Next Article in Journal
Evaluation of Four Lateral Flow Assays for the Detection of Legionella Urinary Antigen
Next Article in Special Issue
Prevalence and Multidrug Resistance Pattern of Methicillin Resistant S. aureus Isolated from Frozen Chicken Meat in Bangladesh
Previous Article in Journal
Development of a Well-Characterized Rhesus Macaque Model of Ebola Virus Disease for Support of Product Development
Previous Article in Special Issue
Phenotypic Antimicrobial Susceptibility of Escherichia coli from Raw Meats, Ready-to-Eat Meats, and Their Related Samples in One Health Context
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Microorganisms
Volume 9
Issue 3
10.3390/microorganisms9030491
microorganisms-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Exploring Antibiotic Resistance Diversity in Leuconostoc spp. by a Genome-Based Approach: Focus on the lsaA Gene

by
Elisa Salvetti
1,†,
Ilenia Campedelli
2,†,
Ilaria Larini
1,
Giada Conedera
1 and
Sandra Torriani
1,*
1
Department of Biotechnology, University of Verona, 37134 Verona, Italy
2
Microbion srl, San Giovanni Lupatoto, 37057 Verona, Italy
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Microorganisms 2021, 9(3), 491; https://doi.org/10.3390/microorganisms9030491
Submission received: 10 February 2021 / Revised: 19 February 2021 / Accepted: 22 February 2021 / Published: 26 February 2021
(This article belongs to the Special Issue Antimicrobial Resistance in the Food Production Chain )
Browse Figures
Versions Notes

Abstract

:
Leuconostoc spp. are environmental microorganisms commonly associated with fermented foods. Absence of antibiotic resistance (AR) in bacteria is a critical issue for global food safety. Herein, we updated the occurrence of AR genes in the Leuconostoc genus through in silico analyses of the genomes of 17 type strains. A total of 131 putative AR traits associated with the main clinically relevant antibiotics were detected. We found, for the first time, the lsaA gene in L. fallax ATCC 700006T and L. pseudomesenteroides NCDO 768T. Their amino acid sequences displayed high similarities (59.07% and 52.21%) with LsaA of Enterococcus faecalis V583, involved in clindamycin (CLI) and quinupristin-dalfopristin (QUD) resistance. This trait has different distribution patterns in Leuconostoc nontype strains—i.e., L. pseudomesenteroides, L. lactis and L. falkenbergense isolates from fermented vegetables, cheeses, and starters. To better explore the role of lsaA, MIC for CLI and QUD were assessed in ATCC 700006T and NCDO 768T; both strains were resistant towards CLI, potentially linking lsaA to their resistant phenotype. Contrarily, NCDO 768T was sensitive towards QUD; however, expression of lsaA increased in presence of this antibiotic, indicating an active involvement of this trait and thus suggesting a revision of the QUD thresholds for this species.

1. Introduction

Leuconostoc spp. belong to the functional group of Lactic Acid Bacteria (LAB) and are generally found on green vegetation and roots; from this natural habitat, they disseminate to various plant niches, such as lychee fruits (L. litchi [1]), palm wine (L. palmae [2]) cabbage and rutabaga (L. rapi [3]), cucumbers, carrots, olives, silage, soybeans (L. mesenteroides strains [4,5]) coffee beans (L. holzapfelii [6]) and quinoa samples (L. lactis and L. mesenteroides isolates, [7]) where they can actively participate in the fermentation process. In particular, Leuconostoc spp. are added as starters cultures for the production of sauerkraut and kimchi, from which the type strains of L. fallax [8], L. kimchii [9], L. inhae [10], L. mesenteroides subsp. jonggajibkimchii [11], and L. miyukkimchii [12], have been isolated.
Leuconostoc spp. have been also associated with foods of animal origin including dairy (L. citreum, L. lactis, L. mesenteroides, L. falkebergense [13,14]), fish (i.e., L. mesenteroides in molluscs, [5]) and both in fresh and fermented meat products (L. carnosum, L. citreum, L. mesenteroides and L. gelidum; [15,16,17]). In particular, their impact on dairy technology is mainly related to their ability to produce CO2, which is responsible for the eye formation in some cheeses, and other aroma compounds, such as diacetyl and acetoin, thus significantly contributing to the flavor of the final product [18].
Due to their presence in fermented foods and associated history of safe consumption, leuconostocs are Generally Regarded As Safe (GRAS) microorganisms by the US Food and Drug Administration (FDA); further, some species have the Qualified Presumption of Safety (QPS) status by the European Food Safety Authority (EFSA) (https://zenodo.org/record/3828466#.YAhMB-lKgc8; accessed in 26 February 2021) and are also included in the Inventory of Microbial Food Cultures with Safety Demonstration in Fermented Food Products by the International Dairy Federation [13].
Despite their important roles and safety in the production of fermented foods, these strains have been also associated with negative aspects on human health, including the production of undesirable compounds, such as biogenic amines [19], and the expression of antimicrobial resistance mechanisms [20]. Leuconostoc spp. have been frequently found in infections caused by multiple microorganisms in patients following vancomycin treatment, towards which they are intrinsically resistant due to the presence of pentadepsipeptide with D-Lactate at the C-terminal in the peptidoglycan instead of a D-Alanine [18]. Generally, leuconostocs are susceptible to beta-lactams (ampicillin and penicillin [21]), and to antibiotics inhibiting protein synthesis (i.e., erythromycin, chloramphenicol, clindamycin and tetracycline [22,23]). However, resistant phenotypes were detected in strains of L. pseudomesenteroides, L. citreum and L. mesenteroides isolated from table olives and dairy products towards chloramphenicol, ciprofloxacin, clindamycin, erythromycin, gentamicin, kanamycin, oxacillin, nitrofurantoin, rifampicin, streptomycin, tetracycline, teicoplanin, trimethoprim and virginiamycin [20,21,22,24,25]; further, acquired resistance to tetracycline and erythromycin has been reported for L. mesenteroides strains from artisanal cheeses [20].
From this perspective, the present study aimed to explore the occurrence of putative antibiotic resistance genes (ARGs) in the genomes of 17 Leuconostoc type strains through in silico analyses. This genome-wide comprehensive survey allowed the detection of the lsaA gene, responsible for clindamycin and quinupristin-dalfopristin resistance, whose distribution pattern was further investigated in L. pseudomesenteroides, L. fallax and related strains, and its role in antibiotic resistance was phenotypically validated. The critical evaluation of genotypic and phenotypic data as it is performed within this study may represent an essential step to counteract the horizontal spread of antibiotic resistance (AR) traits from food-grade technological Leuconostoc strains towards foodborne commensals and other pathogenic bacteria.

2. Materials and Methods

2.1. Genome Sequence Analysis to Retrieve the Antibiotic Resistance Genes

The genome sequences of the 17 available type strains and their annotations for the Leuconostoc genus (13 species and 4 subspecies) were downloaded from NCBI using the accession number reported in Table 1. The annotated sequences were employed to query the Comprehensive Antibiotic Resistance Database (CARD, version 3.1.0, https://card.mcmaster.ca/download, protein homolog model; downloaded in December 2020) [26], through the Basic Local Alignment Search Tool (BLAST, https://blast.ncbi.nlm.nih.gov, accessed in December 2020) in order to identify all AR genes. A trait was annotated as a putative AR determinant according to its BLASTp hit in CARD with a threshold of amino acid sequence identity > 30%, e-value < 1 × 10−5 and query coverage > 70% [27]. In addition, the amino acid sequences of all ARGs retrieved from CARD, resulting in a reference dataset of 2702 amino acid sequences (including aminoglycosides, lincosamides, macrolides, streptogramins, tetracyclines, phenicols, β-lactams, glycopeptides and folate pathway inhibitors, such as trimethoprim) were aligned against the annotated genome sequences of the dataset, and the BLASTp hits were filtered as described above. To minimize putative false negative or false positive outputs, only the putative AR determinants obtained from both approaches were considered for subsequent analyses. Moreover, the obtained data were filtered for drug class, AMR genes and resistance mechanisms, selecting only recognized EFSA antibiotics and discarding efflux pumps genes, which are too generic.

2.2. Analysis of the lsaA Gene

All the amino acid sequences of lsaA, lsaB and lsaC retrieved in the annotated genomes were aligned with Clustal Omega online tool, fully gap-removed with Jalview (v 2.11.1.3), and then evolutionary trees were constructed with MEGAX (v 10.1.8) using the UPGMA method with default parameters [28].
WP_031941011.1 of L. pseudomesenteroides NCDO 768T and WP_010008491.1 of L. fallax ATCC 700006T were used as queries to perform a BLASTp search against the nonredundant protein sequences (nr) database in NCBI, selecting “Leuconostoc (taxid:1243)” in the “organisms” section, query coverage > 60% and identity > 50%. To further explore intraspecies similarity, WP_031941011.1 and WP_010008491.1 were used as queries in a BLASTp search with the same parameters but restricting to organism “Leuconostoc pseudomesenteroides (taxid:33968)” for the first one and “Leuconostoc fallax (taxid:1251)” for the last. The search results at the time of the study (29 January 2021) were downloaded for phylogenetic analysis, adding the LsaA protein of Enterococcus faecalis V583 [29]. Sequence alignments and phylogenetic tree construction were performed as described above [28]. Finally, the genomes associated with the previous BLASTp hits and the genome of E. faecalis V583 were downloaded from NCBI and annotated through Rapid Annotations using Subsystems Technology (RAST, http://RAST.nmpdr.org, accessed on 26 February 2021) server [30] in order to characterize 30 kpb upstream and downstream sequences flanking the lsaA gene. A tBLASTx alignment against genomes to search lsaA was performed, then a BLASTx analysis of the mobile elements detected was carried out to identify transposases or other elements that could be responsible for the transfer of this trait (File S1).

2.3. Bacterial Strains and Growth Conditions

A collection of 11 type strains of the Leuconostoc genus was set up based on the available strains in the collection of the Dept. of Biotechnology, University of Verona (obtained from the BCCM/LMG Bacteria Collection, Ghent, Belgium and from the Spanish Type Culture Collection CECT, Valencia, Spain). Leuconostoc strains were grown in de Man–Rogosa–Sharpe (MRS, Fluka, Italy) medium at 27 °C for 48 h and kept in liquid cultures with 20% (w/vol) glycerol at −80 °C for long term storage.

2.4. Antimicrobial Susceptibility Testing

The minimum inhibitory concentrations (MICs) of clindamycin-CLI and quinupristin-dalfopristin-QUD were determined using microdilution broth methods according to Clinical and Laboratory Standard Institute (CLSI; www.clsi.org, accessed on 26 February 2021), the European Committee on Antimicrobial Susceptibility Testing (EUCAST), and ISO standard. In particular, 96-well microtiter plates containing serial two-fold dilutions of CLI and QUD antibiotics were prepared following the instructions reported by [31]. Briefly, 320 μg/mL for CLI and 160 μg/mL for QUD antibiotic stocks at different concentrations were prepared; starting from each initial stock, 10 dilutions were produced to obtain all the antibiotic solutions necessary for the preparation of the microtiter plates. Finally, 50 μL of each antibiotic solution in the 10 different concentrations were distributed in the microtiter plates. MICs were evaluated in LAB susceptibility test medium (LSM) [32], a mixed formulation containing Iso-Sensitest broth (90%) and MRS broth (10%) as described in ISO 10932 IDF 223 document and recommended by EFSA [33]. Briefly, individual Leuconostoc colonies were grown overnight at 27 °C in MRS broth; thus, the suspension’s turbidity was adjusted to an OD600 equal to 0.2, corresponding to a concentration of about 1 × 108 cfu/mL. This suspension was diluted 1:100 in LSM broth, and then 50 μL of this inoculum was added to each well of the microtiter plates prepared as described above (final concentration 5 × 105 cfu/mL). This test was performed in triplicate for each strain of the collection. Plates were incubated under aerobic conditions at 27 °C for 48 h. MICs were read as the lowest concentration of an antimicrobial agent at which visible growth was inhibited. Epidemiological cut-off (ECOFF) values for CLI were retrieved from [33], while breakpoint for QUD was adopted from [23] and [34].

2.5. RNA Isolation and Real-Time PCR in L. pseudomesenteroides LMG 11482T (=NCDO 768T)

The relative quantification of the lsaA gene expression was performed for the strain L. pseudomesenteroides LMG 11482T (=NCDO 768T). Cell cultures of this strain were grown at 27 °C in MRS broth under three different conditions: in free-antibiotic medium, in the presence of CLI (4 μg/mL) and QUD (1 μg/mL). The cells were collected in two different growth stages corresponding to OD600 values equal to 0.2 and 0.8. For total RNA extraction, cells were washed with 1 mL of 10 mM Tris (pH = 8), which was prepared in sterile diethyl pyrocarbonate (DEPC)-treated water. The pellet was treated with 500 μL of lysozyme (10 mg/mL) and was incubated at 37 °C for 1 h. After centrifugation (4 °C, 8000 rpm, 4 min) and elimination of the supernatant, the pellet was treated with 1 mL of Trizol solution and was incubated for 5 min at room temperature. Subsequently, 200 μL of chloroform were added and vigorously mixed. After centrifugation (4 °C, 10,000 rpm, 15 min), the supernatant was treated with 500 μL of isopropyl alcohol and left for 10 min at room temperature. Total RNA was pelleted by centrifugation at 13,000 rpm for 10 min at 4 °C, washed with 1 mL of ethanol 75%, and dissolved in 35 μL of sterile water (RNAse- and DNAse-free). The purification and transcription of the RNA was performed using, respectively, Turbo DNA-free (ThermoFisher Scientific Inc., Waltham, MA, USA) and ImProm-IITM Reverse Transcriptase (Promega, Madison, WI, USA) kit, following the manufacturer’s instructions.
All real-time PCR reactions were performed using a Light Cycler Nano (Roche, Switzerland) with a FastStart Essential DNA Green Master added with the primers 16S-F /16S-R (amplicon size: 157 pb, [35]) and lsaA-F (5′-CCCCAGACAATTCAAGACTC-3′) and lsaA-R (5′-CTCGAAAATTTGCGCCAGAG-3′), specifically designed in the present study using the Oligo Analyzer software (https://eu.idtdna.com, accessed on 26 February 2021) (amplicon size: 137 bp). The amplification program included an initial incubation at 94 °C for 6 min followed by 45 cycles at 95 °C for 30 s, 60 °C for 30 s and 72 °C for 45 s, and finally 95 °C for 10 s. At the end of the PCR, a dissociation curve was generated to verify the presence of unspecific products or primer dimers. Two independent biological replicates were performed for each growth condition and data were obtained from three technical replicates per sample. The analysis of gene expression was performed using the 2−∆∆ct method [36] with 16S rRNA as internal control.

3. Results

3.1. In Silico Prediction of ARGs in the Leuconostoc Genus

The annotated sequences of the 17 type strains of the Leuconostoc genus were downloaded from NCBI database and aligned against the protein sequences in CARD to retrieve all putative AR genes carried by these strains. Based on the selection criteria described in the Materials and Methods section, a total of 3197 hits belonging to 131 protein sequences were identified and they were mainly putatively involved in the resistance for aminoglycosides (Am) (n = 1), beta-lactams (Bl) (n = 1), diaminopyrimidines (Di) (n = 33), glycopeptides (Gl) (n = 46), lincosamides (Li) (n = 1), erythromycin (Li-Ma-St) (n = 6), chloramphenicol (Ph) (n = 8), rifampicin (Ri) (n = 2) and streptogramins (St) (n = 8). Moreover, several genes annotated as ABC-F ATP-binding cassette ribosomal protection protein ABC cassettes (n = 25) were retrieved due to their roles in resistance to lincosamides, macrolides, oxazolidinones, chloramphenicol, streptogramins and tetracyclines (Figure 1 and Table S1).
The analysis revealed the presence of 1361 hits corresponding to 59 drug efflux pumps proteins in the 17 type strains examined, belonging to the Major Facilitator Superfamily (MFS) antibiotic efflux pump, Outer Membrane Porin (Opr), Resistance-Nodulation-cell Division (RND) antibiotic efflux pump, Small Multidrug Resistance (SMR) antibiotic efflux pump, ATP-Binding Cassette (ABC) antibiotic efflux pump and Multidrug And Toxic compound Extrusion (MATE) transporter (Figure S1).
Among the hits obtained, WP_031941011.1 of L. pseudomesenteroides NCDO 768T and WP_010008491.1 of L. fallax ATCC 700006T were found to have high similarities (51.8% and 58.9%, respectively) with the LsaA protein of E. faecalis ATCC 29212 in the CARD database and as such were further investigated.

3.2. Distribution Patterns of the lsaA Gene in the Leuconostoc Genus

ARG search results showed that all the genomes in the dataset displayed genes annotated as lsaA, lsaB and lsaC, coding for ATP-binding cassette. In Gram-positive bacteria, these genes code for a subgroup of ABC (ATP-binding cassette) transporters which can mediate resistance to antibiotics that bind to the 50S subunit of the ribosome, including ketolides, lincosamides, macrolides, oxazolidinones, phenicols, pleuromutilins and group A and B streptogramins [37]. To better understand the relationship between these traits, a more targeted evolutionary analysis based on the amino acid sequences of genes annotated as lsaA, lsaB and lsaC in the Leuconostoc type strains was conducted, using as references amino acid sequences of antibiotic-resistant genes lsaA, lsaB and lsaC of E. faecalis V583, Mammaliicoccus sciuri (plasmid) pSCFS1 and Streptococcus agalactiae UCN70, respectively [29]. The phylogenetic analysis revealed that the LsaA proteins in L. pseudomesenteroides NCDO 768T and in L. fallax ATCC 700006T are related to LsaA of E. faecalis, involved in CLI and QUD resistance, displaying 52% and 59% similarities (query coverage of 97% and 98%), respectively (Figure 2).
The alignment of the LsaA amino acid sequences of the two Leuconostoc type strains and E. faecalis V583 revealed the presence of conserved Walker A and B motifs, which are peculiar for ABC transporters, and they are involved in the binding and hydrolysis of ATP [29] (Figure 3).
In addition to its presence in the type strains of L. pseudomesenteroides and L. fallax, the analysis of distribution patterns of LsaA in the Leuconostoc genus (BLASTp, coverage > 60% and identity > 50%) showed that this trait occurs in 10 other strains of L. pseudomesenteroides. Nontype isolates are mainly associated with plant-derived fermented foods (strains TR070 and CBA3630, isolated from sourdough and kimchi, respectively), dairy products (1159 and PS12, isolated from a Danish dairy starter culture; 4882, derived from a French dairy starter culture; KMB_610, isolated from Bryndza cheese, a Slovak sheep milk cheese), clinical (AMBR10 from human adenoid) and environmental samples (AS01afH2WH_44, from the metagenomic analysis of anaerobic digestion of organic wastes). Interestingly, BLASTp analysis revealed that LsaA proteins with high similarity values were also present in seven strains of L. lactis mainly associated with kimchi (strains CCK940, Wikim40 and CBA3625), raw plant materials (SBC001 and AV1n, isolated from chive and fruit, respectively), and from human sources (strain 10012628_160229_C9 from fecal samples). Plant-derived fermented foods are suppliers of other strains harboring LsaA, such as L. falkebergense LMG 18969, associated with fermented string beans, and “L. garlicum” KFRI01, isolated from kimchi (Figure 4).

3.3. Analysis of Flanking Regions of the lsaA Gene

The genome sequences of the 23 Leuconostoc strains harboring lsaA belonging to species L. lactis, L. falkebergense, L. pseudomesenteroides, and L. fallax (reported in Figure 4) were further explored to characterize the up- and downstream flanking regions of lsaA. Around 60 kb (30kb up- and 30 kb downstream of lsaA) were selected and the open reading frames (orfs) were further investigated through tBLASTn and BLASTx analyses. Strains whose genome regions exhibit putative mobile elements near to lsaA are depicted in Figure 5. Interestingly, the genome analysis of L. lactis CCK940 and Wikim40 and “L. garlicum” KFRI01 revealed the presence of several transposases (two copies in CCK940, three in KFRI01 and four in Wikim40) downstream of lsaA (between ~300 and ~1200 bp), while two genes upstream of lsaA were annotated as hypothetical proteins and a gene annotated as protease were found. In each strain, at least one of the genes annotated as transposases belongs to the IS3 family. Further downstream, the three genomes contained two genes reported as ABC transporter and carboxypeptidase, respectively.
As for the other strains, mobile elements were detected in the flaking regions (but more distant compared to L. lactis and L. garlicum strains) of lsaA in five strains of L. pseudomesenteroides. More specifically, L. pseudomesenteroides 4882 displayed a gene annotated as a IS30 family transposase at 12 kb downstream of lsaA; other downstream genes between lsaA and IS30 were annotated as putative membrane spanning proteins, ABC transporters, hypothetical proteins, GntR transcriptional regulators and ATPase. Strains LMG 11483, TR070, CBA3630 and NCDO 768T showed similar gene dispositions: a mobile element annotated as transposase (two in CBA3630) was detected at 30 kb upstream of lsaA, while other upstream genes were annotated as oxidoreductase, hypothetical protein and PadR transcriptional regulator; downstream of lsaA, genes were annotated as putative membrane proteins, ABC transporters, hypothetical proteins, GntR-like transcriptional regulators and ATPase. Sequence surrounding lsaA in L. fallax ATCC 700006T included genes annotated as general stress protein, MFS multidrug efflux transporter, reductase (upstream of lsaA), Xre transcriptional regulator, hypothetical proteins and, again, reductase (downstream of lsaA). E. faecalis V583 displayed two genes annotated as peptidase and two genes annotated as dehydratase upstream of lsaA, while four genes annotated as an LSU ribosomal protein, cell wall protein, AraC transcriptional regulator and permease were found downstream of lsaA.

3.4. Determination of Phenotypic Resistance towards CLI and QUD

To validate the genomic data, the MIC values for CLI and QUD were determined through broth microdilution plates for 11 type strains of the Leuconostoc genus available in the strain collection of the Dept. of Biotechnology (University of Verona). The MIC values obtained for these two antibiotics and the relative ECOFFs are reported in Table 2. L. fallax LMG 13177T (=ATCC 700006T) and L. pseudomesenteroides LMG 11482T (=NCDO 768T) showed resistance to clindamycin, as they were characterized by MIC values equal to 16 and 4 μg/mL (ECOFF = 1), respectively. In addition, LMG 11482T (= NCDO 768T) also displayed resistance towards quinupristin-dalfopristin (MIC = 8 μg/mL), while LMG 11482T had an MIC = 2, which is below the cut-off value for this antibiotic (ECOFF = 4 μg/mL).

3.5. Quantification of lsaA Expression in L. pseudomesenteroides LMG 11482T (=NCDO 768T)

Since in E. faecalis the lsaA gene is associated with resistance to CLI and QUD [29], it was necessary to clarify its role in L. pseudomesenteroides LMG 11482T (= NCDO 768T), which was resistant to CLI but susceptible to QUD. For this reason, the relative quantification of lsaA expression was performed in the presence and absence of these antimicrobial substances, using the 16S rRNA gene as internal control (Figure 6). This analysis revealed an increased expression of lsaA in the presence of both antibiotics either in the exponential (OD600 = 0.2) and stationary (OD600 = 0.8) growth phase of L. pseudomesenteroides LMG 11482T (= NCDO 768T), indicating an involvement of lsaA in LMG 11482T (= NCDO 768T) when exposed to QUD.

4. Discussion

Antibiotics represent one of the largest therapeutic categories used in human and veterinary medicine for the treatment of infectious diseases caused by bacterial agents. However, overprescribing and misuse of antibiotics in medicine, aquaculture and agriculture has tremendously raised the emergence and spread of antibiotic-resistant bacteria, which constitute a critical worldwide issue in the one-health perspective where human health is directly linked to the health of animals and ecosystems [43]. In this framework, foods may act as vehicles for the transmission of AR bacteria and resistance genes along the food chain to the human gastrointestinal tract where the effectiveness of therapies could be compromised [44]. In particular, AR microorganisms can be present in food as native microbiota of raw materials, or as cultures intentionally added during food processing, or as environmental contaminants [45].
Among food-grade bacteria, Leuconostoc spp. have been extensively used as starter cultures and probiotics due to their long history of safe use and several species have QPS status by EFSA (https://zenodo.org/record/3828466#.YAhMB-lKgc8, accessed in 26 February 2021). However, limited information on the antimicrobial susceptibility profiles of Leuconostoc spp. is available, as well as their possible involvement in the dissemination of AR determinants between bacteria.
To tackle this issue, genome sequence analyses of the 17 Leuconostoc type strains available to date (January 2021) were carried out to improve current knowledge of the AR features of this genus. This analysis revealed the presence of 131 gene sequences putatively associated with resistance to the main important antibiotics used in medicine, including clindamycin, erythromycin, penicillins, streptogramins, and vancomycin (to which Leuconostoc spp. are intrinsically resistant [18]). In particular, the genome sequence analysis revealed the presence of the gene dfr and genes coding for penicillin-binding proteins (PBP) in all the type strains analyzed, which are involved in trimethoprim and β-lactams resistance, respectively. However, the presence of these determinants is not necessary linked to the resistance, as only mutated DHFR enzymes and PBPs are able to avoid the antibiotic effect on microbial growth [46,47]. Concerning the group of macrolides, lincosamides and streptogramins, traits detected included ermD, coding for an rRNA methylase [48], vat genes, coding for acetyltransferase enzymes [48], and vga and lmr genes coding for Major Facilitators Superfamily (MSF) transporters that pump these antibiotics out of cells [49].
Among the hits retrieved, the manual annotation and targeted similarity analysis revealed, for the first time, the presence of the lsaA gene in L. pseudomesenteroides NCDO 768T and L. fallax ATCC 700006T, whose amino acid sequences displayed high similarity values (51.9% and 58.9%) with the corresponding sequence of lsaA in E. faecalis ATCC 29212 available in CARD. This gene encodes an ATP-binding cassette F (ABC-F) protein, where the ABC portions are not fused or genetically associated with transmembrane domains [37]. This genetic makeup is more closely linked to biological processes, such as DNA repair, enzyme regulation and translational control, rather than transport as conventional ABC transporters [37]. In Gram-positive pathogens (staphylococci, streptococci and enterococci), and antibiotic-producing bacteria (e.g., streptomycetes), a subgroup of ABC-F proteins mediates resistance to antibiotics that exert their action on the ribosome, including ketolides, lincosamides, macrolides, oxazolidinones, phenicols, pleuromutilins, and streptogramins of groups A and B [37]. More specifically, the lsaA gene was found to be responsible for the intrinsic resistance towards CLI and QUD in E. faecalis, where the proposed mechanism of protection was related to the ATP-energized efflux of these antibiotics out of the cell [29]. Comparison of LsaA amino acid sequence of L. pseudomesenteroides NCDO 768T and L. fallax ATCC 700006T with that of E. faecalis highlighted the presence of conserved Walker A and B ATP-binding motifs, suggesting that this gene could mediate a phenotypic resistance towards CLI and QUD in these two strains through the efflux of these antibiotics, as observed in E. faecalis.
Distribution analysis of this trait in the genus Leuconostoc revealed that other L. pseudomesenteroides nontype strains (n = 5), as well as isolates of L. lactis (7), L. falkebergenes (1) and “L. garlicum” (1) harbored lsaA; of these, 69.6% originated from raw or fermented foods (which are also the isolation sources of L. fallax [8]), corroborating the prospect that foods constitute vehicles for (putative) ARGs detected in food-grade bacteria. This scenario is further confirmed by a recent metabarcoding analysis carried out on 58 fermented foods which highlighted a large variability in both the counts per million of ARGs and in AR class frequency across the different foods and substrates and in line with the presence/absence of a starter [50]. It is interesting to note that among the strains harboring lsaA isolated from plant-derived fermented foods (eight strains), six of them originated from kimchi. Although Leech and colleagues [50] reported that kimchi showed few detectable ARGs compared to other substrates, a number of AR bacteria have been isolated from this food matrix, such as Pantoea agglomerans KM1, whose genome contains 13 antibiotic resistance genes conferring resistance to clinically important antibiotics, including penicillin G, bacitracin, rifampicin, vancomycin and fosfomycin [51].
As for L. lactis, strains SBC001, isolated from chive, and CCK940, from kimchi, have been studied for their ability to produce gluco-oligosaccharides with prebiotic and anti-inflammatory effects, while AV1n, isolated from fruit, produces high molecular weight dextrans which can have an important impact on the rheological properties of fermented products as well as immunomodulatory and antiviral activity [52]. However, no phenotypic data are available to date related to their antibiotic resistance patterns [53,54]. Contrarily, strain KACC 91922, isolated from kimchi, was characterized for its probiotic properties and thus its safety was also genotypically assessed, confirming the absence of transferable ARGs [55].
The exopolysaccharide producer strain KFRI01, isolated from kimchi [56] was allotted within the species “L. garlicum”, but taxonomically this species has never been validly published [57]. Therefore, a new species description, if substantiated with robust taxonomic data, should be proposed to further use this species name.
Among L. pseudomesenteroides, genome sequences of the strains 1159, PS12 (isolated from traditional Danish cheese starters [58]) and 4882 (from French dairy starter [59]) revealed their adaptations to dairy environments, but similarly to L. lactis, no phenotypic data regarding their antibiotic resistance patterns have been released.
To evaluate the potential transferability of lsaA from these strains (including NCDO 768T and ATCC 700006T) to other bacteria, the flanking regions were investigated to check for the presence of putative mobile elements. A total of 60 kb was selected (30 kb up- and downstream of lsaA), as it was previously observed that the transposable elements can reach a size of 52 kb [60]. L. lactis CCK940, Wikim40 and “L. garlicum” KFRI01, all isolated from kimchi, displayed from two to four copies of transposable elements right downstream of lsaA, including transposases of the IS3 family. Members of this family have been detected in clinically important Enterococcus faecium and E. faecalis strains, as well as in strains of Lactococcus garviae, an opportunistic emerging zoonotic and human pathogen, which is also associated with different food matrices [61,62]. Among L. pseudomesenteroides strains, particular interest emerged from strain 4882, which displayed a mobile element 12 kb downstream of lsaA belonging to the IS30 family. Insertion elements of this family are quite common in LAB, as they were detected in strains of Lactobacillus delbrueckii, Lactiplantibacillus plantarum, Leuconostoc lactis, Pediococcus pentosaceus and Oenococcus oeni [63,64,65].
Presence of mobile elements flanking a putative AR gene in the genomes of these food-grade and technological Leuconostoc strains highlights the need to phenotypically assess the antibiotic resistance patterns, as well as the effective transferability of this trait in filter and in food mating trials [20]. In this framework, it has already been demonstrated the ability of Leuconostoc strains (belonging to L. mesenteroides) to transfer ARG conferring erythromycin resistance to recipient E. faecalis strains both in lab conditions and in cheese, from which these strains were isolated [20].
To understand the role of lsaA at the phenotypic level, the MIC values of CLI and QUD were determined by broth microdilution plates for the type strains of L. fallax and L. pseudomesenteroides. Both strains showed resistance to CLI, while L. pseudomesenteroides displayed resistance only towards QUD. Even though their MIC values (4 and 16 μg/mL for CLI and 8 and 2 μg/mL for QUD, respectively) are lower than those reported for E. faecalis strains (32–48 μg/mL for CLI and 32 μg/mL for QUD) [29], it is interesting to note that the MIC distributions for E. faecalis reported from the EUCAST website (https://mic.eucast.org/, checked on 2 February 2021) showed that resistant strains displayed MIC values between 4 and 8 μg/mL more frequently for QUD and between 8 and 16 μg/mL for CLI; thus, they are comparable with those observed in the two Leuconostoc strains.
To date, this is the first study reporting a clindamycin-resistant L. pseudomesenteroides strain harboring lsaA; in fact, a previous work on L. pseudomesenteroides strains isolated from fermented table olives, clindamycin-resistant strains did not show the presence of the lsaA gene [21].
The discrepancy between the genotype and phenotype towards QUD for L. pseudomesenteroides was further investigated with the analysis of the expression of lsaA in LMG 11482T, which was found to increase in the presence of both CLI as well as QUD. As such, data obtained may suggest that ECOFF proposed for QUD for the genus Leuconostoc, 4 μg/mL, might be not appropriate to distinguish resistant from susceptible strains belonging to the L. pseudomesenteroides species. Therefore, an update of the quinupristin-dalfopristin ECOFF should be performed, analyzing the MIC values of a larger number of L. pseudomesenteroides isolates.

5. Conclusions

The results obtained in this study represent a starting point for the generation of new and more focused scientific protocols and regulatory procedures based on WGS approaches for the genotype–phenotype safety assessment of Leuconostoc strains employed as starter cultures, probiotic or food preservatives.
In this framework, the phenotypic data obtained (MIC values and lsaA expression analysis) surely open the way to a wider validation of these observations, which necessarily has to be carried out on a higher number of L. pseudomesenteroides and L. fallax strains, as well as on all the isolates (belonging to L. lactis and L. falkebergense) that were found to display the lsaA gene. Further phenotypic analysis should include gene cloning, knock-out vector development and MIC determination in strains with the disrupted gene as it was performed both by Singh and colleagues in 2002 to characterize lsaA in almost 500 strains of Enterococcus strains [29] and by Shi and coauthors in 2020 to characterize lsaD (responsible for resistance to lincosamides, streptogramins and pleuromutilins) in Lactococcus garvieae strains [66].
We showed that ARG searches against CARD databases are not sufficient and accurate as they could be for some pathogenic bacteria [67,68]. Therefore, the implementation of ARGs available for LAB could result in a paradigm shift from phenotype- to genotype-based assessments of the resistance for food-grade and technological bacteria in order to enrich the number of AR determinants included in the database. This research is expected to improve the effectiveness of genome sequence analysis as a tool for the prediction of AR characters even in foodborne bacteria.
In this perspective, WGS-based approaches could be used as a tool for the surveillance of the emergence and spread of AR determinants in bacteria, providing an important initial contribution to the identification of genes potentially associated with resistance as well as relevant information about the possibility of AR genes being spread along the food chain.

Supplementary Materials

The following are available online at https://www.mdpi.com/2076-2607/9/3/491/s1: Table S1: Putative AR genes identified in the Leuconostoc type strains analyzed; Figure S1: Distribution of drug efflux pumps proteins in the Leuconostoc type strains dataset; File S1: Analysis of the flanking regions of strains belonging to Leuconostoc falkebergense, L. fallax, “L. garlicum”, L. lactis, L. pseudomesenteroides and Enterococcus faecalis.

Author Contributions

Conceptualization, E.S., I.C. and S.T.; methodology, I.C.; formal analysis, I.L. and E.S.; investigation, I.C. and G.C.; writing—original draft preparation, E.S., I.C. and I.L.; writing—review and editing, S.T; supervision, E.S. and S.T.; funding acquisition, S.T. All authors have read and agreed to the published version of the manuscript.

Funding

This research received no external funding.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Publicly available datasets were analyzed in this study. Accession numbers of genomes and gene sequences used are reported in Table 1, Figure 2 and Figure 4.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Chen, Y.; Wang, L.; Wu, Y.-C.; Mori, K.; Tamura, T.; Chang, C.; Chang, Y.-C.; Wu, H.-C.; Yi, H.-H.; Wang, P.-Y. Leuconostoc litchii sp. nov., a novel lactic acid bacterium isolated from lychee. Int. J. Syst. Evol. Microbiol. 2020, 70. [Google Scholar] [CrossRef] [PubMed]
  2. Ehrmann, M.A.; Freiding, S.; Vogel, R.F. Leuconostoc palmae sp. nov., a novel lactic acid bacterium isolated from palm wine. Int. J. Syst. Evol. Microbiol. 2009, 59. [Google Scholar] [CrossRef] [Green Version]
  3. Lyhs, U.; Snauwaert, I.; Pihlajaviita, S.; Vuyst, L.; De Vandamme, P. Leuconostoc rapi sp. nov., isolated from sous-vide-cooked rutabaga. Int. J. Syst. Evol. Microbiol. 2015, 65. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  4. Beganović, J.; Pavunc, A.L.; Gjuračić, K.; Špoljarec, M.; Šušković, J.; Kos, B. Improved sauerkraut production with probiotic strain Lactobacillus plantarum L4 and Leuconostoc mesenteroides LMG 7954. J. Food Sci. 2011, 76. [Google Scholar] [CrossRef] [PubMed]
  5. Kaur, J.; Lee, S.; Park, Y.-S.; Sharma, A. RAPD analysis of Leuconostoc mesenteroides strains associated with vegetables and food products from Korea. LWT 2017, 77. [Google Scholar] [CrossRef]
  6. De Bruyne, K.; Schillinger, U.; Caroline, L.; Boehringer, B.; Cleenwerck, I.; Vancanneyt, M.; De Vuyst, L.; Franz, C.M.A.P.; Vandamme, P. Leuconostoc holzapfelii sp. nov., isolated from Ethiopian coffee fermentation and assessment of sequence analysis of housekeeping genes for delineation of Leuconostoc species. Int. J. Syst. Evol. Microbiol. 2007, 57. [Google Scholar] [CrossRef]
  7. Vera-Pingitore, E.; Jimenez, M.E.; Dallagnol, A.; Belfiore, C.; Fontana, C.; Fontana, P.; Von Wright, A.; Vignolo, G.; Plumed-Ferrer, C. Screening and characterization of potential probiotic and starter bacteria for plant fermentations. LWT Food Sci. Technol. 2016, 71. [Google Scholar] [CrossRef]
  8. Martinez-Murcia, A.; Collins, M. A phylogenetic analysis of an atypical leuconostoc: Description of Leuconostoc fallax sp. nov. FEMS Microbiol. Lett. 1991, 82. [Google Scholar] [CrossRef]
  9. Kim, J.; Chun, J.; Han, H.U. Leuconostoc kimchii sp. nov., a new species from kimchi. Int. J. Syst. Evol. Microbiol. 2000, 50. [Google Scholar] [CrossRef] [Green Version]
  10. Kim, B.; Lee, J.; Jang, J.; Kim, J.; Han, H. Leuconostoc inhae sp. nov., a lactic acid bacterium isolated from kimchi. Int. J. Syst. Evol. Microbiol. 2003, 53, 1123–1126. [Google Scholar] [CrossRef] [PubMed]
  11. Jeon, H.H.; Kim, K.H.; Chun, B.H.; Ryu, B.H.; Han, N.S.; Jeon, C.O. A proposal of Leuconostoc mesenteroides subsp. jonggajibkimchii subsp. nov. and reclassification of Leuconostoc mesenteroides subsp. suionicum (Gu et al., 2012) as Leuconostoc suionicum sp. nov. based on complete genome sequences. Int. J. Syst. Evol. Microbiol. 2017, 67. [Google Scholar] [CrossRef]
  12. Lee, S.H.; Park, M.S.; Jung, J.Y.; Jeon, C.O. Leuconostoc miyukkimchii sp. nov., isolated from brown algae (Undaria pinnatifida) kimchi. Int. J. Syst. Evol. Microbiol. 2012, 62. [Google Scholar] [CrossRef]
  13. Inventory of Microbial Food Cultures with Safety Demonstration in Fermented Food Products; 495/2018; Intnational Dairy Federation: Brussels, Belgium, 2018; Available online: https://store.fil-idf.org/product/bulletin-idf-n-495-2018-inventory-microbial-food-cultures-safety-demonstration-fermented-food-products/ (accessed on 26 February 2021).
  14. Wu, Y.; Gu, C.T. Leuconostoc falkenbergense sp. nov., isolated from a lactic culture, fermentating string beans and traditional yogurt. Int. J. Syst. Evol. Microbiol. 2021, 71. [Google Scholar] [CrossRef] [PubMed]
  15. Shaw, B.G.; Harding, C.D. Leuconostoc gelidum sp. nov. and Leuconostoc carnosum sp. nov. from chill-stored meats. Int. J. Syst. Bacteriol. 1989, 39. [Google Scholar] [CrossRef] [Green Version]
  16. Oki, K.; Rai, A.K.; Sato, S.; Watanabe, K.; Tamang, J.P. Lactic acid bacteria isolated from ethnic preserved meat products of the Western Himalayas. Food Microbiol. 2011, 28. [Google Scholar] [CrossRef]
  17. Rahkila, R.; De Bruyne, K.; Johansson, P.; Vandamme, P.; Björkroth, J. Reclassification of Leuconostoc gasicomitatum as Leuconostoc gelidum subsp. gasicomitatum comb. nov., description of Leuconostoc gelidum subsp. aenigmaticum subsp. nov., designation of Leuconostoc gelidum subsp. gelidum subsp. nov. and emended description of Leuconostoc gelidum. Int. J. Syst. Evol. Microbiol. 2014, 64. [Google Scholar] [CrossRef] [Green Version]
  18. Ogier, J.; Casalta, E.; Farrok, C.; Saihi, A. Safety assessment of dairy microorganisms: The Leuconostoc genus. Int. J. Food Microbiol. 2008, 126. [Google Scholar] [CrossRef] [PubMed]
  19. Barbieri, F.; Montanari, C.; Gardini, F.; Tabanelli, G. Biogenic amine production by lactic acid bacteria: A review. Foods 2019, 8, 17. [Google Scholar] [CrossRef] [Green Version]
  20. Flórez, A.B.; Campedelli, I.; Delgado, S.; Alegría, Á.; Salvetti, E.; Felis, G.E.; Mayo, B.; Torriani, S. Antibiotic susceptibility profiles of dairy Leuconostoc, analysis of the genetic basis of atypical resistances and transfer of genes in vitro and in a food matrix. PLoS ONE 2016, 11. [Google Scholar] [CrossRef] [Green Version]
  21. Muñoz, M.C.C.; Benomar, N.; Lerma, L.L.; Gálvez, A.; Abriouel, H. Antibiotic resistance of Lactobacillus pentosus and Leuconostoc pseudomesenteroides isolated from naturally-fermented Aloreña table olives throughout fermentation process. Int. J. Food Microbiol. 2014, 172. [Google Scholar] [CrossRef]
  22. Flórez, A.B.; Delgado, S.; Mayo, B. Antimicrobial susceptibility of lactic acid bacteria isolated from a cheese environment. Can. J. Microbiol. 2005, 51. [Google Scholar] [CrossRef]
  23. Ammor, M.S.; Gueimonde, M.; Danielsen, M.; Zagorec, M.; van Hoek, A.H.A.M.; de los Reyes-Gavilán, C.G.; Mayo, B.; Margolles, A. Two different tetracycline resistance mechanisms, plasmid-carried tet(L) and chromosomally located transposon-associated tet(M), coexist in Lactobacillus sakei Rits 9. Appl. Environ. Microbiol. 2008, 74. [Google Scholar] [CrossRef] [Green Version]
  24. Morandi, S.; Cremonesi, P.; Silvetti, T.; Brasca, M. Technological characterisation, antibiotic susceptibility and antimicrobial activity of wild-type Leuconostoc strains isolated from north Italian traditional cheeses. J. Dairy Res. 2013, 80. [Google Scholar] [CrossRef] [PubMed]
  25. El Issaoui, K.; Khay, E.O.; Abrini, J.; Zinebi, S.; Amajoud, N.; Senhaji, N.S.; Abriouel, H. Molecular identification and antibiotic resistance of bacteriocinogenic lactic acid bacteria isolated from table olives. Arch. Microbiol. 2020. [Google Scholar] [CrossRef]
  26. Alcock, B.P.; Raphenya, A.R.; Lau, T.T.Y.; Tsang, K.K.; Bouchard, M.; Edalatmand, A.; Huynh, W.; Nguyen, A.-L.V.; Cheng, A.A.; Liu, S.; et al. CARD 2020: Antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 2019. [Google Scholar] [CrossRef] [PubMed]
  27. Salvetti, E.; Orrù, L.; Capozzi, V.; Martina, A.; Lamontanara, A.; Keller, D.; Cash, H.; Felis, G.E.; Cattivelli, L.; Torriani, S.; et al. Integrate genome-based assessment of safety for probiotic strains: Bacillus coagulans GBI-30, 6086 as a case study. Appl. Microbiol. Biotechnol. 2016, 100. [Google Scholar] [CrossRef]
  28. Cao, L.; Chen, H.; Wang, Q.; Li, B.; Hu, Y.; Zhao, C.; Hu, Y.; Yin, Y. Literature-based phenotype survey and in silico genotype investigation of antibiotic resistance in the genus Bifidobacterium. Curr. Microbiol. 2020, 77, 4104–4113. [Google Scholar] [CrossRef]
  29. Singh, K.V.; Weinstock, G.M.; Murray, B.E. An Enterococcus faecalis ABC homologue (Lsa) is required for the resistance of this species to clindamycin and quinupristin-dalfopristin. Antimicrob. Agents Chemother. 2002, 46, 1845–1850. [Google Scholar] [CrossRef] [Green Version]
  30. Aziz, R.K.; Bartels, D.; Best, A.A.; DeJongh, M.; Disz, T.; Edwards, R.A.; Formsma, K.; Gerdes, S.; Glass, E.M.; Kubal, M.; et al. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genom. 2008, 9. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  31. Wiegand, I.; Hilpert, K.; Hancock, R.E.W. Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances. Nat. Protoc. 2008, 3. [Google Scholar] [CrossRef]
  32. Klare, I.; Konstabel, C.; Müller-Bertling, S.; Reissbrodt, R.; Huys, G.; Vancanneyt, M.; Swings, J.; Goossens, H.; Witte, W. Evaluation of new broth media for microdilution antibiotic susceptibility testing of lactobacilli, pediococci, lactococci, and bifidobacteria. Appl. Environ. Microbiol. 2005, 71. [Google Scholar] [CrossRef] [Green Version]
  33. EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP); Rychen, G.; Aquilina, G.; Azimonti, G.; Bampidis, V.; de Bastos, M.L.; Bories, G.; Chesson, A.; Cocconcelli, P.S.; Flachowsky, G.; et al. Guidance on the characterisation of microorganisms used as feed additives or as production organisms. EFSA J. 2018, 16. [Google Scholar] [CrossRef]
  34. Danielsen, M.; Wind, A. Susceptibility of Lactobacillus spp. to antimicrobial agents. Int. J. Food Microbiol. 2003, 82. [Google Scholar] [CrossRef]
  35. Yan, M.; Han, J.; Xu, X.; Liu, L.; Gao, C.; Zheng, H.; Chen, Y.; Tao, Y.; Zhou, H.; Li, Y.; et al. Gsy, a novel glucansucrase from Leuconostoc mesenteroides, mediates the formation of cell aggregates in response to oxidative stress. Sci. Rep. 2016, 6. [Google Scholar] [CrossRef] [PubMed]
  36. Schmittgen, T.D.; Livak, K.J. Analyzing real-time PCR data by the comparative CT method. Nat. Protoc. 2008, 3. [Google Scholar] [CrossRef]
  37. Sharkey, L.K.R.; Edwards, T.A.; O’Neill, A.J. ABC-F proteins mediate antibiotic resistance through ribosomal protection. MBio 2016, 7. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  38. Sneath, P.H.A.; Sokal, R. Numerical Taxonomy: The Principles and Practice of Numerical Classification; WF Freeman & Co.: San Francisco, CA, USA, 1973. [Google Scholar]
  39. Felsenstein, J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985, 39. [Google Scholar] [CrossRef] [PubMed]
  40. Zuckerkandl, E.; Pauling, L. Evolutionary divergence and convergence in proteins. In Evolving Genes and Proteins; Bryson, V., Vogel, H.J., Eds.; Elsevier: Amsterdam, The Netherlands, 1965. [Google Scholar] [CrossRef]
  41. Kumar, S.; Stecher, G.; Li, M.; Knyaz, C.; Tamura, K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol. Biol. Evol. 2018, 35. [Google Scholar] [CrossRef]
  42. Stecher, G.; Tamura, K.; Kumar, S. Molecular Evolutionary Genetics Analysis (MEGA) for macOS. Mol. Biol. Evol. 2020, 37. [Google Scholar] [CrossRef] [PubMed]
  43. Berendonk, T.U.; Manaia, C.M.; Merlin, C.; Fatta-Kassinos, D.; Cytryn, E.; Walsh, F.; Buergmann, H.; Sørum, H.; Norström, M.; Pons, M.-N.; et al. Tackling antibiotic resistance: The environmental framework. Nat. Rev. Microbiol. 2015, 13. [Google Scholar] [CrossRef]
  44. Founou, L.L.; Founou, R.C.; Essack, S.Y. Antibiotic resistance in the food chain: A developing country-perspective. Front. Microbiol. 2016, 7. [Google Scholar] [CrossRef] [PubMed]
  45. Verraes, C.; Van Boxstael, S.; Van Meervenne, E.; Van Coillie, E.; Butaye, P.; Catry, B.; De Schaetzen, M.-A.; Van Huffel, X.; Imberechts, H.; Dierick, K.; et al. Antimicrobial resistance in the food chain: A review. Int. J. Environ. Res. Public Health 2013, 10, 2643. [Google Scholar] [CrossRef] [Green Version]
  46. Stanhope, M.J.; Lefébure, T.; Walsh, S.L.; Becker, J.A.; Lang, P.; Pavinski Bitar, P.D.; Miller, L.A.; Italia, M.J.; Amrine-Madsen, H. Positive selection in penicillin-binding proteins 1a, 2b, and 2x from Streptococcus pneumoniae and its correlation with amoxicillin resistance development. Infect. Genet. Evol. 2008, 8. [Google Scholar] [CrossRef]
  47. Rosander, A.; Connolly, E.; Roos, S. Removal of antibiotic resistance gene-carrying plasmids from Lactobacillus reuteri ATCC 55730 and characterization of the resulting daughter strain, L. reuteri DSM 17938. Appl. Environ. Microbiol. 2008, 74. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  48. Roberts, M.C. Update on macrolide-lincosamide-streptogramin, ketolide, and oxazolidinone resistance genes. FEMS Microbiol. Lett. 2008, 282. [Google Scholar] [CrossRef] [Green Version]
  49. Roberts, M.C. Resistance to tetracycline, macrolide-lincosamide-streptogramin, trimethoprim, and sulfonamide drug classes. Mol. Biotechnol. 2002, 20. [Google Scholar] [CrossRef]
  50. Leech, J.; Cabrera-Rubio, R.; Walsh, A.M.; Macori, G.; Walsh, C.J.; Barton, W.; Finnegan, L.; Crispie, F.; O’Sullivan, O.; Claesson, M.J.; et al. Fermented-food metagenomics reveals substrate-associated differences in taxonomy and health-associated and antibiotic resistance determinants. MSystems 2020, 5. [Google Scholar] [CrossRef]
  51. Guevarra, R.B.; Magez, S.; Peeters, E.; Chung, M.S.; Kim, K.H.; Radwanska, M. Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes in Pantoea agglomerans KM1, a potential opportunistic pathogen. PLoS ONE 2021, 16, e0239792. [Google Scholar] [CrossRef]
  52. Besrour-Aouam, N.; Fhoula, I.; Hernández-Alcántara, A.M.; Mohedano, M.L.; Najjari, A.; Prieto, A.; Ruas-Madiedo, P.; López, P.; Ouzari, H.-I. The role of dextran production in the metabolic context of Leuconostoc and Weissella Tunisian strains. Carbohydr. Polym. 2021, 253. [Google Scholar] [CrossRef]
  53. Lee, S.; Park, J.; Jang, J.K.; Lee, B.H.; Park, Y.S. Structural analysis of gluco-oligosaccharides produced by Leuconostoc lactis and their prebiotic effect. Molecules 2019, 24, 3998. [Google Scholar] [CrossRef] [Green Version]
  54. Kim, M.; Jang, J.-K.; Park, Y.-S. Production optimization, structural analysis, and prebiotic- and anti-inflammatory effects of gluco-oligosaccharides produced by Leuconostoc lactis SBC001. Microorganisms 2021, 9, 200. [Google Scholar] [CrossRef]
  55. Moon, J.S.; Choi, H.S.; Shin, S.Y.; Noh, S.J.; Jeon, C.O.; Han, N.S. Genome sequence analysis of potential probiotic strain Leuconostoc lactis EFEL005 isolated from kimchi. J. Microbiol. 2015, 53, 337–342. [Google Scholar] [CrossRef] [PubMed]
  56. Hong, S.P.; Shin, S.C.; Kang, W.-K.; Chin, Y.-W.; Turner, T.L.; Choi, H.W.; Song, K.M.; Kim, H.J. Complete genome sequence of Leuconostoc garlicum KCCM 43211 producing exopolysaccharide. J. Biotechnol. 2017, 246. [Google Scholar] [CrossRef]
  57. Kumar, A.; Augustine, D.; Mehta, A.; Dinesh, K.R.; Viswam, D.; Philip, R. Leuconostoc garlicum: An unusual pathogen in the era of vancomycin therapy. Indian J. Chest Dis. Allied Sci. 2012, 2, 127–130. [Google Scholar]
  58. Pedersen, T.B.; Kot, W.P.; Hansen, L.H.; Sørensen, S.J.; Broadbent, J.R.; Vogensen, F.K.; Ardö, Y. Genome sequences of two Leuconostoc pseudomesenteroides strains isolated from Danish dairy starter cultures. Genome Announc. 2014, 2. [Google Scholar] [CrossRef] [Green Version]
  59. Meslier, V.; Loux, V.; Renault, P. Genome sequence of Leuconostoc pseudomesenteroides strain 4882, isolated from a dairy starter culture. J. Bacteriol. 2012, 194. [Google Scholar] [CrossRef] [Green Version]
  60. Land, M.; Hauser, L.; Jun, S.R.; Nookaew, I.; Leuze, M.R.; Ahn, T.H.; Karpinets, T.; Lund, O.; Kora, G.; Wassenaar, T.; et al. Insights from 20 years of bacterial genome sequencing. Funct. Integr. Genom. 2015, 15, 141–161. [Google Scholar] [CrossRef] [Green Version]
  61. Mikalsen, T.; Pedersen, T.; Willems, R.; Coque, T.M.; Werner, G.; Sadowy, E.; Van Schaik, W.; Jensen, L.B.; Sundsfjord, A.; Hegstad, K. Investigating the mobilome in clinically important lineages of Enterococcus faecium and Enterococcus faecalis. BMC Genom. 2015, 16. [Google Scholar] [CrossRef] [Green Version]
  62. Eraclio, G.; Ricci, G.; Fortina, M.G. Insertion sequence elements in Lactococcus garvieae. Gene 2015, 555. [Google Scholar] [CrossRef]
  63. Nicoloff, H.; Bringel, F. ISLpl1 is a functional IS30-related insertion element in Lactobacillus plantarum that is also found in other lactic acid bacteria. Appl. Environ. Microbiol. 2003, 69, 6032–6040. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  64. Ravin, V.; Alatossava, T. Three new insertion sequence elements ISLdl2, ISLdl3, and ISLdl4 in Lactobacillus delbrueckii: Isolation, molecular characterization, and potential use for strain identification. Plasmid 2003, 49. [Google Scholar] [CrossRef]
  65. Kumar, R.; Grover, S.; Kaushik, J.K.; Batish, V.K. IS30-related transposon mediated insertional inactivation of bile salt hydrolase (bsh1) gene of Lactobacillus plantarum strain Lp20. Microbiol. Res. 2014, 169. [Google Scholar] [CrossRef]
  66. Shi, Y.-Z.; Yoshida, T.; Fujiwara, A.; Nishiki, I. Characterization of lsa(D), a novel gene responsible for resistance to lincosamides, streptogramins A, and pleuromutilins in fish pathogenic Lactococcus garvieae Serotype II. Microb. Drug Resist. 2020, 1–10. [Google Scholar] [CrossRef] [PubMed]
  67. McDermott, P.F.; Tyson, G.H.; Kabera, C.; Chen, Y.; Li, C.; Folster, J.P.; Ayers, S.L.; Lam, C.; Tate, H.P.; Zhao, S. Whole-genome sequencing for detecting antimicrobial resistance in nontyphoidal Salmonella. Antimicrob. Agents Chemother. 2016, 60. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  68. Liu, L.; Zhu, W.; Cao, Z.; Xu, B.; Wang, G.; Luo, M. High correlation between genotypes and phenotypes of environmental bacteria Comamonas testosteroni strains. BMC Genom. 2015, 16. [Google Scholar] [CrossRef] [PubMed] [Green Version]
Microorganisms 09 00491 g001 550
Figure 1. Putative antibiotic resistance (AR) genes identified in Leuconostoc spp. Putative antibiotic resistance genes (ARGs) detected are reported for each strain of the dataset. They are involved in the resistance towards aminoglycosides (Am), beta-lactams (Bl), diaminopyrimidines (Di), glycopeptides (Gl), lincosamides (Li), ABC-F ATP-binding cassette ribosomal protection protein ABC cassettes (Li-Ma-Ox-Ph-St-Te), erythromycin (Li-Ma-St), chloramphenicol (Ph), rifampicin (Ri) and streptogramins (St). The number of hits per drug class is reported on each barplot.
Figure 1. Putative antibiotic resistance (AR) genes identified in Leuconostoc spp. Putative antibiotic resistance genes (ARGs) detected are reported for each strain of the dataset. They are involved in the resistance towards aminoglycosides (Am), beta-lactams (Bl), diaminopyrimidines (Di), glycopeptides (Gl), lincosamides (Li), ABC-F ATP-binding cassette ribosomal protection protein ABC cassettes (Li-Ma-Ox-Ph-St-Te), erythromycin (Li-Ma-St), chloramphenicol (Ph), rifampicin (Ri) and streptogramins (St). The number of hits per drug class is reported on each barplot.
Microorganisms 09 00491 g001
Microorganisms 09 00491 g002 550
Figure 2. Evolutionary relationships of LsaA, LsaB and LsaC proteins in Leuconostoc type strains. The evolutionary history was inferred using the UPGMA method [38]. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches [39]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method [40] and are in the units of the number of amino acid substitutions per site. All positions containing gaps and missing data were eliminated (complete deletion option). Evolutionary analyses were conducted in MEGA X [41,42] by using Enterococcus faecalis V583, Mammaliicoccus sciuri (plasmid) pSCFS1 and Streptococcus agalactiae UCN70 as outgroups. The phylogenetic group including LsaA of L. pseudomesenteroides NCDO 768T and L. fallax ATCC 700006T is highlighted in red.
Figure 2. Evolutionary relationships of LsaA, LsaB and LsaC proteins in Leuconostoc type strains. The evolutionary history was inferred using the UPGMA method [38]. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches [39]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method [40] and are in the units of the number of amino acid substitutions per site. All positions containing gaps and missing data were eliminated (complete deletion option). Evolutionary analyses were conducted in MEGA X [41,42] by using Enterococcus faecalis V583, Mammaliicoccus sciuri (plasmid) pSCFS1 and Streptococcus agalactiae UCN70 as outgroups. The phylogenetic group including LsaA of L. pseudomesenteroides NCDO 768T and L. fallax ATCC 700006T is highlighted in red.
Microorganisms 09 00491 g002
Microorganisms 09 00491 g003 550
Figure 3. Alignment of LsaA amino acid sequence of L. pseudomesenteroides NCDO 768T, L. fallax ATCC 700006T and E. faecalis V583. The red boxes highlight the Walker A (WA) and Walker B (WB) domains conserved in the three sequences.
Figure 3. Alignment of LsaA amino acid sequence of L. pseudomesenteroides NCDO 768T, L. fallax ATCC 700006T and E. faecalis V583. The red boxes highlight the Walker A (WA) and Walker B (WB) domains conserved in the three sequences.
Microorganisms 09 00491 g003
Microorganisms 09 00491 g004 550
Figure 4. Distribution analysis of LsaA in Leuconostoc nontype strains. The evolutionary history was inferred using the UPGMA method [38]. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches [39]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method [40] and are in the units of the number of amino acid substitutions per site. All positions containing gaps and missing data were eliminated (complete deletion option). Evolutionary analyses were conducted in MEGA X [41,42]. Colors refer to isolation sources: Green: raw plant material; Grey: environmental samples, Olive green: fermented foods; Orange: dairy products; Pink: clinical isolates.
Figure 4. Distribution analysis of LsaA in Leuconostoc nontype strains. The evolutionary history was inferred using the UPGMA method [38]. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches [39]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method [40] and are in the units of the number of amino acid substitutions per site. All positions containing gaps and missing data were eliminated (complete deletion option). Evolutionary analyses were conducted in MEGA X [41,42]. Colors refer to isolation sources: Green: raw plant material; Grey: environmental samples, Olive green: fermented foods; Orange: dairy products; Pink: clinical isolates.
Microorganisms 09 00491 g004
Microorganisms 09 00491 g005 550
Figure 5. Genetic organization of the region surrounding the lsaA gene in nine Leuconostoc strains. The picture shows the genetic organization of the regions (30 kpb downstream and 30 kpb upstream) surrounding the lsaA gene identified in the genomes of “L. garlicum KFRI01”, L. lactis CCK940, L. lactis Wikim40 (in reverse strand), L. pseudomesenteroides 4882, L. pseudomesenteroides LMG 11483, L. pseudomesenteroides TR070, L. pseudomesenteroides CBA3630, L. pseudomesenteroides NCDO 768T L. fallax ATCC 700006T and E. faecalis V583.
Figure 5. Genetic organization of the region surrounding the lsaA gene in nine Leuconostoc strains. The picture shows the genetic organization of the regions (30 kpb downstream and 30 kpb upstream) surrounding the lsaA gene identified in the genomes of “L. garlicum KFRI01”, L. lactis CCK940, L. lactis Wikim40 (in reverse strand), L. pseudomesenteroides 4882, L. pseudomesenteroides LMG 11483, L. pseudomesenteroides TR070, L. pseudomesenteroides CBA3630, L. pseudomesenteroides NCDO 768T L. fallax ATCC 700006T and E. faecalis V583.
Microorganisms 09 00491 g005
Microorganisms 09 00491 g006 550
Figure 6. Relative quantification of lsaA expression for L. pseudomesenteroides LMG 11482T (=NCDO 768T) grown in free-antibiotic culture (sa) in the presence of clindamycin 4 μg/mL (CLI) or quinupristin-dalphopristin 1 μg/mL (QUD). The cells were collected in the exponential and stationary growth phases 0.2 and 0.8 OD600, respectively. The expression of lsaA was normalized based on the expression of the 16S rRNA and calculated using the 2−ΔΔct method. *: p-value < 0.05.
Figure 6. Relative quantification of lsaA expression for L. pseudomesenteroides LMG 11482T (=NCDO 768T) grown in free-antibiotic culture (sa) in the presence of clindamycin 4 μg/mL (CLI) or quinupristin-dalphopristin 1 μg/mL (QUD). The cells were collected in the exponential and stationary growth phases 0.2 and 0.8 OD600, respectively. The expression of lsaA was normalized based on the expression of the 16S rRNA and calculated using the 2−ΔΔct method. *: p-value < 0.05.
Microorganisms 09 00491 g006
Table
Table 1. Genome features of the 17 type-strains of the Leuconostoc genus analyzed in this study. The genome sequences of the type strains of L. gelidum aenigmaticum LMG 27840T, L. miyukkimchii DSM 25624T, L. palmae DSM 21144T, L. rapi DSM 27776T are not publicly available.
Table 1. Genome features of the 17 type-strains of the Leuconostoc genus analyzed in this study. The genome sequences of the type strains of L. gelidum aenigmaticum LMG 27840T, L. miyukkimchii DSM 25624T, L. palmae DSM 21144T, L. rapi DSM 27776T are not publicly available.
SpeciesType StrainIsolation SourceGenBank Accession Number
Leuconostoc carnosumDSM 5576TChill-stored meatJACHGL000000000.1
Leuconostoc citreumATCC 49370TFood and clinical sources PUFH00000000.1
Leuconostoc falkenbergenseLMG 10779TLactic culture BMBS00000000.1
Leuconostoc fallaxATCC 700006TSauerkrautPUFI00000000.1
Leuconostoc gelidum subsp. gasicomitatumLMG 18811TPackaged meat FN822744.1
Leuconostoc gelidum subsp. gelidumKCTC 3527TKimchi (a traditional Korean food made by fermentation of Chinese cabbage)AEMI00000000.1
Leuconostoc holzapfeliiCCUG 54536TEthiopian coffee fermentationJAAXPO000000000.1
Leuconostoc inhaeKCTC 3774TKimchiAEMJ00000000.1
Leuconostoc kimchiiIMSNU 11154TKimchichromosome: NC_014136.1/CP001758.1
plasmid: LkipL4701: NC_014131.1/CP001753.1
LkipL4704: NC_014132.1/CP001754.1
LkipL4719: NC_014133.1/CP001755.1
LkipL4726: NC_014134.1/CP001756.1
LkipL48: NC_014135.1/CP001757.1
Leuconostoc lactisDSM 20202TMilkAEOR00000000.1
Leuconostoc litchiiMB7TLycheeSDGY00000000.1
Leuconostoc mesenteroides subsp. cremorisATCC 19254THansen’s dried starter powderACKV00000000.1
Leuconostoc mesenteroides subsp. cremorisDSM 20484TMissing (isolated in 1912)chromosome: NZ_CP012009.1/CP012009.1
plasmid pDSM20484: NZ_CP012010.1/CP012010.1
Leuconostoc mesenteroides subsp. JonggajibkimchiiDRC1506TKimchichromosome: NZ_CP014611.1/CP014611.1
plasmid pDRC1: NZ_CP014612.1/CP014612.1
pDRC2: NZ_CP014613.1/CP014613.1
pDRC3: NZ_CP014614.1/CP014614.1
Leuconostoc mesenteroides subsp. mesenteroidesATCC 8293TFermenting oliveschromosome: NC_008531.1/CP000414.1
plasmid pLEUM1: NC_008496.1/CP000415.1
Leuconostoc pseudomesenteroidesNCDO 768TCane juiceJAAXPY000000000.1
Leuconostoc suionicumDSM 20241TMissing (isolated in 1972)chromosome: NZ_CP015247.1/CP015247.1
plasmid unnamed: NZ_CP015248.1/CP015248.1
Table
Table 2. Minimum inhibitory concentration (MIC) values for clindamycin (CLI) and quinupristin-dalfopristin (QUD) of 11 type strains determined through the broth microdilution method. MICs higher than the Epidemiological cut-off (ECOFF) values are reported in bold.
Table 2. Minimum inhibitory concentration (MIC) values for clindamycin (CLI) and quinupristin-dalfopristin (QUD) of 11 type strains determined through the broth microdilution method. MICs higher than the Epidemiological cut-off (ECOFF) values are reported in bold.
SpeciesMIC (µg/mL)
CLIQUD
Leuconostoc carnosum CECT 4024T (=DSM 5576T)<0.031
Leuconostoc fallax LMG 13177T (=ATCC 700006T)48
Leuconostoc gelidum subsp. gasicomitatum CECT 5767T (=LMG 18811T)<0.031
Leuconostoc gelidum subsp. gelidum CECT 4026T (=KCTC 3527T)<0.030.5
Leuconostoc inhae CECT 7026T (=KCTC 3774T)<0.031
Leuconostoc lactis LMG 8894T (=DSM 20202T)<0.031
Leuconostoc mesenteroides subsp. cremoris LMG 6909T (=ATCC 19254T)0.121
Leuconostoc mesenteroides subsp. dextranicum LMG 6908T (=ATCC 19254T)0.120.5
Leuconostoc mesenteroides subsp. mesenteroides LMG 6893T (=ATCC 8293T)0.121
Leuconostoc pseudomesenteroides LMG 11482T (=NCDO 768T)162
Leuconostoc suionicum CECT 8146T (=DSM 20241T)0.121
ECOFF14
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Share and Cite

MDPI and ACS Style

Salvetti, E.; Campedelli, I.; Larini, I.; Conedera, G.; Torriani, S. Exploring Antibiotic Resistance Diversity in Leuconostoc spp. by a Genome-Based Approach: Focus on the lsaA Gene. Microorganisms 2021, 9, 491. https://doi.org/10.3390/microorganisms9030491

AMA Style

Salvetti E, Campedelli I, Larini I, Conedera G, Torriani S. Exploring Antibiotic Resistance Diversity in Leuconostoc spp. by a Genome-Based Approach: Focus on the lsaA Gene. Microorganisms. 2021; 9(3):491. https://doi.org/10.3390/microorganisms9030491

Chicago/Turabian Style

Salvetti, Elisa, Ilenia Campedelli, Ilaria Larini, Giada Conedera, and Sandra Torriani. 2021. "Exploring Antibiotic Resistance Diversity in Leuconostoc spp. by a Genome-Based Approach: Focus on the lsaA Gene" Microorganisms 9, no. 3: 491. https://doi.org/10.3390/microorganisms9030491

APA Style

Salvetti, E., Campedelli, I., Larini, I., Conedera, G., & Torriani, S. (2021). Exploring Antibiotic Resistance Diversity in Leuconostoc spp. by a Genome-Based Approach: Focus on the lsaA Gene. Microorganisms, 9(3), 491. https://doi.org/10.3390/microorganisms9030491

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