indicated in white font

To analyze the isolation dates, geographical distribution, and bacterial hosts and origin of these hosts, a subset of 865 assemblies with unambiguous above four kinds of data was selected for further analysis. We observed that the number of assembly datasets increased over recent years, a trend likely associated with the advancements in whole-genome sequencing technology (Fig. 5). Of which, mcr-9.1 gene was prevalent across from 29 countries, the USA, the UK, and China were at the forefront of countries reporting the assemblies. Salmonella enterica has emerged as the primary bacterial host for mcr-9.1 genes, followed by Enterobacter, E. coli, Shigella, Citrobacter freundii, Cronobacter, Klebsiella pneumoniae, and Klebsiella oxytoca. Turkeys (348/865), humans (255/865), and chickens (120/865) were identified as the principal bacterial host sources, mcr-9.1 gene is also present in environment, swine, food, and other sources. (Fig. 4B).

Fig. 5
figure 5

A Line chart of the numbers of mcr-9.1-positive assemblies in the NCBI database over time (total: 865). B Top 10 serotypes of mcr-9.1-producing NTS in the NCBI database (total: 1,435)

To identify and analyze the dominant serotypes of mcr-9.1-producing NTS, the serotypes of the assemblies in the NCBI pathogen database were predicted. Serotypes Typhimurium and 1,4,[5],12:i:- (448/1,435), Saint Paul (258/1,435), and Heidelberg (191/1,435) were among the most prevalent globally. Among our isolates, we identified three predominant serotypes: Thompson (5/11), Typhimurium (4/11), and 1,4, [5],12:i:- (2/11). These serotypes are currently the most popular and dominant; hence, we speculate that these predominant NTS serotypes are likely to be the main bacterial hosts for mcr-9.1 [27].


The existence and spread of bacterial resistance pose a major public health threat in the twenty-first century. It makes common infections potentially more difficult to treat, leading to an increased risk of death. Additionally, developing new and effective antibiotics is expensive as well as time-consuming. The emergence of plasmid-mediated colistin resistance exacerbates this situation [28]. Colistin, which is used to treat MDR gram-negative bacterial infections, may lose its effectiveness due to the existence and spread of mcr genes [12]. NTS can infect food animals such as pigs and chickens, as well as humans, intercontinental spreading and proliferating among animals, humans, and the environment through foodborne transmission and contaminated water [29]. Although infection with NTS often results in self-limiting disease, such as diarrhea, in humans and the mortality rate is not high, it can cause severe disease, even death, in children or immune-compromised individuals [30]. While all risk factors alone constitute a significant public health threat, when combined, they can undoubtedly inflict severe damage to global health.

Multiple studies have shown that mcr-9.1 does not confer colistin resistance to bacterial strains, but rather reduces their sensitivity to colistin; however, the silent circulation of mcr-9.1 in the environment warrants close attention [13, 31]. Genome assembly results in the NCBI database show that mcr-9.1 is the most prevalent among mcr genes, even surpassing the initially discovered mcr-1 gene. mcr-9.1 is highly prevalent in the USA and Australia, whereas mcr-1 is more prevalent in China [32]. Unfortunately, Chinese researchers often overlook newly discovered mcr variants, such as mcr-9.1/10, during ARGs screening. Therefore, we speculate that the prevalence of mcr-9.1 may be underestimated, particularly in China. However, according to NCBI genome data, the prevalence of mcr-9.1 is the highest in NTS. Thus, NTS seems to be the dominant bacterial host for mcr-9.1, and we should be especially vigilant about silent mcr-9.1 transmission in NTS. More importantly, we found that the flanking sequence of mcr-9.1 is highly conserved, consistently showing the rcnR-rcnA-pcoS-IS903-mcr-9.1-wbuC pattern [20].

Same as mcr-1, the mcr-9.1 gene is generally located on IncHI2 plasmids, which are the most prevalent in mcr-1- and mcr-9.1-producing NTS and approximately 300 kb in length. The co-adaptive evolution of large plasmid IncHI2 and NTS improved the stability of the plasmid in bacteria [33]. These plasmids encode multidrug resistance. Although mcr-9.1 does not induce colistin resistance in bacterial strains, it often coexists with genes that cause resistance to commonly used treatment drugs, such as ESBLs (blaTEM-1B, blaCTX-M, blaSHV-12) [11], macrolide (mph(A)) and PMQR(qnrA1) [25] genes [34]. Also, severe residual antibiotics in the environment, for example, tetracycline (tet(D)) and sulfonamide (sul1). The pattern of coexistence of resistance genes on plasmid IncHI2 is also the same as that of mcr-1 genes [35].

Therefore, even without using colistin to treat NTS infections, the selective pressure from commonly used drugs may still promote the spread of plasmids carrying mcr-9.1, the transfer of a single plasmid amongst bacterial strains can result in the simultaneous transfer of multiple resistance genes. This increases the risk of propagation of these resistance genes, posing a significant public health threat.

In this study, we comprehensively surveyed the prevalence and transmission of NTS strains that harbor the mcr-9.1 gene in Chinese hospitals over the last decade. We identified 11/7,106 isolates carrying mcr-9.1, all of which displayed multidrug resistance but remained sensitive to colistin, the last-resort antibiotic. We found varied distributions of Salmonella serotypes and STs. To our knowledge, mcr-9.1 has only been reported in serotypes Thompson, Minnesota [36], Senftenberg [37], and Typhimurium [19]. This study is the first to demonstrate the existence of mcr-9.1 in NTS serotype 1,4,[5],12:i:-. This is the most extensive report on mcr-9.1-producing NTS in China to date. Previous investigations only detailed the epidemiological characteristics of one or two mcr-9.1-producing NTS strains [19]. Additionally, this study identified novel hybrid plasmids carrying mcr-9.1, suggesting a continuous expansion of mcr-9.1 plasmids.


The prevalence of mcr-9-positive NTS isolates in China appears to be relatively low. Additionally, the level of resistance conferred by mcr-9 is not notably high. It is noteworthy that the mcr-9 gene can propagate through conservative flanking sequences, allowing for silent dissemination. On a global scale, the presence of mcr-9 is primarily concentrated in specific Salmonella serovars, including Typhimurium, 1,4,[5],12:i:-, Saint Paul, and Heidelberg. In contrast, in China, the prevalence of mcr-9-positive NTS strains is mainly restricted to serovars Typhimurium, 1,4,[5],12:i:-, and Thompson. Our findings underscore the imperative for continuous surveillance and call for more research on mcr-9.1 gene dynamics, particularly considering its potential co-transfer under antimicrobial pressure. Future efforts should focus on multidisciplinary approaches, integrating human health, animal health, and environmental factors to effectively curtail the spread of antibiotic resistance.

Material and methods

Source of NTS’s data, screening of ARGs and Antimicrobial susceptibility test (AST)

As per the National Foodborne Disease Surveillance Plan of China, 32 provincial Centers for Disease Control and Prevention (CDC) laboratories are advised to submit epidemiological information and experimental data on the isolates to the China Food Safety Authority (CFSA) via the National Molecular Tracing Network for Foodborne Disease Surveillance (TraNet). In this study, 7,106 NTS isolates were sourced from diarrhea cases reported under the active foodborne disease surveillance framework from 2010 to 2020. ARGs were screened by ABRicate (Version 1.0.1) ( ASTs and minimal inhibitory concentrations (MICs) for mcr-9.1-producing isolates were performed and interpreted as previously described [38]. Serotypes were predicted by SISTR_cmd (Version 1.1.2) [39], sequence types were identified by MLST (Version 2.23.0) [40].

Datasets of mcr-9.1-producing assemblies and mcr-9.1-producing plasmids based on the NCBI database

To clarify the spreading of mcr-9.1 gene across from the world, mcr-9.1-producing assemblieswere downloaded from NCBI pathogen database, mcr-9.1-producing plasmids were obtained from Refseq database by BLASTn as previously described [38], on January 19, 2022.

Long-read sequencing and plasmid sequence analysis

To locate the mcr-9.1 gene, eight representative isolates, having unique mcr-9.1-positive contigs as previously described [38], were choose to long-read sequence. Unicycler (Version 0.4.8) was used to long-read assembling. ABRicate (Version 1.0.1) ( in PlasmidFinder database, with 90% identification threshold and 60% minimum coverage. Mashtree (Version 1.2.0) were used to create a tree for plasmids based on Mash distance. BLAST Ring Image Generator (BRIG) (Version 0.95) was used to aligned and visualized for all plasmids in this study and a referenced plasmid obtained from NCBI.

Conjugation experiment

To test the transferability of mcr-9.1 genes, conjugation experiment was performed by the donor strain mcr-9.1-producing isolates and the recipient strain sodium azide-resistant E. coli J53. Briefly, the donor and recipient strains at log phase were mixed at the donor/recipient ratio of 1/3, applied to a 0.22 µm filter on antibiotic free Brain–Heart Infusion Agar (BHA) plates, followed by culture at 37 °C for 16 h. The putative transconjugants were selected by BHA supplemented with colistin (0.5 μg/mL) and sodium azide (150 μg/mL), further confirmed by Polymerase chain reaction (PCR) screening for cdgR genes, which were found in E. coli but not in NTS.

Availability of data and materials

All genome assemblies of mcr-9-positive NTS isolates in China were registered under BioProject accession no. PRJNA1026158.


mcr :

Mobilized colistin resistance


Non-typhoidal Salmonella


Sequence type


Antimicrobial resistance genes


Multi-drug resistant




Extended-spectrum beta-lactamases


Plasmid-mediated quinolone resistance

E. coli :

Escherichia coli


Antimicrobial susceptibility test


Centers for Disease Control and Prevention


Minimal inhibitory concentrations


China Food Safety Authority


Tracing Network


BLAST Ring Image Generator


Polymerase chain reaction




  1. Issenhuth-Jeanjean S, Roggentin P, Mikoleit M, Guibourdenche M, de Pinna E, Nair S, et al. Supplement 2008–2010 (no. 48) to the white-Kauffmann-Le minor scheme. Res Microbiol. 2014;165(7):526–30.

    Article  PubMed  Google Scholar 

  2. Li W, Han H, Liu J, Ke B, Zhan L, Yang X, et al. Antimicrobial resistance profiles of Salmonella isolates from human diarrhea cases in China: an eight-year surveilance study. One Health Adv. 2023;1:2.

    Article  Google Scholar 

  3. Gal-Mor O. Persistent infection and long-term carriage of typhoidal and nontyphoidal Salmonellae. Clin Microbiol Rev. 2019;32(1):e00088-18.

    CAS  PubMed  Google Scholar 

  4. Crump JA, Sjölund-Karlsson M, Gordon MA, Parry CM. Epidemiology, clinical presentation, laboratory diagnosis, antimicrobial resistance, and antimicrobial management of invasive Salmonella infections. Clin Microbiol Rev. 2015;28:901–37.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Wang Y, Zhang A, Yang Y, Lei C, Jiang W, Liu B, et al. Emergence of Salmonella enterica serovar Indiana and California isolates with concurrent resistance to cefotaxime, amikacin and ciprofloxacin from chickens in China. Int J Food Microbiol. 2017;262:23–30.

    Article  CAS  PubMed  Google Scholar 

  6. Bush K, Bradford PA. Epidemiology of β-Lactamase-producing pathogens. Clin Microbiol Rev. 2020;33:e00047-e119.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Rodríguez-Martínez JM, Cano ME, Velasco C, Martínez-Martínez L, Pascual A. Plasmid-mediated quinolone resistance: an update. J Infect Chemother. 2011;17(2):149–82.

    Article  PubMed  Google Scholar 

  8. Kim JS, Kwon MJ, Jeon SJ, Park SH, Han S, Park SH, et al. Identification of a carbapenem-resistant Enterobacter kobei clinical strain co-harbouring mcr-4.3 and mcr-9 in Republic of Korea. J Glob Antimicrob Resist. 2021;26:114–6.

    Article  CAS  PubMed  Google Scholar 

  9. Jackson BR, Griffin PM, Cole D, Walsh KA, Chai SJ. Outbreak-associated Salmonella enterica serotypes and food Commodities, United States, 1998–2008. Emerg Infect Dis. 2013;19(8):1239–44.

    Article  PubMed  PubMed Central  Google Scholar 

  10. Liebana E, Carattoli A, Coque TM, Hasman H, Magiorakos A-P, Mevius D, et al. Public health risks of Enterobacterial isolates producing extended-spectrum β-Lactamases or AmpC β-Lactamases in food and food-producing animals: an EU perspective of epidemiology, analytical methods, risk factors, and control options. Clin Infect Dis. 2013;56:1030–7.

    Article  PubMed  Google Scholar 

  11. Pan Y, Fang Y, Song X, Lyu N, Chen L, Feng Y, et al. Co-occurrence of mcr-9, extended spectrum β-lactamase (ESBL) and AmpC genes in a conjugative IncHI2A plasmid from a multidrug-resistant clinical isolate of Salmonella diarizonae. J Infect. 2021;82(4):84–123.

    Article  CAS  PubMed  Google Scholar 

  12. Liu YY, Wang Y, Walsh TR, Yi LX, Zhang R, Spencer J, et al. 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.

    Article  PubMed  Google Scholar 

  13. Carroll LM, Gaballa A, Guldimann C, Sullivan G, Henderson LO, Wiedmann M. Identification of novel mobilized colistin resistance gene mcr-9 in a multidrug-resistant, colistin-susceptible Salmonella enterica serotype typhimurium isolate. mBio. 2019;10:e00853-19.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Kieffer N, Royer G, Decousser JW, Bourrel AS, Palmieri M, Ortiz De La Rosa JM, et al. mcr-9, an inducible gene encoding an acquired phosphoethanolamine transferase in Escherichia coli, and its origin. Antimicrob Agents chemother. 2019;63(9):10–128.

    Article  Google Scholar 

  15. Osei Sekyere J, Maningi NE, Modipane L, Mbelle NM. Emergence of mcr-9.1 in extended-spectrum-β-lactamase-producing clinical Enterobacteriaceae in Pretoria, South Africa: global evolutionary phylogenomics, resistome, and mobilome. mSystems. 2020;5(3):10–128.

    Article  Google Scholar 

  16. Elbediwi M, Pan H, Zhou X, Rankin SC, Schifferli DM, Yue M. Detection of mcr-9-harbouring ESBL-producing Salmonella Newport isolated from an outbreak in a large-animal teaching hospital in the USA. J Antimicrob Chemother. 2021;76(4):1107–9.

    Article  CAS  PubMed  Google Scholar 

  17. Leite EL, Araújo WJ, Vieira TR, Zenato KS, Vasconcelos PC, Cibulski S, et al. First reported genome of an mcr-9-mediated colistin-resistant Salmonella Typhimurium isolate from Brazilian livestock. J Glob Antimicrob Resist. 2020;23:394–7.

    Article  PubMed  Google Scholar 

  18. Guarneri F, Bertasio C, Romeo C, Formenti N, Scali F, Parisio G, et al. First detection of mcr-9 in a multidrug-resistant Escherichia coli of animal origin in Italy is not related to colistin usage on a pig farm. Antibiotics. 2023;12(4):689.

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Fan J, Cai H, Fang Y, He J, Zhang L, Xu Q, et al. Molecular genetic characteristics of plasmid-borne mcr-9 in Salmonella enterica serotype Typhimurium and Thompson in Zhejiang. China Front Microbiol. 2022;13:852434.

    Article  ADS  PubMed  Google Scholar 

  20. Li Y, Dai X, Zeng J, Gao Y, Zhang Z, Zhang L. Characterization of the global distribution and diversified plasmid reservoirs of the colistin resistance gene mcr-9. Sci Rep. 2020;10:8113.

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  21. Zhou H, Wang S, Wu Y, Dong N, Ju X, Cai C, et al. Carriage of the mcr-9 and mcr-10 genes in clinical strains of the Enterobacter cloacae complex in China: a prevalence and molecular epidemiology study. Int J Antimicrob Agents. 2022;60(4):106645.

    Article  CAS  PubMed  Google Scholar 

  22. Lin M, Yang Y, Chen G, He R, Wu Y, Zhong LL, et al. Co-occurrence of mcr-9 and blaNDM-1 in Enterobacter cloacae isolated from a patient with bloodstream infection. Infect Drug Resist. 2020;13:1397–402.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Li X, Wang Q, Huang J, Zhang X, Zhou L, Quan J, et al. Clonal outbreak of NDM-1-producing Enterobacter hormaechei belonging to high-risk international clone ST78 with the coexistence of tmexCD2-toprJ2 and mcr-9 in China. Int J Antimicrob Agents. 2023;61(6):106790.

    Article  CAS  PubMed  Google Scholar 

  24. Parra-Flores J, Holý O, Riffo F, Lepuschitz S, Ruppitsch W, Forsythe S. Draft genome sequences of seven Cronobacter sakazakii strains carrying the mcr-9.1 gene isolated in Chile. Microbiol Resour Announc. 2021;10(28):e00506-21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Yuan Q, Xia P, Xiong L, Xie L, Lv S, Sun F, et al. First report of coexistence of blaKPC-2, blaNDM-1- and mcr-9-carrying plasmids in a clinical carbapenem-resistant Enterobacter hormaechei isolate. Front Microbiol. 2023;14:1153366.

    Article  PubMed  PubMed Central  Google Scholar 

  26. Page DT, Whelan KF, Colleran E. Mapping studies and genetic analysis of transfer genes of the multi-resistant IncHI2 plasmid, R478. FEMS Microbiol Lett. 1999;179(1):21–9.

    Article  CAS  PubMed  Google Scholar 

  27. Koutsoumanis K, Allende A, Alvarez-Ordóñez A, Bolton D, Bover-Cid S, Chemaly M, et al. Salmonella control in poultry flocks and its public health impact. EFSA J Eur Food Saf Author. 2019;17(2):e05596.

    Google Scholar 

  28. Nordmann P, Poirel L. Plasmid-mediated colistin resistance: an additional antibiotic resistance menace. Clin Microbiol Infect. 2016;22:398–400.

    Article  CAS  PubMed  Google Scholar 

  29. Chen K, Xie M, Wang H, Chan EW-C, Chen S. Intercontinental spread and clonal expansion of ColRNA1 plasmid-bearing Salmonella Corvallis ST1541 strains: a genomic epidemiological study. One Health Adv. 2023;1:16.

    Article  Google Scholar 

  30. GBD 2017 Non-Typhoidal Salmonella Invasive Disease Collaborators. The global burden of non-typhoidal salmonella invasive disease: a systematic analysis for the global burden of disease study 2017. Lancet Infect Dis. 2019;19(12):1312–24.

    Article  Google Scholar 

  31. Macesic N, Blakeway LV, Stewart JD, Hawkey J, Wyres KL, Judd LM, et al. Silent spread of mobile colistin resistance gene mcr-9.1 on IncHI2 “superplasmids” in clinical carbapenem-resistant Enterobacterales. Clin Microbiol Infect. 2021;27(12):1856-e7.

    Article  Google Scholar 

  32. Zhang Z, Tian X, Shi C. Global spread of MCR-producing Salmonella enterica isolates. Antibiotics. 2022;11:998.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Zhang JF, Fang LX, Chang MX, Cheng M, Zhang H, Long TF, et al. A trade-off for maintenance of multidrug-resistant IncHI2 plasmids in Salmonella enterica serovar typhimurium through adaptive evolution. mSystems. 2022;7(5):e00248-22.

    Article  PubMed  PubMed Central  Google Scholar 

  34. Vázquez X, Fernández J, Alkorta M, de Toro M, Rosario Rodicio M, Rodicio R. Spread of blaCTX-M-9 and other clinically relevant resistance genes, such as mcr-9 and qnrA1, driven by IncHI2-ST1 plasmids in clinical isolates of monophasic Salmonella enterica serovar typhimurium ST34. Antibiotics (Basel, Switzerland). 2023;12(3):547.

    Google Scholar 

  35. Yang L, Shen Y, Jiang J, Wang X, Shao D, Lam MMC, et al. Distinct increase in antimicrobial resistance genes among Escherichia coli during 50 years of antimicrobial use in livestock production in China. Nat Food. 2022;3(3):197–205.

    Article  Google Scholar 

  36. Alzahrani KO, Alshdokhi EA, Mujallad MI, Al-Reshoodi FM, Alhamed AS, Alswaji AA, et al. Complete genome sequence of a colistin-susceptible Salmonella enterica serovar minnesota strain harboring mcr-9 on an IncHI2/IncHI2A plasmid, isolated from chicken meat. Microbiol Resour Announc. 2021;10(45):e00826-21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Maguire M, Khan AS, Adesiyun AA, Georges K, Gonzalez-Escalona N. Closed genome sequence of a Salmonella enterica serotype senftenberg strain carrying the mcr-9 gene isolated from broken chicken eggshells in Trinidad and Tobago. Microbiol Resour Announc. 2021;10(21):10–128.

    Article  Google Scholar 

  38. Yang T, Li W, Cui Q, Qin X, Li B, Li X, et al. Distribution and transmission of colistin resistance genes mcr-1 and mcr-3 among nontyphoidal Salmonella isolates in China from 2011 to 2020. Microbiol Spectr. 2023;11:e0383322.

    Article  PubMed  Google Scholar 

  39. Yoshida CE, Kruczkiewicz P, Laing CR, Lingohr EJ, Gannon VPJ, Nash JHE, et al. The Salmonella In Silico typing resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies. PLoS One. 2016;11:e0147101.

    Article  PubMed  PubMed Central  Google Scholar 

  40. Ibarz Pavón AB, Maiden MCJ. Multilocus sequence typing. Methods Mol Biol. 2009;551:129–40.

    Article  PubMed  Google Scholar 

Download references


Our thanks go out to all the public health staff from participant CDCs for their efforts in isolate identification, data validation, and submission.


The financial backing for this research was provided by the National Key Research and Development Program of China (Grant No. 2022YFC2303900), along with the National Natural Science Foundation of China (Grant Nos. 32141001 and 32225048). The funders had no role in study design, data collection, and interpretation, or the decision to submit the work for publication.

Author information

Authors and Affiliations



Q.C. and W.L.: Methodology, investigation, data curation and visualization of these results, writing the original draft. X.Q., X.J. and X.G.: Investigation into identifying mcr-9.1-producing isolates, formal analysis, assisting in drafting of the manuscript. T.Y. and L.Y.: Conducted plasmid analysis. T.Y. and X.Z.: carried out conjugation assays. C.W., G.Z. and Q.Y.: These authors contributed to data curation. M.F.: contributed to the methodology. Z.S. and Y.G.: Conceptualization, supervision, funding acquisition, project administration, review and editing of the manuscript. This author provided overarching guidance throughout the project and ensured the strategic relevance and scientific rigor of the research. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Yunchang Guo or Zhangqi Shen.

Ethics declarations

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

All authors declare that they have no conflicts of interest.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Additional file 1:

Figure S1. Antimicrobial resistance rate of mcr-9.1-positive isolates in this study.

Additional file 2:

Table S1. Characterizations of 11 mcr-9.1-producing isolates in this study.

Additional file 3:

Table S2. Profiles of 8 mcr-9.1-producing plasmids in this study.

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Cui, Q., Li, W., Yang, T. et al. Prevalence and dissemination of mcr-9.1-producing non-typhoidal Salmonella strains from diarrhea patients throughout China during 2010–2020. One Health Adv. 2, 4 (2024).

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: