Next Article in Journal
Stapling of Peptides Potentiates the Antibiotic Treatment of Acinetobacter baumannii In Vivo
Next Article in Special Issue
Whole-Genome Sequencing of a Colistin-Resistant Acinetobacter baumannii Strain Isolated at a Tertiary Health Facility in Pretoria, South Africa
Previous Article in Journal
Microbiological Diagnoses on Clinical Mastitis—Comparison between Diagnoses Made in Veterinary Clinics versus in Laboratory Applying MALDI-TOF MS
Previous Article in Special Issue
Genomic Changes within a Subset of IncI2 Plasmids Associated with Dissemination of mcr-1 Genes and Other Important Antimicrobial Resistance Determinants
 
 
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Low Level of Colistin Resistance and mcr Genes Presence in Salmonella spp.: Evaluation of Isolates Collected between 2000 and 2020 from Animals and Environment

by
Fabrizio Bertelloni
*,
Giulia Cagnoli
,
Barbara Turchi
and
Valentina Virginia Ebani
Department of Veterinary Science, University of Pisa, 56124 Pisa, Italy
*
Author to whom correspondence should be addressed.
Antibiotics 2022, 11(2), 272; https://doi.org/10.3390/antibiotics11020272
Submission received: 30 December 2021 / Revised: 11 February 2022 / Accepted: 16 February 2022 / Published: 19 February 2022
(This article belongs to the Special Issue Colistin Resistance: The Need for a One Health Approach)

Abstract

:
Salmonellosis is one of the most important zoonoses in Europe and the world. Human infection may evolve in severe clinical diseases, with the need for hospitalization and antimicrobial treatment. Colistin is now considered an important antimicrobial to treat infections from multidrug- resistant Gram-negative bacteria, but the spreading of mobile colistin-resistance (mcr) genes has limited this option. We aimed to evaluate colistin minimum inhibitory concentration and the presence of mcr (mcr-1 to mcr-9) genes in 236 Salmonella isolates previously collected from different animals and the environment between 2000 and 2020. Overall, 17.79% of isolates were resistant to colistin; no differences were observed in relation to years of isolation (2000–2005, 2009–2014, and 2015–2020), Salmonella enterica subspecies (enterica, salamae, diarizonae, and houtenae), origin of samples (domestic animals, wildlife, and environment), or animal category (birds, mammals, and reptiles); only recently isolated strains from houseflies showed the most resistance. Few isolates (5.93%) scored positive for mcr genes, in particular for mcr-1, mcr-2, mcr-4, mcr-6, and mcr-8; furthermore, only 2.54% of isolates were mcr-positive and colistin-resistant. Detected resistance to colistin was equally distributed among all examined Salmonella isolates and not always related to the presence of mcr genes.

1. Introduction

Colistin is an old antibiotic, discovered in 1947, and belonging to the class of polymyxins. The target of this antimicrobial is the outer membrane lipopolysaccharides (LPS) of Gram-negative bacteria [1]. In human medicine, colistin use has been largely abandoned since the mid-1970s as a consequence of some adverse events, primarily nephrotoxicity and neurotoxicity, combined with the discovery of new antibiotics [2]. In contrast, colistin was largely used in veterinary medicine worldwide to treat infections, mainly from Enterobacteriaceae, in terrestrial and aquatic animals. Furthermore, it was used for decades as a growth promoter in farm animals in many countries; this practice is still allowed in some territories [3]. The increase in antimicrobial resistance led, by the mid-1990s, to the rediscovery of colistin for human therapy as a last-resort antibiotic in multidrug-resistant Gram-negative infections [2,4]. Consequently, policies for the reduction in use of colistin in animals were advanced in many countries, although the resistance to this antimicrobial was not so diffuse [1,5]. Resistance to colistin remained a rare event for years, probably because it is encoded chromosomally and consequently transferred only vertically [2,5].
In 2015, the first plasmid gene able to confer resistance to colistin, mcr-1, was detected in Escherichia coli in China [6]. Subsequently, different variants of this gene, from mcr-2 to mcr-10, and numerous subvariants have been reported [7,8]. Surprisingly, retrospective investigations highlighted the presence of mcr genes in strains isolated from the 1980s, but particularly in bacteria cultured in the last twenty years [9,10,11]. However, before 2015, colistin resistance was not considered a serious threat and resistance levels were generally low [12]. Starting in 2015, reports of colistin-resistant and mcr-positive bacteria increased; now, these events are reported worldwide in many Gram-negative bacteria [12,13].
Despite E. coli remaining the main bacterial species involved in this phenomenon, colistin resistance and mcr-mediated resistance were also reported in Salmonella [14]. Phenotypic resistance to colistin in Salmonella is variable in relation to serotypes, year of isolation, source (humans, animals, food, and environment), and geographic area. However, percentages of resistant strains are generally low, ranging between about 1% and 12% [15,16,17,18], with some exceptions (40%) [19]. The gene mcr-1 was the most frequently detected in Salmonella, but mcr-2, mcr-3, mcr-4, mcr-5, and mcr-9 were also detected [20]. Domestic animals were identified as the main reservoir of mcr-positive salmonellae and S. ser Typhimurium as the most frequent serovar carrying these genes [14,20]. However, detection rate of mcr-positive Salmonella strains is generally low [17,18,21], with some exceptions [22]. As reported for other bacteria, the direct relation between the presence of mcr genes and colistin resistance in Salmonella has not been fully clarified; these genes have also been found in susceptible strains [15], and, frequently, only a small number of resistant strains carry these genes [16,17,18], suggesting other mechanisms of resistance [2]. In S. enterica, different chromosomally encoded mechanisms were identified as conferring resistance to colistin. In particular, the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine (PEtN) to the phosphate groups of lipid A causes the alteration of the LPS structure; this event alters the primary target of colistin. The arnBCADTEF and pmrCAB operons are responsible for this process; they are up-regulated by the two-component regulatory systems (TCSs) PmrA/PmrB and PhoP/PhoQ. Overactivation of TCSs by external stimuli or by mutations may lead to the hyper-expression of arnBCADTEF and pmrCAB. Mutations in mgrB, a suppressor gene of the PhoP/PhoQ system, may produce the same result. Deacylation of lipid A, mediated by pagL, rpoN, and ipxM genes, may be another mechanism mediating colistin resistance, although less common in S. enterica than in other bacteria, such as Acinetobacter baumannii. Finally, it has been proposed that alteration of efflux pumps (sapABCDF operon) and porins by cytoplasmic molecules (ydeI/ompD system) can increase bacterial resistance to polymyxins [2,13,23,24].
The aim of this study was to investigate the colistin resistance and presence of mcr genes (mcr-1 to mcr-9) in Salmonella strains isolated from animals or related environments, including strains cultured from atypical samples (reptiles and wild animals) and belonging to serotypes that are not frequently detected or investigated, collected between 2000 and 2020.

2. Results

2.1. Evaluation of Minimum Inhibitory Concentration (MIC) for Colistin

Overall, 42/236 (17.79%) isolates showed resistance to colistin; most of them, 33/236 (13.98%), showed an MIC equal to the breakpoint, 4 µg/mL. Consequently, only nine (3.81%) strains had a higher MIC. In particular, one (0.42%) isolate had an MIC of 8 µg/mL, one (0.42%) isolate of 16 µg/mL, one (0.42%) isolate of 256 µg/mL and six (2.54%) isolates had an MIC higher than 256 µg/mL.
Considering the years of isolation of the investigated strains and the first report of mcr genes in 2015, to evaluate the distribution over time of colistin resistance, isolates were arranged in three groups: salmonellae collected between 2000 and 2005, between 2009 and 2014, and finally, between 2015 and 2020 (no isolates were collected between 2006 and 2008). Percentages of resistant strains collected between 2000–2005 and 2009–2014 were very similar, 15.17% (17/112) and 15.27% (11/72), respectively, and no statistical differences emerged (p > 0.05). Although the percentage of resistant salmonellae isolated in the period 2015–2020 was higher, 28.00% (14/50), this difference was not statistically significant (p > 0.05). Table 1 shows detailed data on distribution of MICs over time in examined Salmonella strains.
Considering the source of the strains, 174 isolates were from domestic animals, including pets, 51 isolates were from wild animals, including houseflies and crayfish, and 11 isolates were from environmental and feed samples. In detail, 13 isolates were cultured from Arthropoda (housefly and crayfish), 51 from birds, 63 from mammals, and 98 from reptiles. Of strains from domestic animals, 16.67% (29/174) showed resistance to colistin, whereas 23.53% (12/51) and 9.09% (1/11) of isolates from wild animals and environmental samples were resistant, respectively (Table 2); no statistical differences were observed (p > 0.05). Likewise, 38.46% (5/13), 21.57% (11/51), 22.22% (14/63), and 11.22% (11/98) of Salmonella isolates from Arthropoda, birds, mammals, and reptiles showed resistance to colistin, respectively (Table 3); no statistical differences emerged among strains from birds, mammals, and reptiles (p > 0.05), whereas isolates from Arthropoda appeared more resistant than salmonellae from other animals (p < 0.05).
All analyzed strains belonged to the species S. enterica. In particular, 202 isolates belonged to subspecies enterica, 7 to subspecies salamae, 9 to subspecies diarizonae, and 14 to subspecies houtenae; finally, 4 strains were in the R phase. Table 4 shows the distribution of MIC values in relation to Salmonella subspecies. Considering the MIC results, 16.83% (34/202) of S. enterica sub. enterica isolates showed resistance, 14.29% (1/7) of S. enterica sub. salamae isolates, 22.22% (2/9) of S. enterica sub. diarizonae isolates, and 21.43% (3/14) of S. enterica sub. houtenae isolates showed resistance to colistin; 50.00% of R-phase strains were resistant. No statistical differences emerged among the different subspecies (p > 0.05).
A serovar-to-serovar comparison was not feasible because, for most serovars, only one isolate was available. We compared the data relating to the six serovars most frequently detected in human infections in EU between 2015 and 2019: Enteritidis, Typhimurium, Typhimurium monophasic variants, Infantis, Derby, and Newport [25]. As shown in Table 5, 40.00% of S. ser. Enteritidis, 20.69% (6/29) of S. ser. Typhimurium, 14.9% (1/7) of S. ser. Typhimurium monophasic variants, 25.00% (2/8) of S. ser. Infantis, 12.50% (2/16) of S. ser. Derby, and 0.00% (0/3) of S. ser. Newport showed resistance to colistin; no statistical differences were observed (p > 0.05).

2.2. Molecular Detection of mcr Genes

None of the isolates were positive for mcr-3, mcr-5, mcr-7, or mcr-9 genes. The most detected gene was mcr-2, with 7/236 (2.96%) positive isolates, followed by mcr-4, with 4/236 (1.69%) positive isolates, and mcr-1 and mcr-8, with 2/236 (0.84%) positive isolates each; only 1/236 (0.42%) scored positive for mcr-6. Overall, 14/236 (5.93%) isolates were positive for mcr genes; only two isolates scored positive for more than one gene. Six isolates were collected in 2019 from different specimens and showed phenotypic resistance to colistin. Eight Salmonella strains, collected in 2002 from reptiles, showed susceptibility to colistin, although they were positive for the investigated resistance genes. Table 6 shows detailed information about mcr-positive strains.

3. Discussion

Salmonella is one of the most important food-borne zoonotic pathogens worldwide. In Europe, salmonellosis is the second most prevalent zoonosis considering the total number of confirmed cases and the most prevalent considering the total number of outbreaks. In 2019, in EU, Salmonella was responsible for 87,923 confirmed human cases, 16,628 hospitalizations, and 140 deaths [25]. In Europe, antimicrobial resistance, mainly multidrug resistance, was generally lower in Salmonella than in other Enterobacteriaceae, with differences related to serotype and geographic territory [26]. Colistin was recently reintroduced in human therapy and it is now considered a critically important antimicrobial [27]. For this reason, the discovery of mobile genes conferring colistin resistance caused many concerns. These genes were more commonly observed among E. coli strains, but they were also detected in other Gram-negative bacteria, such as Salmonella [28].
The number of studies on phenotypic colistin resistance in Salmonella is limited. Past works were usually based on the disk diffusion test, a method not suitable for colistin resistance detection [1]; on the other hand, recent investigations usually focused on mcr-positive strains. In our study, the percentage of colistin-resistant strains was 17.79%, which is slightly higher than the data reported in recent literature. Recent surveys registered percentages of colistin-resistant Salmonella strains ranging between 1% and 12% [15,17,18,29,30]. These differences may be due to many factors: source, geographic area, and serotype. It is interesting to note that no differences were observed in relation to years of isolation, suggesting a basal level of diffused resistance. Unfortunately, our study suffers from the heterogeneity of samples from which Salmonella isolates were cultured; thus, it was not possible to draw a conclusion in terms of monitoring over time. However, this limitation may also represent a strength of the study, showing a condition largely spread among the Salmonella genus and not restricted to strains coming from a particular matrix. To underline this hypothesis, no differences were observed among strains from wild animals, domestic animals, or environment, or from different animal categories: birds, mammals, and reptiles. Salmonella isolates from houseflies (Musca domestica) were statistically the most resistant strains. Considering the behavior of houseflies, the obtained results may suggest that these insects might be involved in the diffusion of colistin-resistant salmonellae.
Most of the available studies in the literature focused on a subset of serovars, the ones mainly involved in human and animal salmonellosis, such as Typhimurium and Enteritidis [14,16,20]. Few data are available on colistin resistance in Salmonella belonging to uncommon serovars or subspecies [31]. In our investigation, more than 70 different serovars, belonging to four subspecies, were included. In relation to phenotypic colistin resistance, no statistical differences were observed among the subspecies. Furthermore, no statistical differences emerged among the six serovars most frequently detected in human infections in EU between 2015 and 2019 [25]. These findings support the hypothesis of a diffused resistance among tested salmonellae. Moreover, our results show that the less investigated serovars may also be involved in the phenomenon of colistin resistance.
Regarding mobile colistin-resistance genes, few isolates scored positive (5.93%) for one or more genes. This finding is in agreement with other studies reporting a percentage of mcr-positive Salmonella strains ranging between 0.6% and 3.3% [15,17,18,19,29]. The slightly higher positivity detected in our survey may be related to the extended set of investigated genes. Our data confirm the low circulation of these genes in the Salmonella genus compared to other Enterobacteriaceae, especially E. coli. E. coli seems to be the primary species having mcr genes [9,28,32], also confirmed by the high prevalence of mcr-positive E. coli strains (44.6%) isolated from wild boar from the same geographic area [33].
The low detection rate of mcr genes compared to found phenotypic resistance suggests the low involvement of these genes in colistin resistance in Salmonella, as also supposed by other authors [17,29]. Detected resistance may be related to other chromosome-related mechanisms. From this point of view, the TCSs (pmrA/pmrB and phoP/phoQ) play a key role in colistin resistance in Salmonella. Mutations occurring in these genes or in their regulatory genes, such as mgrB for PhoP/Q, lead to the modification of lipid A and, consequently, the alteration of the colistin target [2,13,24]. Up-regulation of TCSs may also be the consequence of environmental stimuli, including low Mg2+ concentrations [2]. For this reason, cation-adjusted Mueller–Hinton medium was employed in MIC tests, as recommended by CLSI [34]. Other resistance mechanisms reported in Salmonella are related to efflux pumps and porins, but they seem to play a secondary role in colistin resistance in these bacteria [1].
Only 6/14 mcr-positive isolates were resistant to colistin. All mcr-positive and colistin-susceptible strains were from reptiles sampled in 2002. The gene mcr-1 was detected for the first time in E. coli in 2015 [6]. However, studies performed since 2015 have also shown the presence of this gene in previously obtained isolates [9], including Salmonella strains [14,20]. Currently, the exact relation between the presence of mcr genes and phenotypic resistance to colistin is controversial and far from being fully understood. In most studies, only colistin-resistant strains were screened for mcr and this aspect may cause a lack of information. Recent investigations also showed the abundant presence of these genes in susceptible bacteria [35]; furthermore, some mcr variants are unable to confer colistin resistance [31]. The obtained results highlighted the importance of carrying out both phenotypic and genotypic analyses to investigate the antimicrobial resistance.
The present research, which focused on the resistance to colistin in Salmonella strains cultured from different sources, suffers from some limitations. It would be useful to investigate if colistin-resistant and mcr-positive strains are also resistant to other antibiotics and whether they harbor other resistant genes, particularly at the plasmid level. Furthermore, we investigated only the involvement of mcr genes in colistin resistance. As reported above, other chromosomally related mechanisms induce resistance to colistin; the study of these systems may explain some resistances that were phenotypically detected.

4. Materials and Methods

4.1. Salmonella Strains Included in the Study

This investigation was conducted on 236 Salmonella spp. strains preserved in the biobank of the Laboratory of Infectious Disease of the Department of Veterinary Sciences, University of Pisa, Italy. All strains were collected during routine investigations or specific research. Most of the isolates came from apparently healthy animals. The strains were selected based on their pulsotype profile and/or taking into consideration epidemiological information. All strains were isolated from feces or organs of various domestic or wild animals (mammals, birds, reptiles, and arthropods), with the exception of 11 strains coming from environmental or feed samples collected at animal farms. Supplementary Table S1 shows information for each strain related to the type of sample, isolation year, species, subspecies, and serotype.

4.2. Evaluation of Minimum Inhibitory Concentration for Colistin

The broth microdilution method was employed for evaluation of minimum inhibitory concentrations (MICs) of colistin. The protocol described by CLSI was adopted [34]; cation-adjusted Mueller–Hinton (MH) broth (Oxoid, Milan, Italy) was used and colistin sulfate (CARLO ERBA Reagents, Cornaredo, Italy) was diluted 2-fold from 256 to 0.5 µg/mL. Isolates showing an MIC > 2 μg/mL were recorded as resistant [36].

4.3. Molecular Detection of mcr Genes

DNA was extracted from overnight agar cultures with a commercial kit, DNA Plus Kits (Zymo Research, Irvine, CA, USA), following the manufacturer’s guidelines.
Two multiplex PCR assays were employed: the first for the detection of genes mcr-1, mcr-2, mcr-3, mcr-4, and mcr-5; and the second to detect mcr-6, mcr-7, mcr-8, and mcr-9 genes. The assays were executed using primers and protocols published elsewhere [37,38] and are shown in Table 7. PCR reactions were carried out in a volume of 50 µL including 25 µL EconoTaq PLUS GREEN 2X Master Mixes (Lucigen Corporation, Middleton, WI, USA), 0.5 µL of each primer (10 µM concentration), 3 µL of template DNA, and PCR-grade water to reach the final volume.

4.4. Statistical Analyses

Chi-square (X2) and Fisher (F) tests were used to evaluate the obtained data. In particular, statistical tests were used to compare distribution of resistant strains and positivity to mcr genes in relation to: year of isolation, source of isolates, Salmonella subspecies, and serovars. The statistical significance threshold was set at a p-value ≤ 0.05.

5. Conclusions

In the present study, we focused on the resistance to colistin in Salmonella strains isolated and collected over the last twenty years. No relevant differences emerged among the investigated isolates, suggesting a broad resistance in strains from different sources belonging to different serovars and isolated in different years. Phenotypic resistance was not always associated with mcr genes, confirming that this rising issue marginally involves Salmonella strains. The results of the resistance of the studied isolates to other antimicrobials have been reported in previous surveys. However, the present investigation may be improved by further data about other possible genetic mechanisms responsible for colistin resistance, as suggested by some authors who assumed that chromosomally related mechanisms are involved [2,13,24]. Programs of antibiotic-resistance monitoring should include Salmonella of uncommon serovars and isolated from atypical hosts to obtain more real and valuable information.

Supplementary Materials

The following are available online at https://www.mdpi.com/article/10.3390/antibiotics11020272/s1, Table S1: Detailed information about analyzed Salmonella isolates.

Author Contributions

Conceptualization, F.B.; formal analysis, F.B. and G.C.; investigation, F.B. and G.C.; resources, V.V.E.; data curation, F.B. and B.T.; writing—original draft preparation, F.B. and B.T.; writing—review and editing, F.B. and V.V.E.; supervision, V.V.E.; funding acquisition, V.V.E. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by University of Pisa, Fondi di Ateneo.

Data Availability Statement

The data presented in this study are available within the article and Supplementary Material.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Poirel, L.; Jayol, A.; Nordmanna, P. Polymyxins: Antibacterial activity, susceptibility testing, and resistance mechanisms encoded by plasmids or chromosomes. Clin. Microbiol. Rev. 2017, 30, 557–596. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  2. El-Sayed Ahmed, M.A.E.G.; Zhong, L.L.; Shen, C.; Yang, Y.; Doi, Y.; Tian, G.B. Colistin and its role in the Era of antibiotic resistance: An extended review (2000–2019). Emerg. Microbes Infect. 2020, 9, 868–885. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  3. Kempf, I.; Jouy, E.; Chauvin, C. Colistin use and colistin resistance in bacteria from animals. Int. J. Antimicrob. Agents 2016, 48, 598–606. [Google Scholar] [CrossRef] [PubMed]
  4. Falagas, M.E.; Kasiakou, S.K. Colistin: The Revival of Polymyxins for the Management of Multidrug-Resistant Gram-Negative Bacterial Infections. Clin. Infect. Dis. 2005, 40, 1333–1341. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  5. Venter, H.; Henningsen, M.L.; Begg, S.L. Antimicrobial resistance in healthcare, agriculture and the environment: The biochemistry behind the headlines. Essays Biochem. 2017, 61, 1–10. [Google Scholar] [CrossRef]
  6. Liu, Y.Y.; Wang, Y.; Walsh, T.R.; Yi, L.X.; Zhang, R.; Spencer, J.; Doi, Y.; Tian, G.; Dong, B.; Huang, X.; 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, 161–168. [Google Scholar] [CrossRef]
  7. Partridge, S.R.; Di Pilato, V.; Doi, Y.; Feldgarden, M.; Haft, D.H.; Klimke, W.; Kumar-Singh, S.; Liu, J.H.; Malhotra-Kumar, S.; Prasad, A.; et al. Proposal for assignment of allele numbers for mobile colistin resistance (mcr) genes. J. Antimicrob. Chemother. 2018, 73, 2625–2630. [Google Scholar] [CrossRef] [PubMed]
  8. Shen, Y.; Zhang, R.; Schwarz, S.; Wu, C.; Shen, J.; Walsh, T.R.; Wang, Y. Farm animals and aquaculture: Significant reservoirs of mobile colistin resistance genes. Environ. Microbiol. 2020, 22, 2469–2484. [Google Scholar] [CrossRef] [Green Version]
  9. Nang, S.C.; Li, J.; Velkov, T. The rise and spread of mcr plasmid-mediated polymyxin resistance. Crit. Rev. Microbiol. 2019, 45, 131–161. [Google Scholar] [CrossRef]
  10. Macori, G.; Nguyen, S.V.; Naithani, A.; Hurley, D.; Bai, L.; Garch, F.E.; Woehrlé, F.; Miossec, C.; Roques, B.; O’gaora, P.; et al. Characterisation of early positive mcr-1 resistance gene and plasmidome in escherichia coli pathogenic strains associated with variable phylogroups under colistin selection. Antibiotics 2021, 10, 1041. [Google Scholar] [CrossRef]
  11. Fan, R.; Li, C.; Duan, R.; Qin, S.; Liang, J.; Xiao, M.; Lv, D.; Jing, H.; Wang, X. Retrospective Screening and Analysis of mcr-1 and blaNDM in Gram-Negative Bacteria in China, 2010–2019. Front. Microbiol. 2020, 11, 121. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  12. Gharaibeh, M.H.; Shatnawi, S.Q. An overview of colistin resistance, mobilized colistin resistance genes dissemination, global responses, and the alternatives to colistin: A review. Vet. World 2019, 12, 1735. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  13. Hamel, M.; Rolain, J.M.; Baron, S.A. The History of Colistin Resistance Mechanisms in Bacteria: Progress and Challenges. Microorganisms 2021, 9, 442. [Google Scholar] [CrossRef] [PubMed]
  14. Lima, T.; Domingues, S.; DaSilva, G. Plasmid-mediated colistin resistance in salmonella enterica: A review. Microorganism 2019, 7, 55. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  15. Pungpian, C.; Lee, S.; Trongjit, S.; Sinwat, N.; Angkititrakul, S.; Prathan, R.; Srisanga, S.; Chuanchuen, R. Colistin resistance and plasmid-mediated mcr genes in Escherichia coli and Salmonella isolated from pigs, pig carcass and pork in Thailand, Lao PDR and Cambodia border provinces. J. Vet. Sci. 2021, 22, 1–15. [Google Scholar] [CrossRef] [PubMed]
  16. Sevilla, E.; Vico, J.P.; Delgado-Blas, J.F.; González-Zorn, B.; Marín, C.M.; Uruén, C.; Martín-Burriel, I.; Bolea, R.; Mainar-Jaime, R.C. Resistance to colistin and production of extended-spectrum β-lactamases and/or AmpC enzymes in Salmonella isolates collected from healthy pigs in Northwest Spain in two periods: 2008–2009 and 2018. Int. J. Food Microbiol. 2021, 338, 108967. [Google Scholar] [CrossRef] [PubMed]
  17. Carnevali, C.; Morganti, M.; Scaltriti, E.; Bolzoni, L.; Pongolini, S.; Casadei, G. Occurrence of mcr-1 in Colistin-Resistant Salmonella enterica Isolates Recovered from Humans and Animals in Italy, 2012 to 2015. Antimicrob. Agents Chemother. 2016, 60, 7532. [Google Scholar] [CrossRef] [Green Version]
  18. Garcia-Graells, C.; De Keersmaecker, S.C.J.; Vanneste, K.; Pochet, B.; Vermeersch, K.; Roosens, N.; Dierick, K.; Botteldoorn, N. Detection of Plasmid-Mediated Colistin Resistance, mcr-1 and mcr-2 Genes, in Salmonella spp. Isolated from Food at Retail in Belgium from 2012 to 2015. Foodborne Pathog. Dis. 2018, 15, 114–117. [Google Scholar] [CrossRef]
  19. Luk-in, S.; Chatsuwan, T.; Kueakulpattana, N.; Rirerm, U.; Wannigama, D.L.; Plongla, R.; Lawung, R.; Pulsrikarn, C.; Chantaroj, S.; Chaichana, P.; et al. Occurrence of mcr-mediated colistin resistance in Salmonella clinical isolates in Thailand. Sci. Rep. 2021, 11, 14170. [Google Scholar] [CrossRef]
  20. Portes, A.B.; Rodrigues, G.; Leitão, M.P.; Ferrari, R.; Conte Junior, C.A.; Panzenhagen, P. Global distribution of plasmid-mediated colistin resistance mcr gene in Salmonella: A systematic review. J. Appl. Microbiol. 2021, 132, 872–889. [Google Scholar] [CrossRef] [PubMed]
  21. Arnott, A.; Wang, Q.; Bachmann, N.; Sadsad, R.; Biswas, C.; Sotomayor, C.; Howard, P.; Rockett, R.; Wiklendt, A.; Iredell, J.R.; et al. Multidrug-Resistant Salmonellaenterica 4,[5],12:i:- Sequence Type 34, New South Wales, Australia, 2016–2017. Emerg. Infect. Dis. 2018, 24, 751. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  22. Yi, L.; Wang, J.; Gao, Y.; Liu, Y.; Doi, Y.; Wu, R.; Zeng, Z.; Liang, Z.; Liu, J.H. mcr-1−Harboring Salmonella enterica Serovar Typhimurium Sequence Type 34 in Pigs, China. Emerg. Infect. Dis. 2017, 23, 291. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  23. Pilonieta, M.C.; Erickson, K.D.; Ernst, R.K.; Detweiler, C.S. A Protein Important for Antimicrobial Peptide Resistance, YdeI/OmdA, Is in the Periplasm and Interacts with OmpD/NmpC. J. Bacteriol. 2009, 191, 7243. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  24. Baron, S.; Hadjadj, L.; Rolain, J.M.; Olaitan, A.O. Molecular mechanisms of polymyxin resistance: Knowns and unknowns. Int. J. Antimicrob. Agents 2016, 48, 583–591. [Google Scholar] [PubMed]
  25. EFSA, (European Food Safety Authority); ECDC, (European Centre for Disease Prevention and Control). The European Union One Health 2019 Zoonoses Report. EFSA J. 2021, 19, 6406. [Google Scholar]
  26. EFSA, (European Food Safety Authority); ECDC, (European Centre for Disease Prevention and Control). The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2018/2019. EFSA J. 2021, 19, 179. [Google Scholar]
  27. WHO (World Health Organization-Advisory Group on Integrated Surveillance of Antimicrobial Resistance). Critically Important Antimicrobials for Human Medicine, 6th Revision 2018; World Health Organization: Geneva, Switzerland, 2019. [Google Scholar]
  28. Khondker, A.; Rheinstädter, M.C. How do bacterial membranes resist polymyxin antibiotics? Commun. Biol. 2020, 3, 77. [Google Scholar] [CrossRef] [PubMed]
  29. Moreno, L.Z.; Gomes, V.T.M.; Moreira, J.; de Oliveira, C.H.; Peres, B.P.; Silva, A.P.S.; Thakur, S.; La Ragione, R.M.; Moreno, A.M. First report of mcr-1-harboring Salmonella enterica serovar Schwarzengrund isolated from poultry meat in Brazil. Diagn. Microbiol. Infect. Dis. 2019, 93, 376–379. [Google Scholar] [CrossRef] [PubMed]
  30. Li, X.P.; Fang, L.X.; Song, J.Q.; Xia, J.; Huo, W.; Fang, J.T.; Liao, X.P.; Liu, Y.H.; Feng, Y.; Sun, J. Clonal spread of mcr-1 in PMQR-carrying ST34 Salmonella isolates from animals in China. Sci. Rep. 2016, 6, 38511. [Google Scholar] [CrossRef]
  31. Tyso, G.H.; Li, C.; Hsu, C.H.; Ayers, S.; Borenstein, S.; Mukherjee, S.; Tran, T.T.; McDermot, P.F.; Zhao, S. The mcr-9 gene of salmonella and escherichia coli is not associated with colistin resistance in the United States. Antimicrob. Agents Chemother. 2020, 64, e00573-20. [Google Scholar]
  32. Elbediwi, M.; Li, Y.; Paudyal, N.; Pan, H.; Li, X.; Xie, S.; Rajkovic, A.; Feng, Y.; Fang, W.; Rankin, S.C.; et al. Global burden of colistin-resistant bacteria: Mobilized colistin resistance genes study (1980–2018). Microorganisms 2019, 7, 461. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  33. Cilia, G.; Turchi, B.; Fratini, F.; Ebani, V.V.; Turini, L.; Cerri, D.; Bertelloni, F. Phenotypic and genotypic resistance to colistin in E. coli isolated from wild boar (Sus scrofa) hunted in Italy. Eur. J. Wildl. Res. 2021, 67, 1–7. [Google Scholar] [CrossRef]
  34. CLSI (Clinical and Laboratory Standards Institute). M07-A10 Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria That Grow Aerobically; Approved Standard, 10th ed.; CLSI Document M07-A10; Clinical and Laboratory Standards Institute: Wayne, PA, USA, 2015. [Google Scholar]
  35. Aguirre, L.; Vidal, A.; Seminati, C.; Tello, M.; Redondo, N.; Darwich, L.; Martín, M. Antimicrobial resistance profile and prevalence of extended-spectrum beta-lactamases (ESBL), AmpC beta-lactamases and colistin resistance (mcr) genes in Escherichia coli from swine between 1999 and 2018. Porc. Health Manag. 2020, 6, 8. [Google Scholar] [CrossRef] [Green Version]
  36. EUCAST, (The European Committee on Antimicrobial Susceptibility Testing). Breakpoint Tables for Interpretation of MICs and Zone Diameters; Version 10.0; The European Committee on Antimicrobial Susceptibility Testing: Basel, Switzerland, 2020. [Google Scholar]
  37. Borowiak, M.; Baumann, B.; Fischer, J.; Thomas, K.; Deneke, C.; Hammerl, J.A.; Szabo, I.; Malorny, B. Development of a Novel mcr-6 to mcr-9 Multiplex PCR and Assessment of mcr-1 to mcr-9 Occurrence in Colistin-Resistant Salmonella enterica Isolates From Environment, Feed, Animals and Food (2011–2018) in Germany. Front. Microbiol. 2020, 11, 80. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  38. Rebelo, A.R.; Bortolaia, V.; Kjeldgaard, J.S.; Pedersen, S.K.; Leekitcharoenphon, P.; Hansen, I.M.; Guerra, B.; Malorny, B.; Borowiak, M.; Hammerl, J.A.; et al. Multiplex PCR for detection of plasmid-mediated colistin resistance determinants, mcr-1, mcr-2, mcr-3, mcr-4 and mcr-5 for surveillance purposes. Eurosurveillance 2018, 23, 17-00672. [Google Scholar] [CrossRef]
Table 1. Distribution of the tested Salmonella strains in relation to minimum inhibitory concentration (MIC) values and years of isolation.
Table 1. Distribution of the tested Salmonella strains in relation to minimum inhibitory concentration (MIC) values and years of isolation.
Years of IsolationMIC Values (µg/mL)Total
≤0.51248163264128256>256
2000–2005302639140100011112
2009–201416261910100000072
2015–2020128169000000550
Total58617533110001658
Table 2. Distribution of the tested Salmonella strains in relation to minimum inhibitory concentration (MIC) values and origin of samples.
Table 2. Distribution of the tested Salmonella strains in relation to minimum inhibitory concentration (MIC) values and origin of samples.
MIC Values (µg/mL)Total
≤0.51248163264128256>256
Domestic animals434854221100014174
Wild animals14101510000000251
Environment1361000000011
Total586175331100016236
Table 3. Distribution of the tested Salmonella strains in relation to minimum inhibitory concentration (MIC) values and animal categories.
Table 3. Distribution of the tested Salmonella strains in relation to minimum inhibitory concentration (MIC) values and animal categories.
MIC Values (µg/mL)Total
≤0.51248163264128256>256
Arthropoda3145000000013
Birds10161410100000051
Mammals1415208000000663
Reptiles3026319010001098
Environment/
Feed
1361000000011
Total586175331100016236
Table 4. Distribution of the tested Salmonella strains in relation to minimum inhibitory concentration (MIC) values and subspecies.
Table 4. Distribution of the tested Salmonella strains in relation to minimum inhibitory concentration (MIC) values and subspecies.
SubspeciesMIC Values (µg/mL)Total
≤0.51248163264128256>256
enterica485961301100002202
salamae303100000007
diarizonae313000000029
houtenae3170000001214
R phase101200000004
Total586175331100016236
Table 5. Minimum inhibitory concentration (MIC) values obtained for Salmonella serovars most frequently detected in human infections in EU between 2015 and 2019.
Table 5. Minimum inhibitory concentration (MIC) values obtained for Salmonella serovars most frequently detected in human infections in EU between 2015 and 2019.
SerovarMIC Values (µg/mL)Total
≤0.51248163264128256>256
Derby4821000000116
Enteritidis0333100000010
Infantis123200000008
Newport120000000003
TMV051100000007
Typhimurium9595000000129
Legend: TMV = Typhimurium monophasic variant.
Table 6. Detailed information about the mcr-positive Salmonella isolates.
Table 6. Detailed information about the mcr-positive Salmonella isolates.
IsolateSubspeciesSerovarAnimalSampleYearMIC
(µg/mL)
mcr-1mcr-2mcr-4mcr-6mcr-8
S356houtenae1,40:z4,z23:-DonkeyOrgans2019>256-+---
S358houtenae1,40:z4,z23:-SheepOrgans2019>256-+---
S374entericaNapoliHousefly 20194-++--
S375 R phaseHousefly 20194--+--
S378 R phaseHousefly 20194--+--
S386diarizonae50:r:1,5,7Wild boarFeces2019>256+----
R43entericaTrimndonReptileFeces2002≤0.5---+-
R108entericaMemphisReptileFeces2002≤0.5-+---
R164houtenae44:z4,z23:-ReptileFeces20022----+
R161houtenae44:z4,z23:-ReptileFeces20022-+---
R173entericaSenftenbergReptileFeces2002≤0.5----+
R300diarizonae50:z:z52ReptileFeces20021+-+--
R112houtenae18:z36,z23:-ReptileFeces2002≤0.5-+---
R126diarizonae48:z4,z23:-ReptileFeces20022-+---
Total27412
Table 7. Primers and protocols employed in PCR assays.
Table 7. Primers and protocols employed in PCR assays.
Target GenePrimer NameSequence (5′-3′)Expected
Size (bp)
ProtocolsReferences
Multiplex 1mcr-1mcr1_320bp_fwAGTCCGTTTGTTCTTGTGGC320Initial denaturation at 95 °C for 10 min,
25 cycles: denaturation at 95 °C for 30 s,
annealing at 58 °C for 90 s,
elongation at 72 °C for 60 s,
Final elongation at 72 °C for 10 min.
[38]
mcr1_320bp_revAGATCCTTGGTCTCGGCTTG
mcr-2mcr2_700bp_fwCAAGTGTGTTGGTCGCAGTT715
mcr2_700bp_revTCTAGCCCGACAAGCATACC
mcr-3mcr3_900bp_fwAAATAAAAATTGTTCCGCTTATG929
mcr3_900bp_revAATGGAGATCCCCGTTTTT
mcr-4mcr4_1100bp_fwTCACTTTCATCACTGCGTTG1116
mcr4_1100bp_revTTGGTCCATGACTACCAATG
mcr-5MCR5_fwATGCGGTTGTCTGCATTTATC1644
MCR5_revTCATTGTGGTTGTCCTTTTCTG
Multiplex 2mcr-6mcr-6_mp_fwAGCTATGTCAATCCCGTGAT252Initial denaturation at 95 °C for 10 min,
30 cycles: denaturation at 95 °C for 30 s,
annealing at 55 °C for 30 s,
elongation at 72 °C for 60 s,
Final elongation step at 72 °C for 10 min.
[37]
mcr-6_mp_revATTGGCTAGGTTGTCAATC
mcr-7mcr-7_mp_fwGCCCTTCTTTTCGTTGTT551
mcr-7_mp_revGGTTGGTCTCTTTCTCGT
mcr-8mcr-8_mp_fwTCAACAATTCTACAAAGCGTG856
mcr-8_mp_revAATGCTGCGCGAATGAAG
mcr-9mcr-9_mp_fwTTCCCTTTGTTCTGGTTG1011
mcr-9_mp_revGCAGGTAATAAGTCGGTC
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Share and Cite

MDPI and ACS Style

Bertelloni, F.; Cagnoli, G.; Turchi, B.; Ebani, V.V. Low Level of Colistin Resistance and mcr Genes Presence in Salmonella spp.: Evaluation of Isolates Collected between 2000 and 2020 from Animals and Environment. Antibiotics 2022, 11, 272. https://doi.org/10.3390/antibiotics11020272

AMA Style

Bertelloni F, Cagnoli G, Turchi B, Ebani VV. Low Level of Colistin Resistance and mcr Genes Presence in Salmonella spp.: Evaluation of Isolates Collected between 2000 and 2020 from Animals and Environment. Antibiotics. 2022; 11(2):272. https://doi.org/10.3390/antibiotics11020272

Chicago/Turabian Style

Bertelloni, Fabrizio, Giulia Cagnoli, Barbara Turchi, and Valentina Virginia Ebani. 2022. "Low Level of Colistin Resistance and mcr Genes Presence in Salmonella spp.: Evaluation of Isolates Collected between 2000 and 2020 from Animals and Environment" Antibiotics 11, no. 2: 272. https://doi.org/10.3390/antibiotics11020272

APA Style

Bertelloni, F., Cagnoli, G., Turchi, B., & Ebani, V. V. (2022). Low Level of Colistin Resistance and mcr Genes Presence in Salmonella spp.: Evaluation of Isolates Collected between 2000 and 2020 from Animals and Environment. Antibiotics, 11(2), 272. https://doi.org/10.3390/antibiotics11020272

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop