Journal Home Online First Current Issue Archive For Authors Journal Information 中文版

Engineering >> 2022, Volume 15, Issue 8 doi: 10.1016/j.eng.2022.05.006

Genomic Epidemiology of ST34 Monophasic Salmonella enterica Serovar Typhimurium from Clinical Patients from 2008 to 2017 in Henan, China

a Henan Center for Disease Control and Prevention, Zhengzhou 450016, China
b Key Laboratory of Food Safety Risk Assessment & China National Center for Food Safety Risk Assessment, National Health Commission of the People’s Republic of China,
Beijing 100021, China
c Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University,
Yangzhou 225009, China
d Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
e Department of Food Science, National Institutes for Food and Drug Control, Beijing 100050, China
f Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin D04 N2E5, Ireland

Received: 2022-03-13 Revised: 2022-05-04 Accepted: 2022-05-15 Available online: 2022-05-29

Next Previous


Salmonella enterica serovar 4,[5],12:i:- (S. 4,[5],12:i:-) is a monophasic variant of Salmonella enterica serovar Typhimurium that has emerged as a global serovar causing public health concern. To date, the epidemiology and genomic characterization of this pathogen in China have not been well described. We investigated the prevalence, antimicrobial resistance (AMR) phenotypes, and population genomics of sequence type 34 (ST34) S. 4,[5],12:i:- among cases of human salmonellosis in Henan Province, China. A total of 100 ST34 S. 4,[5],12:i:- isolates were studied from 2008 to 2017 and found mostly resistant to ampicillin (AMP), streptomycin (STR), sulfonamides (SUL), and tetracycline (TET) (ASSuT). Bayesian phylogenetic analysis demonstrated that isolates identified in China were mostly related to the European lineage and evolved into two major clades with different resistance genes and plasmid profiles. Notably, clade 1 showed a significantly higher rate of mutations in gyrA and plasmid-mediated quinolone resistance genes. The carrying of the resistance-containing region (encoding R-type ASSuT), including blaTEM-1B (conferring resistance to AMP), strAB (STR), sul2 (SUL), and tet(B) (TET) inserted into the fljBA operon, was responsible for most of the monophasic variants in clade 2. IncHI2 plasmids were the dominant multi-drug resistance mobile genetic elements accounting for the transmission of acquired resistance genes in this serovar, and these were more prevalent in clade 1. Our findings highlighted the increasing prevalence of multi-drug resistant S. 4,[5],12:i:- in China, along with the differential characteristics of resistance gene acquisition among various lineages. Based on our data, control measures are required to address the spread of this zoonotic pathogen. Further owing to its potential origin in food-producing animals, a "One Health" approach, should be implemented to support surveillance whilst informing interventional strategies.



Fig. 1

Fig. 2

Fig. 3

Fig. 4

Fig. 5

Fig. 6


[ 1 ] Havelaar AH, Kirk MD, Torgerson PR, Gibb HJ, Hald T, Lake RJ, et al. World Health Organization Global Estimates and Regional Comparisons of the Burden of Foodborne Disease in 2010. PLoS Med 2015;12(12):e1001923. link1

[ 2 ] Sun H, Wan Y, Du P, Bai L. The epidemiology of monophasic Salmonella Typhimurium. Foodborne Pathog Dis 2020;17(2):87–97. link1

[ 3 ] Petrovska L, Mather AE, AbuOun M, Branchu P, Harris SR, Connor T, et al. Microevolution of monophasic Salmonella Typhimurium during epidemic, United Kingdom, 2005–2010. Emerg Infect Dis 2016;22(4):617–24. link1

[ 4 ] FDA. 2019 NARMS Update: Integrated Report Summary [Internet]. Silver Spring: FDA; 2022 Apr 22 [cited 2022 May 1]. Available from: https://www.

[ 5 ] World Health Organization. Disease Outbreak News; Multicountry outbreak of Salmonella Typhimurium linked to chocolate products- Europe and the United States of America [Internet]. Geneva: World Health Organizatio; 2022 Apr 26 [cited 2022 May 1]. Available from: emergencies/ disease-outbreak-news/item/2022-DON369.

[ 6 ] Laorden L, Herrera-Leo´n S, Marti´nez I, Sanchez A, Kromidas L, Bikandi J, et al. Genetic evolution of the Spanish multidrug-resistant Salmonella enterica 4,5,12:i:- monophasic variant. J Clin Microbiol 2010;48(12):4563–6. link1

[ 7 ] Lucarelli C, Dionisi AM, Filetici E, Owczarek S, Luzzi I, Villa L. Nucleotide sequence of the chromosomal region conferring multidrug resistance (R-type ASSuT) in Salmonella Typhimurium and monophasic Salmonella Typhimurium strains. J Antimicrob Chemother 2012;67(1):111–4. link1

[ 8 ] Boland C, Bertrand S, Mattheus W, Dierick K, Jasson V, Rosseel T, et al. Extensive genetic variability linked to IS26 insertions in the fljB promoter region of atypical monophasic variants of Salmonella enterica serovar Typhimurium. Appl Environ Microbiol 2015;81(9):3169–75. link1

[ 9 ] Ingle DJ, Ambrose RL, Baines SL, Duchene S, Gonçalves da Silva A, Lee DYJ, et al. Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4, [5],12:i:- in Australia. Nat Commun 2021;12:4786. link1

[10] Van Puyvelde S, Pickard D, Vandelannoote K, Heinz E, Barbé B, de Block T, et al. An African Salmonella Typhimurium ST313 sublineage with extensive drugresistance and signatures of host adaptation. Nat Commun 2019;10:4280. link1

[11] Van Boeckel TP, Pires J, Silvester R, Zhao C, Song J, Criscuolo NG, et al. Global trends in antimicrobial resistance in animals in low- and middle-income countries. Science 2019;365(6459):eaaw1944. link1

[12] Kuehn B. Multidrug-resistant Salmonella. JAMA 2019;322(14):1344. link1

[13] Zeng X, Lv S, Qu C, Lan L, Tan D, Li X, et al. Serotypes, antibiotic resistance, and molecular characterization of non-typhoidal Salmonella isolated from diarrheic patients in Guangxi Zhuang Autonomous Region, China, 2014–2017. Food Control 2021;120:107478. link1

[14] He J, Sun F, Sun D, Wang Z, Jin S, Pan Z, et al. Multidrug resistance and prevalence of quinolone resistance genes of Salmonella enterica serotypes 4,[5],12:i:- in China. Int J Food Microbiol 2020;330:108692. link1

[15] Xie X, Wang Z, Zhang K, Li Y, Hu Y, Pan Z, et al. Pig as a reservoir of CRISPR type TST4 Salmonella enterica serovar Typhimurium monophasic variant during 2009–2017 in China. Emerg Microbes Infect 2020;9(1):1–4. link1

[16] Jiang Z, Anwar TM, Peng X, Biswas S, Elbediwi M, Li Y, et al. Prevalence and antimicrobial resistance of Salmonella recovered from pig-borne food products in Henan. China Food Control 2021;121:107535. link1

[17] Zheng D, Ma K, Du J, Zhou Y, Wu G, Qiao X, et al. Characterization of human origin Salmonella serovar 1,4,[5],12:i:- in eastern China, 2014 to 2018. Foodborne Pathog Dis 2021;18(11):790–7. link1

[18] Liu JK, Bai L, Li WW, Han HH, Fu P, Ma XC, et al. Trends of foodborne diseases in China: lessons from laboratory-based surveillance since 2011. Front Med 2018;12(1):48–57. link1

[19] Xia S, Hendriksen RS, Xie Z, Huang L, Zhang J, Guo W, et al. Molecular characterization and antimicrobial susceptibility of Salmonella isolates from infections in humans in Henan Province. China J Clin Microbiol 2009;47 (2):401–9. link1

[20] Nucera DM, Maddox CW, Hoien-Dalen P, Weigel RM. Comparison of API 20E and invA PCR for identification of Salmonella enterica isolates from swine production units. J Clin Microbiol 2006;44(9):3388–90. link1

[21] Prendergast DM, Hand D, Ghallchóir EN, McCabe E, Fanning S, Griffin M, et al. A multiplex real-time PCR assay for the identification and differentiation of Salmonella enterica serovar Typhimurium and monophasic serovar 4,[5],12:-. Int J Food Microbiol 2013;166(1):48–53. link1

[22] CLSI. Performance Standards for Antimicrobial Susceptibility Testing. 28th ed. CLSI supplement M100. CLSI, Wayne, PA, USA. 2018.

[23] The European Committee on Antimicrobial Susceptibility Testing. Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020 [Internet]. Växjö: The European Committee on Antimicrobial Susceptibility Testing; 2022 Apr 21 [cited 2022 May 1]. Available from:

[24] Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012;19(5):455–77. link1

[25] Wick RR, Judd LM, Gorrie CL, Holt KE, Phillippy AM. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017;13(6):e1005595. link1

[26] Li R, Chen K, Chan EWC, Chen S. Resolution of dynamic MDR structures among the plasmidome of Salmonella using MinION single-molecule, long-read sequencing. J Antimicrob Chemother 2018;73(10):2691–5. link1

[27] Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30(14):2068–9. link1

[28] Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V, et al. ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 2020;75(12):3491–500. link1

[29] Kichenaradja P, Siguier P, Perochon J, Chandler M. ISbrowser: an extension of ISfinder for visualizing insertion sequences in prokaryotic genomes. Nucleic Acids Res 2010;38(Database issue):D62–8. link1

[30] Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, Villa L, et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 2014;58 (7):3895–903. link1

[31] Liu B, Zheng D, Jin Q, Chen L, Yang J. VFDB 2019: a comparative pathogenomic platform with an interactive web interface. Nucleic Acids Res 2019;47(D1): D687–92. link1

[32] Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009;25 (16):2078–9. link1

[33] Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012;9(4):357–U54. link1

[34] Elbediwi M, Wu B, Pan H, Jiang Z, Biswas S, Li Y, et al. Genomic characterization of mcr-1-carrying Salmonella enterica serovar 4,[5],12:i:- ST34 clone isolated from pigs in China. Front Bioeng Biotechnol 2020;8:663. link1

[35] Price MN, Dehal PS, Arkin AP, Poon AF. FastTree 2—approximately maximumlikelihood trees for large alignments. PLoS ONE 2010;5(3):e9490. link1

[36] Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 2016;44 (W1):W242–5. link1

[37] Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 2007;7(1):1–8. link1

[38] Yoshida CE, Kruczkiewicz P, Laing CR, Lingohr EJ, Gannon VP, Nash JH, 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(1):e0147101. link1

[39] Garcia P, Malorny B, Rodicio MR, Stephan R, Hachler H, Guerra B, et al. Horizontal acquisition of a multidrug-resistance module (R-type ASSuT) is responsible for the monophasic phenotype in a widespread clone of Salmonella serovar 4,[5],12:i:-. Front Microbiol 2016;7:680. link1

[40] Fang LX, Li XP, Deng GH, Li SM, Yang RS, Wu ZW, et al. High genetic plasticity in multidrug-resistant sequence type 3-IncHI2 plasmids revealed by sequence comparison and phylogenetic analysis. Antimicrob Agents Chemother 2018;62 (4):e02068-17. link1

[41] Li R, Lu X, Peng K, Liu Y, Xiao X, Wang Z. Reorganization of mcr-1-bearing large MDR plasmids resolved by nanopore sequencing. J Antimicrob Chemother 2020;75(6):1645–7. link1

[42] Guo Q, Ding B, Jové T, Stoesser N, Cooper VS, Wang M, et al. Characterization of a novel IncHI2 plasmid carrying tandem copies of blaCTX-M-2 in a fosA6- harboring Escherichia coli sequence type 410 strain. Antimicrob Agents Chemother 2016;60(11):6742–7. link1

[43] Elnekave E, Hong S, Mather AE, Boxrud D, Taylor AJ, Lappi V, et al. Salmonella enterica serotype 4,[5],12:i:- in swine in the United States Midwest: an emerging multidrug-resistant clade. Clin Infect Dis 2018;66(6):877–85. link1

[44] Patchanee P, Tanamai P, Tadee P, Hitchings MD, Calland JK, Sheppard SK, et al. Whole-genome characterisation of multidrug resistant monophasic variants of Salmonella Typhimurium from pig production in Thailand. PeerJ 2020;8:e9700. link1

[45] Elnekave E, Hong SL, Lim S, Boxrud D, Rovira A, Mather AE, et al. Transmission of multidrug-resistant Salmonella enterica subspecies enterica 4,[5],12:i:- sequence type 34 between Europe and the United States. Emerg Infect Dis 2020;26(12):3034–8. link1

[46] Mather AE, Phuong TLT, Gao Y, Clare S, Mukhopadhyay S, Goulding DA, et al. New variant of multidrug-resistant Salmonella enterica serovar Typhimurium associated with invasive disease in immunocompromised patients in Vietnam. mBio 2018;9(5):e01056-18. link1

[47] Diaconu EL, Alba P, Feltrin F, Di Matteo P, Iurescia M, Chelli E, et al. Emergence of IncHI2 plasmids with mobilized colistin resistance (mcr)-9 gene in ESBLproducing, multidrug-resistant Salmonella Typhimurium and its monophasic variant ST34 from food-producing animals in Italy. Front Microbiol 2021;12:705230. link1

[48] 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.e7-13. link1

[49] Li L, Liao XP, Liu ZZ, Huang T, Li X, Sun J, et al. Co-spread of oqxAB and blaCTX-M-9G in non-typhi Salmonella enterica isolates mediated by ST2-IncHI2 plasmids. Int J Antimicrob Agents 2014;44(3):263–8. link1

[50] Garcia-Fernandez A, Carattoli A. Plasmid double locus sequence typing for IncHI2 plasmids, a subtyping scheme for the characterization of IncHI2 plasmids carrying extended-spectrum beta-lactamase and quinolone resistance genes. J Antimicrob Chemother 2010;65(6):1155–61. link1

[51] Billman-Jacobe H, Liu Y, Haites R, Weaver T, Robinson L, Marenda M, et al. pSTM6-275, a conjugative IncHI2 plasmid of Salmonella enterica that confers antibiotic and heavy-metal resistance under changing physiological conditions. Antimicrob Agents Chemother 2018;62(5):e02357–17. link1

[52] Branchu P, Charity OJ, Bawn M, Thilliez G, Dallman TJ, Petrovska L, et al. SGI-4 in monophasic Salmonella Typhimurium ST34 is a novel ICE that enhances resistance to copper. Front Microbiol 2019;10:1118. link1

[53] Bearson BL, Trachsel JM, Shippy DC, Sivasankaran SK, Kerr BJ, Loving CL, et al. The role of Salmonella genomic Island 4 in metal tolerance of Salmonella enterica serovar I 4,[5],12:i:- pork outbreak isolate USDA15WA-1. Genes 2020;11(11):1291. link1

[54] Arnott A, Wang Q, Bachmann N, Sadsad R, Biswas C, Sotomayor C, et al. Multidrug-resistant Salmonella enterica 4,[5],12:i:- sequence type 34, New South Wales, Australia, 2016–2017. Emerg Infect Dis 2018;24(4):751–3. link1

Related Research