Mem Inst Oswaldo Cruz, Rio de Janeiro, 113(6) june 2018
Short communication

Detection of blaNDM-1 in Stenotrophomonas maltophilia isolated from Brazilian soil

João Pedro Rueda Furlan, André Pitondo-Silva, Eliana Guedes Stehling+

Universidade de São Paulo, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Ribeirão Preto, SP, Brasil

DOI: 10.1590/0074-02760170558
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ABSTRACT

This study reports the presence of the blaNDM-1 gene in an isolate of Stenotrophomonas maltophilia obtained from a Brazilian soil, inside an IncA/C plasmid with ~ 45 Kb. To the best of our knowledge, this is the second report in the world and the first in Brazil of NDM-producing bacterium isolated from soil.

The main mechanism of resistance to β-lactams is the production of β-lactamases, which hydrolyzes these antibiotics with consequent loss of the antimicrobial effect against bacteria. Bush and Jacoby (2010) 3 classified the β-lactamases into three functional groups and New Delhi Metallo-β-Lactamase (NDM) is one of the most important and worrying of group three, due to its wide spectrum of action on β-lactam antibiotics, except for aztreonam. NDM has been extensively researched and, although it is mostly described in clinical isolates, it has also been reported in bacteria isolated from soil and water (Wang and Sun 2015 28 , Mahon et al. 2017 17 ).

The great majority of NDM-producing bacteria belongs to the Enterobacteriaceae family and nonfermenting Gram-negative bacilli (NFGNB), including Acinetobacter baumannii (Wang and Sun 2015 28 , Mahon et al. 2017 17 ). In some locations in India and China, NDM is considered endemic. In other countries such as Colombia, Egypt and Saudi Arabia there are reports of outbreaks and some cases are described worldwide, including Brazil (Dortet et al. 2014 10 ).

Due to the high levels of antimicrobial resistance, research on the mechanisms of acquisition and transfer of resistance by different species of bacteria has been increasingly widespread; however, the great majority of studies has been carried out with clinical bacteria. In the meantime, the soil microbiota is considered a great reservoir of antimicrobial resistance genes with clinical relevance, which can disseminate to other sources, such as some β-lactamases encoding genes (Humeniuk et al. 2002 12 , Wright 2007 30 ). Although the origin of Metallo-β-lactamases (MBLs) is unknown, a recent study showed the characterisation of new MBLs in bacteria isolated from soil (Gudeta et al. 2015 11 ). For this reason, this study aimed to investigate in bacteria isolated from soil the presence of the blaNDM gene, which encodes an important β-lactamase little described in soil samples.

One hundred and fifty bacterial isolates from soil samples from different plantation areas in the five Brazilian regions was obtained according to Martins et al. (2014) 18 , using MacConkey Agar (Oxoid, United Kingdom) for to select Gram-negative bacteria. Genomic DNA was extracted using the QIAamp DNA Mini Kit (QIAGEN) according to the manufacturer's instructions and the bacterial identification was performed by polymerase chain reaction (PCR) followed by DNA sequencing of the 16S and 23S rRNA genes (Weisburg et al. 1991 29 , Hunt et al. 2006 13 ). The amplicons were purified using the Illustra GFX PCR DNA Kit (GE Healthcare, USA) and submitted to DNA sequencing on an ABI 3500xL Genetic Analyzer platform (Applied Biosystems, USA). The obtained nucleotide sequences were compared with those available in GenBank using the BLAST algorithm (http://blast.ncbi.nlm.nih.gov/Blast.cgi).

Antimicrobial susceptibility testing was performed by the disc diffusion method, and the minimum inhibitory concentration (MIC) was determined by the broth dilution method, according to the Clinical and Laboratory Standards Institute (CLSI 2015). The genes blaCTX-M - (groups 1, 2, 8, and 9), blaCMY, blaKPC, blaGES, blaSHV, blaPER, blaVEB, blaOXA-48-like, blaOXA-1-like, blaIMP, blaVIM, and blaNDM were investigated by PCR using the primers and conditions described by Dallenne et al. (2010) 9 and Peirano et al. (2011) 21 . The amplicon was purified, sequenced, and aligned using Clustal Omega EMBL-EBI Multiple Sequence Alignment (http://www.ebi.ac.uk/Tools/msa/clustalo/).

Plasmid DNA was extracted using the Plasmid Midi Kit (QIAGEN) and purified after excision of the gel band with the QIAquick Gel Extraction Kit (QIAGEN), according to the manufacturer's instructions. Plasmids were screened by PCR-based replicon typing (Carattoli et al. 2005 4 ). The molecular weight of the plasmid found in the study was determined by comparison with standard plasmids of the reference strains Escherichia coli V517 (Macrina et al. 1978 16 ) and E. coli 39R861 (Pitondo-Silva et al. 2014 23 ) using BioNumerics software 5.1 (Applied Maths, Belgium), after standard 0.8 % agarose gel electrophoresis.

Among the analysed isolates, only one Stenotrophomonas maltophilia named S431 (GenBank accession number MF079262 and KY242787) was the only one that presented the blaNDM-1 gene (GenBank accession number MF589973). In addition, for this isolate, several other β-lactamases encoding genes above cited were researched and none of them was found. The blaNDM-1 gene was detected inside an IncA/C plasmid (repA gene - GenBank accession number MF085557) with ~ 45 Kb, the only plasmid in this isolate. This isolate was obtained in Ribeirão Preto city, São Paulo state, from a soil sample cultivated with corn and soy, which are widely used for animal feeding in the Southeast region of Brazil.

Among the antibiotics recommended for S. maltophilia according to CLSI (2015) 8 , the isolate S431 was resistant to minocycline and sensitive for levofloxacin and trimethoprim-sulfamethoxazole by the disc diffusion method. According to the MIC tests, S431 was resistant to ceftazidime, presenting MIC > 256 μg/mL.

S. maltophilia is an opportunistic pathogen which presents a high level of with intrinsic resistance to different classes of antibiotics. It adapts easily to different environments, and has the ability to form biofilm. This species is most commonly associated with respiratory infection, but there are reports of different types of infections resulting in high mortality rates (Brooke 2012 2 ).

The blaNDM-1 gene was previously reported in a clinical isolate of S. maltophilia from China (Yang et al. 2014 31 ). The first report of NDM-producing bacterium was in 2009 in a clinical isolate from India (Yong et al. 2009 32 ). In Brazil, the first report was in 2013 in a Providencia rettgeri isolate and afterwards, other reports were described in enterobacterial species and also in NFGNB (Carvalho-Assef et al. 2013 6 , Sampaio and Gales 2016 25 ). In the environment, NDM-producing bacteria have been reported, but there is only one report in the world of bacteria isolated from soil (Wang and Sun 2015 28 ). In isolates from different water sources, such as rivers, beach, recreational waters, wastewater and sewage, some reports in different countries have already occurred, including Brazil (Pagano et al. 2015 20 , Kittinger et al. 2016 15 , Islam et al. 2017 14 , Mahon et al. 2017 17 ).

The blaNDM gene has been detected in different plasmids, however IncA/C-type is one of the most prevalent. These plasmids stand out due to the ability of replication in different hosts and because they are commonly reported in multi-drug resistant (MDR) bacteria (Carattoli 2013 5 ). In Brazil, the association between the blaNDM gene and IncA/C (Pereira et al. 2015 22 ) and other groups of plasmids such as IncH12, IncP, IncW, IncN and IncF has already been reported (Carvalho-Assef et al. 2014 7 , Quiles et al. 2015 24 ).

The blaNDM gene is increasingly being reported worldwide, predominantly in clinical isolates, where most of the studies are concentrated. There are few reports of blaNDM in environmental bacteria, probably due to few studies in these sources, being the most of them focused on isolates from water (Walsh et al. 2011 27 , Kittinger et al. 2016 15 , Islam et al. 2017 14 , Mahon et al. 2017 17 ). Among the β-lactam antibiotics, the carbapenems have a broad spectrum of action and are often used against infections caused by bacteria producing other β-lactamases (Meletis 2016 19 ). Resistance to these antibiotics by the production of β-lactamases, especially NDM, has become a major challenge in the treatment of different bacterial infections (Walsh and Toleman 2011 26 ).

The blaNDM gene has been found in different plasmids, which frequently carries other resistance genes causing a rapid spread of these genes (Walsh et al. 2011 27 , Berrazeg et al. 2014 1 ). As the blaNDM-1 gene was found inserted into a plasmid of a soil bacterium, it can potentially be transferred to other bacteria and disseminated in the environment and other sources, including water and humans, being for this reason a human health hazard. Besides that, due to the intrinsic resistance to imipenem, which it is associated with the MBL L1, S. maltophila can act as a silent disseminator of blaNDM-1, avoiding the detection of this gene in laboratories.

MDR bacteria are becoming widespread in the environment due to the incidence of antibiotic used in agriculture and these bacteria can migrate to the hospital environment. Since S431 was isolated from a soil sample cultivated with corn and soy, which are widely used for animal feeding in the Southeast region of Brazil, the blaNDM-1 can spread to different environments, which is of great concern. All reports in Brazil were in clinical isolates, with the exception of Klebsiella pneumoniae isolated from superficial beach water in Rio de Janeiro (Pagano et al. 2015 20 ).

To the best of our knowledge, there is only one study reporting NDM-producing Acinetobacter calcoaceticus and Acinetobacter junii in livestock soil samples from China (Wang and Sun 2015 28 ). As far as we know, this is the second report in the world and the first in Brazil of NDM-producing bacterium isolated from soil.

 

ACKNOWLEDGEMENTS

To JDD Pitout (University of Calgary, Calgary, AB, Canada) for kindly providing the β-lactamase control strain used in this study. We also thank John Carpenter, Ribeirão Preto, SP, Brazil, for the English revision.

 

AUTHORS' CONTRIBUTION

JPRF and APS performed the laboratory work on which this short communication is based; JPRF, APS and EGS analysed the results; EGS supervised the work; JPRF and EGS wrote the paper.

 

REFERENCES
01. Berrazeg M, Diene S, Medjahed L, Parola P, Drissi M, Raoult D, et al. New Delhi Metallo-beta-lactamase around the world: an eReview using Google Maps. Euro Surveill. 2014; 19(20): pii:20809.

02. Brooke JS. Stenotrophomonas maltophilia: an emerging global opportunistic pathogen. Clin Microbiol Rev. 2012; 25(1): 2-41.

03. Bush K, Jacoby GA. Updated functional classification of β-lactamases. Antimicrob Agents Chemother. 2010; 54(3): 969-76.

04. Carattoli A, Bertini A, Villa L, Falbo V, Hopkins KL, Threlfall EJ. Identification of plasmids by PCR-based replicon typing. J Microbiol Methods. 2005; 63(3): 219-28.

05. Carattoli A. Plasmids and the spread of resistance. Int J Med Microbiol. 2013; 303(6-7): 298-304.

06. Carvalho-Assef AP, Pereira PS, Albano RM, Berião GC, Chagas TP, Timm LN, et al. Isolation of NDM-producing Providencia rettgeri in Brazil. J Antimicrob Chemother. 2013; 68(12): 2956-7.

07. Carvalho-Assef AP, Pereira PS, Albano RM, Berião GC, Tavares CP, Chasgas TP, et al. Detection of NDM-1-, CTX-M-15-, and qnrB4-producing Enterobacter hormaechei isolates in Brazil. Antimicrob Agents Chemother. 2014; 58(4): 2475-6.

08. CLSI - Clinical and Laboratory Standards Institute. Performance standards for antimicrobial susceptibility resting: twenty-fifth informational supplement. CLSI document M100-S25. Wayne: Clinical and Laboratory Standards Institute; 2015.

09. Dallenne C, da Costa A, Decré D, Favier C, Arlet G. Development of a set of multiplex PCR assays for the detection of genes enconding important beta-lactamases in enterobacteriaceae. J Antimicrob Chemother. 2010; 65(3): 490-5.

10. Dortet L, Poirel L, Nordmann P. Worldwide dissemination of the NDM-type carbapenemases in Gram-negative bacteria. Biomed Res Int. 2014; 2014: 249856.

11. Gudeta DD, Bortolaia V, Amos G, Wellington EM, Brandt KK, Poirel L, et al. The soil microbiota harbors a diversity of carbapenem-hydrolyzing β-lactamases of potential clinical relevance. Antimicrob Agents Chemother. 2015; 60(1): 151-60.
12. Humeniuk C, Arlet G, Gautier VP, Grimont RL, Philippon A. Beta-lactamases of Kluyvera ascorbata, probable progenitors of some plasmid-encoded CTX-M types. Antimicrob Agents Chemother. 2002; 46(9): 3045-9.
13. Hunt DE, Klepac-Ceraj V, Acinas SG, Gautier C, Bertilsson S, Polz MF. Evaluation of 23S rRNA PCR primers for use in phylogenetic studies of bacterial diversity. Appl Environ Microbiol. 2006; 72(3): 2221-5.
14. Islam MA, Islam M, Hasan R, Hossain MI, Nabi A, Rahman M, et al. Environmental spread of New Delhi metallo-β-lactamase-1-producing multidrug-resistant bacteria in Dhaka, Bangladesh. Appl Environ Microbiol. 2017; 83(15): e00793-17.
15. Kittinger C, Lipp M, Folli B, Kirschner A, Baumert R, Galler H, et al. Enterobacteriaceae isolated from the River Danube: antibiotic resistances, with a focus on the presence of ESBL and carbapenemases. PLoS One. 2016; 11(11): e0165820.
16. Macrina FL, Kopecko DJ, Jones KR, Ayers DJ, McCowen SM. A multiple plasmid-containing Escherichia coli strain: convenient source of size reference plasmid molecules. Plasmid. 1978; 1(3): 417-20.
17. Mahon BM, Brehony C, McGrath E, Killeen J, Cormican M, Hickey P, et al. Indistinguishable NDM-producing Escherichia coli isolated from recreational waters, sewage, and a clinical specimen in Ireland, 2016 to 2017. Euro Surveill. 2017; 22(15): pii: 30513.
18. Martins VV, Pitondo-Silva A, Manço LM, Falcão JP, Freitas SS, da Silveira WD, et al. Pathogenic potential and genetic diversity of environmental and clinical isolates of Pseudomonas aeruginosa. APMIS. 2014; 122(2): 92-100.
19. Meletis G. Carbapenem resistance: overview of the problem and future perspectives. Ther Adv Infect Dis. 2016; 3(1):15-21.
20. Pagano M, Poirel L, Martins AF, Rozales FP, Zavascki AP, Barth AL, et al. Emergence of NDM-1-producing Acinetobacter pittii in Brazil. Int J Antimicrob Agents. 2015; 45(4): 444-5.
21. Peirano G, Ahmed-Bentley J, Woodford N, Pitout JD. New Delhi metallo-β-lactamase from traveler returning to Canada. Emerg Infect Dis. 2011; 17(2): 242-4.
22. Pereira PS, Borghi M, Albano RM, Lopes JC, Silveira MC, Marques EA, et al. Coproduction of NDM-1 and KPC-2 in Enterobacter hormaechei from Brazil. Microb Drug Resist. 2015; 21(2): 234-6.
23. Pitondo-Silva A, Martins VV, Fernandes AF, Stehling EG. High level of resistance to aztreonam and ticarcillin in Pseudomonas aeruginosa isolated from soil of different crops in Brazil. Sci Total Environ. 2014; 1(473-474): 155-8.
24. Quiles MG, Rocchetti TT, Fehlberg LC, Kusano EJ, Chebabo A, Pereira RM, et al. Unusual association of NDM-1 with KPC-2 and armA among Brazilian Enterobacteriaceae isolates. Braz J Med Biol Res. 2015; 48(2): 174-7.
25. Sampaio JL, Gales AC. Antimicrobial resistance in Enterobacteriaceae in Brazil: focus on β-lactams and polymyxins. Braz J Microbiol. 2016; 47(Suppl. 1): 31-7.
26. Walsh TR, Toleman MA. The new medical challenge: why NDM-1? Why Indian? Expert Rev Anti Infect Ther. 2011; 9: 137-41.
27. Walsh TR, Weeks J, Livermore DM, Toleman MA. Dissemination of NDM-1 positive bacteria in the New Delhi environment and its implications for human health: an environmental point prevalence study. Lancet Infect Dis. 2011; 11: 355-62.
28. Wang B, Sun D. Detection of NDM-1 carbapenemase-producing Acinetobacter calcoaceticus and Acinetobacter junii in environmental samples from livestock farms. J Antimicrob Chemother. 2015; 70(2): 611-3.
29. Weisburg WG, Barns SM, Pelletier BA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol. 1991; 173: 697-703.
30. Wright GD. The antibiotic resistome: the nexus of chemical and genetic diversity. Nat Rev Microbiol. 2007; 5: 175-86.
31. Yang Z, Liu W, Cui Q, Niu W, Li H, Zhao X, et al. Prevalence and detection of Stenotrophomonas maltophilia carrying metallo-β-lactamase blaL1 in Beijing, China. Front Microbiol. 2014; 9(5): 692.
32. Yong D, Toleman MA, Giske CG, Cho HS, Sundman K, Lee K, et al. Characterization of a new metallo-beta-lactamase gene, bla(NDM-1), and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India. Antimicrob Agents Chemother. 2009; 53(12): 5046-54.

Financial support: FAPESP [grant no. 2015/18990-2].
+ Corresponding author: elianags@usp.br
Received 22 December 2017
Accepted 9 March 2018

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