Occurrence of mcr-mediated colistin resistance in Salmonella clinical isolates in Thailand

Abstract

Nontyphoidal Salmonella, an important zoonotic pathogen and a major cause of foodborne illnesses, could be a potential reservoir of plasmids harbouring mobile colistin resistance gene (mcr). This study reported, for the first time, a high rate of mcr-carrying Salmonella clinical isolates (3.3%, 24/724) in Thailand, associated with mcr-3 gene (3.0%, 22/724) in S. 4,[5],12:i:-(15.4%, 4/26), S. Typhimurium (8.8%, 5/57), and S. Choleraesuis (5.6%, 13/231). Remarkably, the increasing trends of colistin and extended-spectrum cephalosporin resistances have displayed a high agreement over the years, with a dramatic rise in the mcr-carrying Salmonella from 1.1% (6/563) during 2005-2007 to 11.2% (18/161) during 2014-2018 when CTX-M-55 became abundant. Clonal and plasmid analysis revealed that the self-transferable IncA/C and a novel hybrid IncA/C-FIIs MDR plasmids were the major vehicles to disseminate both mcr-3 and bla_CTX-M55 genes among diverse Salmonella strains, from as early as 2007. To our knowledge the occurrence of mcr-3 and the co-existence of it with bla_CTX-M-55 in S. Choleraesuis are reported here for the first time, leading to clinical concern over the treatment of the invasive salmonellosis. This study provides evidence of the potential reservoirs and vectors in the dissemination of the mcr and highlights the co-selection by colistin and/or cephalosporins.

Figure 1

The AMR among 724 nontyphoidal Salmonella isolated from humans in Thailand during 2005–2007 and 2014–2018. (a) Comparison of AMR frequency in nontyphoidal Salmonella isolates between 2005–2007 and 2014–2018. (b) Frequency of ESC resistance and colistin resistance over time for nontyphoidal Salmonella isolated from patients from 2005–2016. AMP ampicillin, CRO ceftriaxone, CAZ ceftazidime, GEN gentamicin, TE tetracycline, CIP ciprofloxacin, NAL nalidixic acid, CHL chloramphenicol, SXT trimethoprim-sulfamethoxazole, ERT ertapenem, COL colistin, ESCs extended-spectrum cephalosporins.

Figure 2

(a) Comparison of the AMR observed between ESC-resistant Salmonella and non ESC-resistant counterparts from the 724 nontyphoidal Salmonella isolated from patients in Thailand during 2005–2007 and 2012–2016. (b) Resistance mechanisms detected among ESC-resistant Salmonella isolates in 2005–2007 and 2014–2018. AMP ampicillin, GEN gentamicin, TE tetracycline, CIP ciprofloxacin, NAL nalidixic acid, CHL chloramphenicol, SXT trimethoprim-sulfamethoxazole, ERT ertapenem, COL colistin, ESCs extended-spectrum cephalosporins; *, p < 0.05; and **, p < 0.01.

Figure 3

Dendrogram generated by PFGE-XbaI of 24 mcr-harbouring Salmonella isolates from humans in Thailand. Isolate summary information showing antimicrobial susceptibility profiles, colistin MIC, AMR mechanisms, plasmid profiles, and pulsotypes. Black squares represent isolates that were resistant to antimicrobial agents. Antimicrobial agents are abbreviated as follows: AMP ampicillin, CRO ceftriaxone, CAZ ceftazidime, GEN gentamicin, TE tetracycline, CIP ciprofloxacin, NAL nalidixic acid, CHL chloramphenicol, SXT trimethoprim-sulfamethoxazole, ERT ertapenem, COL colistin, BKK Bangkok, CBR Chonburi, ST Satun, CHM Chiang Mai, RBR Ratchaburi, NTB Nonthaburi, PMQR plasmid-mediated quinolone resistance, ND not determined; and -, not found. *Plasmid sizes and AMR mechanisms confirmed for the location on the plasmid by Southern blot and hybridisation are underlined by a single line or a double line.

Figure 4

Plasmid profile analysis of nontyphoidal Salmonella isolates with conjugative plasmid carrying the mcr-3 gene together with bla_CTX-M-55 gene by S1-PFGE and Southern blot hybridisation. Representative (a) PFGE profiles of total DNA digestion with S1 nuclease, and (b,c) relative hybridisation with the (b) mcr-3 probe and (c) bla_CTX-M-55 probe. Lane 1, plasmid profile analysis of S. Choleraesuis strain H-17–072; lane 2, S. Choleraesuis strain H-17–073; lane 3, S. Choleraesuis strain H-17–053; lane 4, S. Typhimurium strain H-07–020; lane 5, S. Typhimurium strain H-07–021; lane 6, S. Typhimurium strain H-07–037; lane 7, S. Typhimurium strain H-07–038; lane 8, S. Typhimurium strain H-07–385; lane 9, S. Typhimurium strain H-07–388; lane M, CHEF DNA Size Standard-Lambda Ladder (#170–3635), marker labels are in kilo-bases. Arrows indicate the locations of AMR plasmids.