Antibiotic resistances of starter and probiotic strains of lactic acid bacteria

Conjugal transfer of erm(B) and multiple tet genes from Lactobacillus spp. to bacterial pathogens in animal gut, in vitro and during food fermentation

Three strains of Lactobacillus comprising Lactobacillus salivarius (CHS-1E and CH7-1E) and Lactobacillus reuteri (CH2-2) previously isolated from chicken meat were analyzed for their transferability of antibiotic resistance (AR) genes to pathogenic strains under in vivo, in vitro, and during food fermentation. For in vivo model, Albino Wistar rats were inoculated with 10¹⁰ CFU/g/ml of Enterococcus faecalis JH2-2 (recipient). After 7 days, either of two donors L. salivarius CH7-1E or L. reuteri [harbouring erythromycin and tetracycline resistance genes] were introduced at a concentration of 10⁹ CFU/ml daily for 1 week. Two days after donor introduction, there was a stable increase in the number of transconjugants in the animal faeces from 10² to 10³ CFU/g and presented erm(B), tet(M), tet(L) and tet(W) in their genome like donor strains. Similar observations were made with in vitro filter mating between CHS-1E, CH2-2 and CH7-1E and E. faecalis JH2-2 with transfer frequencies of 1 × 10^-4, 3.8 × 10^-3 and 2 × 10^-3 per donor cell respectively. With the results obtained in vivo and in vitro, the AR transferability of donor strains was estimated during food fermentation (chicken sausage, fermented milk or idli batter) with pathogenic recipient strains added as contaminants. At the end of mating period, phenotypic resistance to erythromycin and tetracycline in Listeria monocytogenes and Yersinia enterocolitica strains was observed. This study showed the ability of food borne Lactobacillus in diffusing their AR traits in diverse natural environments increasing their concern of AR dissemination in the food chain when used as food additives and/or probiotics.

The unravelled Enterococcus faecalis zoonotic superbugs: Emerging multiple resistant and virulent lineages isolated from poultry environment

This study aimed to investigate the zoonotic potential by virtue of phylogenetic analysis, virulence and resistance gene profiles of Enterococcus faecalis originating from poultry environment. The ERIC, BOX and RAPD PCR analysis showed the clustering of E. faecalis strains (n = 74) into five groups (G1-G5) and fifteen sub-clusters (B1-B15), which share 50%-80% similarities with ATCC E. faecalis and clinical strains of human infection. E. faecalis strains harboured seven enterocins genes including ent1097 (85%), entB (84%), enterolysinA (51%), entSEK4 (51%), entL50 (31%), entA (25.7%) and ent1071 (14.9%). The highest prevalence of gelE-sprE (90%), lip-fl (90%) followed by cylL (62%), hyl (60%), katA (16%) and cylA (5.4%) was observed in poultry isolates. The fsr operon and gelE-sprE was co-associated in 66.2% strains. E. faecalis also harboured biofilm and endocarditis-associated genes, including efaAfs (97%), ebp-pilli (ebpABC and srtC 69.9%-80%), asa1 (71%), agg (55%), ace (54%) and esp-Tim (3%). Despite all found sensitive to vancomycin, 98.6% strains were multi-drug resistant to five to twelve tested antimicrobials. An increased-level of resistance (≥32 μg/ml) was observed to ampicillin (8.1%), meropenem (21.6%), chloramphenicol (73.4%), erythromycin (90.5%), tetracycline (100%) and high-level resistance to kanamycin (79.7%) and gentamicin (52.7%). The multi-drug resistant E. faecalis (MDRe.f) were carried pbp4 (90%), tetL (90%), tetM (70%), ermB (81%), cat (52.7%), acc6-aph2 (58.1%), aaph(3)-III (49.9%), gyrA (97%) and parC (98%) genes. Moreover, these MDRe.f were also harboured, hospital-associated marker IS16 (58%) and pheromone responsive genes, that is ccf (88%), cpd (74%), cob (62%) and eep (66%). Thus, regardless of the distinct phylogenetic background of E. faecalis of poultry origin, ATCC E. faecalis and clinical strains of human origin, we found major similarities in virulence, resistance gene profiles and mobile genetic elements (IS16 and pheromone responsive plasmids), supporting the zoonotic/reverse zoonotic risk associated with this organism.

Potential of Lactobacillus plantarum IBB3036 and Lactobacillus salivarius IBB3154 to persistence in chicken after in ovo delivery

The aim of this study was to characterize and compare selected Lactobacillus strains originating from different environments (cow milk and hen feces) with respect to their applicative potential to colonize gastrointestinal track of chickens before hatching from an egg. In vitro phenotypic characterization of lactobacilli strains included the investigation of the important prerequisites for persistence in gastrointestinal tract, such as a capability to survive in the presence of bile salts and at low pH, enzymatic and sugar metabolic profiles, adhesion abilities, and resistance to osmolytes, temperature, and antibiotics. Regarding the resistance of lactobacilli to most of the various stress factors tested, the milk isolate Lactobacillus plantarum IBB3036 showed better abilities than the chicken feces isolate Lactobacillus salivarius IBB3154. However, regarding the acidification tolerance and adherence ability, L. salivarius IBB3154 revealed better characteristics. Use of these two selected lactobacilli isolates together with proper prebiotics resulted in the preparation of two S1 and S2 bioformulations, which were injected in ovo into hen Cobb500 FF fertilized eggs. Furthermore, in vivo tests assessing the persistence of L. plantarum IBB3036 and L. salivarius IBB3154 in the chicken gastrointestinal tract was monitored by PCR‐based classical and quantitative techniques and revealed the presence of both strains in fecal samples collected 3 days after hatching. Subsequently, the number of L. salivarius IBB3154 increased significantly in the chicken intestine, whereas the presence of L. plantarum IBB3036 was gradually decreased.

Biodiversity and Microbial Resistance of Lactobacilli Isolated From the Traditional Greek Cheese Kopanisti

Kopanisti is a Greek artisan cheese produced from raw milk in the island of Mykonos, Greece. The milk is left to rest for 12–24 h and then the rennet is added. After its formation the curd is left to drain for 2–3 days and is ready either for consumption (as tyrovolia fresh cheese), or with the addition of extra salt, the curd is left to ripen through further fermentation and surface development of Penicillium fungi, aprocess leading to the production of the traditional Greek cheese Kopanisti. From 120 samples of kopanisti, 574 Lactobacillus strains were isolated, distributed in 17 species (16 of them isolated from tyrovolia as well). Strains from 15 species were found resistant or multiresistant against 15 antimicrobial agents, representing all categories of antibiotics. Analysis revealed that the resistance was moderated during ripening of the curd from tyrovolia to Kopanisti. Resistance against penicillin G, ampicillin/sulbactam, clindamycin, chloramphenicol, streptomycin, trimethoprim, metronidazole, vancomycin, teichoplanin, and quinupristin/dalvopristin was significantly enhanced, while the resistance against ampicillin, erythromycin, oxytetracycline, gentamycin, and fucidic acid was significantly reduced. These changes during ripening suggest that resistance to antimicrobials is a dynamic process subjected to environmental factors. The biodiversity of isolated Lactobacillus strains is impressive and explains the exquisite sensorial characteristics of the cheese. However, the extent of the resistance is alarming.

Antibiotic Resistance-Susceptibility Profiles of Streptococcus thermophilus Isolated from Raw Milk and Genome Analysis of the Genetic Basis of Acquired Resistances

The food chain is thought to play an important role in the transmission of antibiotic resistances from commensal and beneficial bacteria to pathogens. Streptococcus thermophilus is a lactic acid bacterium of major importance as a starter for the dairy industry. This study reports the minimum inhibitory concentration (MIC) of 16 representative antimicrobial agents to 41 isolates of S. thermophilus derived from raw milk. Strains showing resistance to tetracycline (seven), erythromycin and clindamycin (two), and streptomycin and neomycin (one) were found. PCR amplification identified tet(S) in all the tetracycline-resistant strains, and ermB in the two erythromycin/clindamycin-resistant strains. Hybridisation experiments suggested each resistance gene to be located in the chromosome with a similar genetic organization. Five antibiotic-resistant strains -two resistant to tetracycline (St-2 and St-9), two resistant to erythromycin/clindamycin (St-5 and St-6), and one resistant to streptomycin/neomycin (St-10)- were subjected to genome sequencing and analysis. The tet(S) gene was identified in small contigs of 3.2 and 3.7 kbp in St-2 and St-9, respectively, flanked by truncated copies of insertion sequence (IS) elements. Similarly, ermB in St-6 and St-5 was found in contigs of 1.6 and 28.1 kbp, respectively. Sequence analysis and comparison of the largest contig showed it to contain three segments (21.9, 3.7, and 1.4 kbp long) highly homologous to non-collinear sequences of pRE25 from Enterococcus faecalis. These segments contained the ermB gene, a transference module with an origin of transfer (oriT) plus 15 open reading frames encoding proteins involved in conjugation, and modules for plasmid replication and segregation. Homologous stretches were separated by short, IS-related sequences, resembling the genetic organization of the integrative and conjugative elements (ICEs) found in Streptococcus species. No gene known to provide aminoglycoside resistance was seen in St-10. Four strain-specific amino acid substitutions in the RsmG methyltransferase were scored in this strain; these might be associated to its streptomycin/neomycin resistance. Under yogurt manufacturing and storage conditions, no transfer of either tet(S) or ermB from S. thermophilus to L. delbrueckii was detected. The present results contribute toward characterisation of the antibiotic resistance profiles in S. thermophilus, provide evidence for the genetic basis of acquired resistances and deepen on their transference capability.

Assessment of antibiotic susceptibility in Lactobacillus isolates from chickens

BACKGROUND

The aim of this study was to determine the susceptibility of 88 Lactobacillus isolates derived from chickens to antibiotic substances and to detect drug-resistance genes.

RESULTS

The minimal inhibitory concentration of 13 antimicrobial substances was determined by the broth microdilution method, and resistance genes were detected by PCR. We recorded a high prevalence of resistance to tiamulin (90% resistant isolates), tetracyclines (74%) and lincomycin (70%), and a moderately high frequency of resistance to enrofloxacin (48%), macrolides (42%), aminoglycosides (12.5-31%), ampicillin (26%) and chloramphenicol (23%). Multi-drug resistance was observed in 79.5% of isolates. The presence of resistance genes was generally correlated with phenotypic resistance, but some molecular determinants were also recorded in susceptible isolates. Among tetracycline resistance genes, the most frequently identified was tetW (45% isolates), followed by tetM (26%) and tetL (24%). The ermB, ermC and lnuA genes, associated with resistance to macrolides and lincosamides, were observed in 39, 12 and 39% of isolates, respectively. Among genes determining resistance to aminoglycoside antibiotics, we identified ant(6)-Ia (10% of isolates), aac(6')-Ie-aph(2')-Ia (8%), aph(2″)-Ic (6%) and aadE (4.5%). The cat gene was present in 32 isolates, including 8 of 20 found to be resistant to chloramphenicol. Two genes encoding efflux pumps were identified-the acrA gene was present in all isolates tested, and 10 of 79 lactobacilli determined to be phenotypically resistant to tiamulin contained the lsaE gene. We were unable to explain the resistance mechanism of Lactobacillus isolates to ampicillin, but showed that it did not involve the production of β-lactamases.

CONCLUSIONS

Our findings indicate that intestinal lactobacilli should be considered a reservoir of resistance genes and that antibiotics must be used prudently in poultry production. The data derived from this study can be used as a basis for reviewing current microbiological breakpoints for categorization of susceptible and resistant strains within the genus Lactobacillus.

Analysis of resistance genes in pan-resistant Myroides odoratimimus clinical strain PR63039 using whole genome sequencing

To clarify the antibiotic resistance mechanisms of Myroides odoratimimus, pan-resistant M. odoratimimus strain PR63039 was isolated and its genome sequenced and analyzed. Antimicrobial susceptibility testing was conducted using the Kirby-Bauer disk diffusion method, and the Phoenix-100 Automated Microbiology System with a NMIC/ID-4 panel including aminoglycosides, β-lactams, polypeptides, quinolones, sulfonamides, chloramphenicols, and tetracyclines. Single-molecule real-time whole genome sequencing was conducted using the PacBio RSII system, and genome annotation was performed using RAST and IMG ER. To characterize the genome features, a number of databases and software programs, including GC-Profile, CG viewer, the VFDB database, ISfinder, RADB, CARD, ResFinder, and PHAST, were used. M. odoratimimus isolate PR63039 was resistant to almost all antibiotics tested, suggesting pan-drug resistance. The genome consisted of a 4,366,950-bp chromosome and a 90,798-bp plasmid (p63039), which contained a large number of resistance genes and virulence factors. The distribution of the resistance genes was distinctive, and a resistance region, designated MY63039-RR, was identified. RAST analysis indicated that 108 of the annotated genes were potentially involved in virulence, disease, and defense, all of which could be associated with resistance and pathogenicity. Prophage analysis also identified two incomplete prophages in the genome of M. odoratimimus PR63039. Multiple antibiotic-resistance genes were identified, including those associated with resistance to tetracycline (tetX), macrolides (ereB, cfrA, lasE), sulfonamides (sul2, sul3), β-lactams (bla_MUS-1, bla_TUS-1, bla_SFB-1, bla_SLB-1, bla_OXA-209, bla_OXA-347), and chloramphenicol (cat). Further, the presence of 18 antibiotic efflux pump-encoding resistance genes, including acrB, acrD, acrF, adeB, adeG, adeJ, amrB, ceoB, cmeB, mdsB, mexB, mexD, mexF, mtrD, smeE, mdtF, macB, likely accounts for the observed quinolone resistance of strain PR63039. To the best of our knowledge, this is the first report of the presence of the bla_SFB-1, bla_SLB-1, bla_OXA-209, bla_OXA-347, and tetX resistance genes in M. odoratimimus.

Comparison of antibiotic resistance and copper tolerance of Enterococcus spp. and Lactobacillus spp. isolated from piglets before and after weaning

In China, antimicrobials and copper are used extensively as growth-promoting agents for piglets. This study aimed to characterize the role of in-feed copper in the emergence of copper-tolerant and antibiotic-resistant Enterococcus and Lactobacillus isolates in Chinese pig farms. Feces of the same eight piglets from four litters at 7 and 55 days old and their mothers were traced in order to isolate Enterococcus spp. and Lactobacillus spp.. The minimum inhibitory concentrations of 10 antimicrobials and copper sulfate were determined using an agar dilution method. The feed levels of Cu²⁺ for lactating sows, suckling piglets, and weaned piglets were 6, 177, and 18 mg/kg, respectively. All the 136 Enterococcus isolates were sensitive to vancomycin; and the resistance rates to penicillin, enrofloxacin, and high level streptomycin resistance increased significantly after weaning. For the 155 Lactobacillus isolates, the resistance rates to ampicillin, chloramphenicol, tetracycline, and enrofloxacin were significantly higher in weaned piglets. The ratios of copper tolerant Enterococcus and Lactobacillus isolates both increased significantly after weaning (P < 0.05). A phenotypic correlation was observed after classifying the isolates into two groups (CuSO₄ MIC₅₀ < 16 or ≧16 for enterococci; CuSO₄ MIC₅₀ < 12 or ≧12 for lactobacilli) and comparing the antimicrobial-resistant percentage of two groups. On species level, a significant increase of E. faecalis to enrofloxacin was observed in line with the increase of copper MIC (P < 0.05). The findings revealed the changes of the antibiotic resistance and copper tolerance level of enterococci and lactobacilli between suckling and weaned piglets and demonstrated that there might be a strong association between in-feed copper and increased antibiotic resistance in enterococci and lactobacilli in Chinese intensive swine farms.

Detection of antibiotic resistance genes in the feces of young adult Japanese

Antibiotic resistance genes in the feces of healthy young adult Japanese were analyzed with polymerase chain reaction using specific primers. Antibiotic resistance genes against macrolides (ermB, ermF, ermX, and mefA/E), tetracyclines (tetW, tetQ, tetO, and tetX), β-lactam antibiotics (blaTEM ), and streptomycin (aadE) were detected in more than 50% of subjects. These antibiotic resistance genes are likely widespread in the large intestinal bacteria of young adult Japanese.

Assessment of virulence factors, antibiotic resistance and amino-decarboxylase activity in Enterococcus faecium MXVK29 isolated from Mexican chorizo

Enterococcus faecium MXVK29 has the ability to produce an antimicrobial compound that belongs to Class IIa of the Klaenhammer classification, and could be used as part of a biopreservation technology through direct inoculation of the strain as a starter or protective culture. However, Enterococcus is considered as an opportunistic pathogen, hence, the purpose of this work was to study the food safety determinants of E. faecium MXVK29. The strain was sensitive to all of the antibiotics tested (penicillin, tetracycline, vancomycin, erythromycin, chloramphenicol, gentamicin, neomycin, kanamycin and netilmicin) and did not demonstrate histamine, cadaverine or putrescine formation. Furthermore, tyrosine-decarboxylase activity was detected by qualitative assays and PCR. Among the virulence factors analysed for the strain, only the genes encoding the sexual pheromone cCF10 precursor lipoprotein (ccf) and cell-wall adhesion (efaA_fm ) were amplified. The presence of these genes has low impact on pathogenesis, as there are no other genes encoding for virulence factors, such as aggregation proteins. Therefore, Enterococcus faecium could be employed as part of a bioconservation method, because it does not produce risk factors for consumer's health; in addition, it could be used as part of the hurdle technology in foods.

SIGNIFICANCE AND IMPACT OF THE STUDY

The use of molecular techniques has allowed, in recent years, to detect pathogenicity genes present in the genome of starter cultures used in food processing and preservation. The presence of these genes is undesirable, because horizontal transfer may occur with the natural biota of consumers. For this reason, it is important to analyse the presence of pathogenicity genes in such cultures. In this work, virulence factors and antibiotic resistance of Enterococcus faecium strain MXVK29, producing an antimicrobial compound with high antilisterial activity, were analysed. The results indicate that the strain is safe to be used in food processing as starter culture.

Antibiotic sensitivity pattern of indigenous lactobacilli isolated from curd and human milk samples

The gut microbiota plays a vital role in host well-being and lactic acid bacteria (LAB) have gained an overwhelming attention as health promoter. This perception has evolved from traditional dairy products to a money-spinning market of probiotics. The safety of probiotics is coupled to their intended use and LAB may act as pool of antimicrobial resistance genes that could be transferred to pathogens, either in food matrix or in gastrointestinal tract, which could be detrimental to host. This study evaluated the antibiotic susceptibility patterns of LAB isolated from curd (20) and human milk (11) samples. Antibiotic susceptibility was determined against 26 common antibiotics, following reference disc diffusion assay. A varied response in terms of susceptibility and resistance towards antibiotics was recorded. Among curd isolates, D7 (Lactobacillus plantarum) was the most resistant followed by D4, D8, D10 and D25. Among human milk isolates, HM-1 (L. casei) showed the highest resistance profile. All LAB isolates displayed high susceptibility pattern towards imipenem and meropenem. In general, high resistivity was exhibited by human milk isolates. The present study showed that antibiotic resistance is widespread among different lactobacilli, which may pose a food safety concern. Therefore, antibiotic sensitivity should be considered as a vital tool for safety assessment of probiotics.

Adaptation to Biocides Cetrimide and Chlorhexidine in Bacteria from Organic Foods: Association with Tolerance to Other Antimicrobials and Physical Stresses

Chlorhexidine (CH) and quaternary ammonium compounds (QAC), such as cetrimide (CE), are widely used as disinfectants because of their broad antimicrobial spectrum. However, their frequent use for disinfection in different settings may promote bacterial drug resistance against both biocides and clinically relevant antibiotics. This study analyzes the effects of stepwise exposure to cetrimide (CE) and chlorhexidine (CH) of bacteria from organic foods and previously classified as biocide-sensitive. Gradual exposure of these strains to biocides resulted in mainly transient decreased antimicrobial susceptibility to other antibiotics and to biocides. Biocide-adapted bacteria also exhibit alterations in physiological characteristics, mainly decreased heat tolerance, or gastric acid tolerance in CE-adapted strains, while bile resistance does not seem to be influenced by biocide adaptation. Results from this study suggest that changes in membrane fluidity may be the main mechanism responsible for the acquisition of stable tolerance to biocides.

Lactic acid bacteria isolated from raw and fermented pork products: Identification and characterization of catalase-producing Pediococcus pentosaceus

Lactic acid bacteria (LAB) from raw and fermented pork samples were screened for their inhibitory activity by an agar spot test in order to obtain a LAB strain with suitable property to be used as meat starter cultures. Among the 174 isolates, 73 were positive to inhibit at least one of the seven indicator bacteria, which were further characterized. The most suitable isolate was isolate P0805, identified as Pediococcus pentosaceus. This bacterium was catalase- and nitrate reductase-positive and amino acid decarboxylase-negative; moreover, it produced inhibitory substances against Salmonella Typhimurium with the activity of the partially purified inhibitory substances of 409,600 AU/mL. To further characterize the catalase-producing ability of P. pentosaceus P0805, the effect of hematin on its catalase activity in Sausage Model Broth (SMB) was evaluated, and it enhanced catalase production. The catalase activity was found in both SMB with and without hematin. It was concluded that catalase produced by this bacterium was heme-independent catalase.

Characterization of Antibiotic Resistance Genes from Lactobacillus Isolated from Traditional Dairy Products

Lactobacilli are widely used as starter cultures or probiotics in yoghurt, cheese, beer, wine, pickles, preserved food, and silage. They are generally recognized as safe (GRAS). However, recent studies have shown that some lactic acid bacteria (LAB) strains carry antibiotic resistance genes and are resistant to antibiotics. Some of them may even transfer their intrinsic antibiotic resistance genes to other LAB or pathogens via horizontal gene transfer, thus threatening human health. A total of 33 Lactobacillus strains was isolated from fermented milk collected from different areas of China. We analyzed (1) their levels of antibiotic resistance using a standardized dilution method, (2) their antibiotic resistance gene profiles by polymerase chain reaction (PCR) using gene-specific primers, and (3) the transferability of some of the detected resistance markers by a filter mating assay. All Lactobacillus strains were found to be resistant to vancomycin, but susceptible to gentamicin, linezolid, neomycin, erythromycin, and clindamycin. Their susceptibilities to tetracycline, kanamycin, ciprofloxacin, streptomycin, quinupristin/dalfopristin, trimethoprim, ampicillin, rifampicin, and chloramphenicol was different. Results from our PCR analysis revealed 19 vancomycin, 10 ciprofloxacin, and 1 tetracycline-resistant bacteria that carried the van(X), van(E), gyr(A), and tet(M) genes, respectively. Finally, no transferal of the monitored antibiotic resistance genes was observed in the filter mating assay. Taken together, our study generated the antibiotic resistance profiles of some milk-originated lactobacilli isolates and preliminarily assessed their risk of transferring antibiotic gene to other bacteria. The study may provide important data concerning the safe use of LAB.

Antibiotic resistance in lactococci and enterococci: phenotypic and molecular-genetic aspects

Extensive use of antibiotics in medicine, veterinary practice and animal husbandry has promoted the development and dissemination of bacterial drug resistance. The number of resistant pathogens causing common infectious diseases increases rapidly and creates worldwide public health problem. Commensal bacteria, including lactic acid bacteria of genera Enterococcus and Lactococcus colonizing gastrointestinal and urogenital tracts of humans and animals may act as vehicles of antibiotic resistance genes similar to those found in pathogens. Lactococci and enterococci are widely used in manufacturing of fermented products and as probiotics, therefore monitoring and control of transmissible antibiotic resistance determinants in industrial strains of these microorganisms is necessary to approve their Qualified Presumption of Safety status. Understanding the nature and molecular mechanisms of antibiotic resistance in enterococci and lactococci is essential, as intrinsic resistant bacteria pose no threat to environment and human health in contrast to bacteria with resistance acquired through horizontal transfer of resistance genes. The review summarizes current knowledge concerning intrinsic and acquired antibiotic resistance in Lactococcus and Enterococcus genera, and discusses role of enterococci and lactococci in distribution of this feature.

Antibiotic resistance mechanisms of Myroides sp

Bacteria of the genus Myroides (Myroides spp.) are rare opportunistic pathogens. Myroides sp. infections have been reported mainly in China. Myroides sp. is highly resistant to most available antibiotics, but the resistance mechanisms are not fully elucidated. Current strain identification methods based on biochemical traits are unable to identify strains accurately at the species level. While 16S ribosomal RNA (rRNA) gene sequencing can accurately achieve this, it fails to give information on the status and mechanisms of antibiotic resistance, because the 16S rRNA sequence contains no information on resistance genes, resistance islands or enzymes. We hypothesized that obtaining the whole genome sequence of Myroides sp., using next generation sequencing methods, would help to clarify the mechanisms of pathogenesis and antibiotic resistance, and guide antibiotic selection to treat Myroides sp. infections. As Myroides sp. can survive in hospitals and the environment, there is a risk of nosocomial infections and pandemics. For better management of Myroides sp. infections, it is imperative to apply next generation sequencing technologies to clarify the antibiotic resistance mechanisms in these bacteria.

Effects of exposure to quaternary-ammonium-based biocides on antimicrobial susceptibility and tolerance to physical stresses in bacteria from organic foods

In the present study, a collection of 76 biocide-sensitive bacterial strains isolated from organically produced food were adapted by repeated exposure to increasing concentrations of the quaternary ammonium compounds (QACs) benzalkonium chloride (BC) and hexadecylpyridinium chloride (HDP). The sensitivity of both wildtype strains and their corresponding QAC-adapted strains to other biocides and to antibiotics was studied. QAC tolerance increased in 88.2% of strains for BC and in 30.3% of strains for HDP, with increases in minimum inhibitory concentrations between 2 and over 100 fold. Adaptive resistance was stable after 20 subcultures in biocide-free medium for 7 and 5 of the BC- and HDP-adapted strains, respectively. Adaptation to BC and HDP also reduced the susceptibility to other biocides, mainly hexachlorophene (CF), didecyldimethylammonium bromide (AB), triclosan (TC) and chlorhexidine (CH). BC-adapted strains showed increased antibiotic resistance to ampicillin (AM) followed by sulfamethoxazol (SXT) and cefotaxime (CTX), and some showed increased sensitivity to ceftazidime (CAZ), CTX, AM and STX. Changes in antibiotic resistance in HDP-adapted strains were more heterogeneous and strain-dependent. Main efflux pump genes detected in QAC-adapted strains were acrB, sugE, norC, qacE and qacH, as well as antibiotic resistance genes aac(6_)-Ie-aph(2_)-Ia, aph(2_)-Ic, ant(4_)-Ia, lsa, mrsA/B, ereA, ermB and cat. Membrane anisotropy experiments revealed that QAC adaptation induced an increase in membrane rigidity in the case of BC, while response to HDP was more heterogeneous and strain-dependent. Growth capacity was significantly higher in some QAC-adapted strains and strain-dependent changes in heat tolerance were also detected in QAC-adapted strains. Gastric acid or bile resistances do not seem to be influenced by QAC adaptation.

Genomic analysis of the multi-drug-resistant clinical isolate Myroides odoratimimus PR63039

Myroides odoratimimus (M. odoratimimus) has been gradually implicated as an important nosocomial pathogen that poses a serious health threat to immunocompromised patients owing to its multi-drug resistance. However, the resistance mechanism is currently unclear. To clarify the antibiotic resistance and infectivity mechanisms of M. odoratimimus, whole genome sequencing was performed on the multi-drug-resistant M. odoratimimus strain PR63039. The genome sequence was completed with single molecule real-time (SMRT) technologies. Then, annotation was performed using RAST and IMG-ER. A number of databases and software programs were used to analyze the genomic characteristics, including GC-Profile, ISfinder, CG viewer, ARDB, CARD, ResFinder, the VFDB database, PHAST and Progressive Mauve. The M. odoratimimus PR63039 genome consisted of a chromosome and a plasmid. The genome contained a large number of resistance genes and virulence factors. The distribution of the resistance genes was distinctive, and a resistance region named MY63039-RR was found. The subsystem features generated by RAST indicated that the annotated genome had 108 genes that were potentially involved in virulence, disease and defense, all of which had strong associations with resistance and pathogenicity. The prophage analysis showed two incomplete prophages in the genome. The genomic analysis of M. odoratimimus PR63039 partially clarified its antibiotic resistance mechanisms and virulence factors. Obtaining a clear understanding of its genomic characteristics will be conducive to the management of multidrug-resistant M. odoratimimus.

Assessment of the in vitro bioactive properties of lactic acid bacteria isolated from native ecological niches of Ecuador

Lactic acid bacteria are known for their biotechnological potential. In various regions of Ecuador numerous indigenous biological resources are largely undocumented. In this study, we evaluated the potential probiotic characteristics and antagonistic in vitro properties of some lactic acid bacteria from native niches of the subtropical rain forests of Ecuador. These isolates were identified according to their morphological properties, standard API50CH fermentation profile and RAPD-DNA polymorphism pattern. The selected isolates were further evaluated for their probiotic potential. The isolates grew at 15°C and 45°C, survived at a pH ranging from 2.5 to 4.5 in the presence of 0.3% bile (>90%) and grew under sodium chloride conditions. All selected isolates were sensitive to ampicillin, amoxicillin and cefuroxime and some showed resistance to gentamicin, kanamycin and tetracycline. Moreover, the agar well diffusion assay showed that the supernatant of each strain at pH 3.0 and pH 4.0, but not at pH 7.0 exhibited increased antimicrobial activity (inhibition zone >15mm) against two foodborne pathogens, Escherichia coli and Salmonella spp. To our knowledge, this is the first report describing the antagonistic activity against two foodborne pathogens and the probiotic in vitro potential of lactic acid bacteria isolated from native biota of Ecuador.

Technological and safety properties of newly isolated GABA-producing Lactobacillus futsaii strains

AIM

To evaluate the technological and safety properties of Lactobacillus futsaii CS3 and CS5 isolated from Thai fermented shrimp products (Kung-Som) in order to develop a valuable gamma-aminobutyric acid (GABA)-producing starter culture.

METHODS AND RESULTS

Both strains showed a high GABA-producing ability (>8 mg ml(-1) ) in MRS broth containing 20 mg ml(-1) monosodium glutamate (MSG) for 120 h. They also exhibited inhibitory activity against foodborne pathogens and spoilage bacteria. Cell surface hydrophobicity and proteolytic activity were observed in both strains. Strain CS3 survived better under simulated gastrointestinal tract conditions with only 1·5 log-units cell decrease over 8 h. Both strains showed the ability to deconjugate taurocholate and taurodeoxycholate acid. Neither virulence genes nor biogenic amine production was detected. Strain CS3 exhibited susceptibility to all tested antibiotics with the exception of vancomycin, while strain CS5 showed resistance to vancomycin, ampicillin and chloramphenicol.

CONCLUSIONS

Based on the results obtained, Lact. futsaii CS3 is very promising as a GABA-producing and potentially probiotic starter culture strain for applications in functional fermented foods.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study focuses on the technological and safety characteristics of Lact. futsaii CS3 and CS5 including their high GABA-producing capacity for the first time. This provides a way of replacing chemical GABA by natural GABA using a GABA-producing starter culture candidate, at the same time offering the consumer new attractive food products.

Anti-bacterial and anti-biofilm activity of probiotic bacteria against oral pathogens

In this study, three lactic acid bacteria (LAB), isolated from barley, traditional dried meat and fermented olive were characterized and tested for their anti-bacterial and anti-biofilm activities against oral bacteria. Our results revealed that the tested LAB were γ-hemolytic and were susceptible to four antibiotics. All the strains were resistant to low pH, bile salt, pepsin and pancreatin. Furthermore, FB2 displayed a high aut-oaggregative phenotype (99.54%) while FF2 exhibited the best co-aggregation rate. Concerning the microbial adhesion to solvent, FB2 was the most hydrophobic strain (data obtained with chloroform and n-hexadecane). In addition Pediococcus pentosaceus FB2 and Lactobacillus brevis FF2 displayed a significant inhibitory effect against Streptococcus salivarius B468 (MIC = 10%). Moreover the selected strains were able to inhibit biofilm formation of Bacillus cereus ATCC14579 (MBIC50 = 28.16%) and S. salivarius B468 (MBIC50 = 42.28%). The selected LAB could be considered as candidate probiotics for further application in functional food and mainly in the prevention of oral diseases.

Adaptive tolerance to phenolic biocides in bacteria from organic foods: Effects on antimicrobial susceptibility and tolerance to physical stresses

The aim of the present study was to analyze the effects of step-wise exposure of biocide-sensitive bacteria from organic foods to phenolic biocides triclosan (TC) and hexachlorophene [2,2'-methylenebis(3,4,6-trichlorophenol)] (CF). The analysis included changes in the tolerance to the biocide itself, the tolerance to other biocides, and cross-resistance to clinically important antibiotics. The involvement of efflux mechanisms was also studied as well as the possible implication of modifications in cytoplasmic membrane fluidity in the resistance mechanisms. The influence of biocide tolerance on growth capacity of the adapted strains and on subsequent resistance to other physical stresses has also been analyzed. Repeated exposure of bacteria from organic foods to phenolic biocides resulted in most cases in partially increased tolerance to the same biocide, to dissimilar biocides and other antimicrobial compounds. Nine TC-adapted strains and six CF-adapted strains were able to develop high levels of biocide tolerance, and these were stable in the absence of biocide selective pressure. Most strains adapted to TC and one CF-adapted strain showed significantly higher anisotropy values than their corresponding wildtype strains, suggesting that changes in membrane fluidity could be involved in biocide adaptation. Exposure to gradually increasing concentrations of CF induced a decrease in heat tolerance. Biocide adaptation had no significant effects of gastric acid or bile resistance, suggesting that biocide adaptation should not influence survival in the gastrointestinal tract.

Physio-chemical, microbiological properties of tempoyak and molecular characterisation of lactic acid bacteria isolated from tempoyak

This study aims to determine physio-chemical properties of tempoyak, characterise the various indigenous species of lactic acid bacteria (LAB) present at different stages of fermentation and also to determine the survival of selected foodborne pathogens in tempoyak. The predominant microorganisms present in tempoyak were LAB (8.88-10.42 log CFU/g). Fructobacillus durionis and Lactobacillus plantarum were the dominant members of LAB. Other LAB species detected for the first time in tempoyak were a fructophilic strain of Lactobacillus fructivorans, Leuconostoc dextranicum, Lactobacillus collinoides and Lactobacillus paracasei. Heterofermentative Leuconostoc mesenteroides and F. durionis were predominant in the initial stage of fermentation, and as fermentation proceeded, F. durionis remained predominant, but towards the end of fermentation, homofermentative Lb. plantarum became the predominant species. Lactic, acetic and propionic acids were present in concentrations ranging from 0.30 to 9.65, 0.51 to 7.14 and 3.90 to 7.31 mg/g, respectively. Genotyping showed a high degree of diversity among F. durionis and Lb. plantarum isolates, suggesting different sources of LAB. All tested Lb. plantarum and F. durionis (except for one isolate) isolates were multidrug resistant. Salmonella spp., Listeria monocytogenes and Staphylococcus aureus were not detected. However, survival study showed that these pathogens could survive up to 8-12 days. The results aiming at improving the quality and safety of tempoyak.

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

In spite of a global concern on the transfer of antibiotic resistances (AR) via the food chain, limited information exists on this issue in species of Leuconostoc and Weissella, adjunct cultures used as aroma producers in fermented foods. In this work, the minimum inhibitory concentration was determined for 16 antibiotics in 34 strains of dairy origin, belonging to Leuconostoc mesenteroides (18), Leuconostoc citreum (11), Leuconostoc lactis (2), Weissella hellenica (2), and Leuconostoc carnosum (1). Atypical resistances were found for kanamycin (17 strains), tetracycline and chloramphenicol (two strains each), and erythromycin, clindamycin, virginiamycin, ciprofloxacin, and rifampicin (one strain each). Surprisingly, L. mesenteroides subsp. mesenteroides LbE16, showed resistance to four antibiotics, kanamycin, streptomycin, tetracycline and virginiamycin. PCR analysis identified tet(S) as responsible for tetracycline resistance in LbE16, but no gene was detected in a second tetracycline-resistant strain, L. mesenteroides subsp. cremoris LbT16. In Leuconostoc mesenteroides subsp. dextranicum LbE15, erythromycin and clindamycin resistant, an erm(B) gene was amplified. Hybridization experiments proved erm(B) and tet(S) to be associated to a plasmid of ≈35 kbp and to the chromosome of LbE15 and LbE16, respectively. The complete genome sequence of LbE15 and LbE16 was used to get further insights on the makeup and genetic organization of AR genes. Genome analysis confirmed the presence and location of erm(B) and tet(S), but genes providing tetracycline resistance in LbT16 were again not identified. In the genome of the multi-resistant strain LbE16, genes that might be involved in aminoglycoside (aadE, aphA-3, sat4) and virginiamycin [vat(E)] resistance were further found. The erm(B) gene but not tet(S) was transferred from Leuconostoc to Enterococcus faecalis both under laboratory conditions and in cheese. This study contributes to the characterization of AR in the Leuconostoc-Weissella group, provides evidence of the genetic basis of atypical resistances, and demonstrates the inter-species transfer of erythromycin resistance.

Key Roles of Human Polymorphonuclear Cells and Ciprofloxacin in Lactobacillus Species Infection Control

Lactobacilli have the potential to act as reservoirs of antibiotic resistance genes similar to those found in human pathogens, with the risk of transferring these genes to many pathogenic bacteria. In this study, we investigated the role of human polymorphonuclear cells (PMNs) against Lactobacillus spp. both resistant and susceptible to ciprofloxacin (a fluoroquinolone) and the effect of ciprofloxacin on the interaction between PMNs and three Lactobacillus spp. with different patterns of susceptibility to this drug. Hence, the primary functions of PMNs, such as phagocytosis and bacterial intracellular killing, against lactobacilli were investigated. The rate of PMN phagocytosis was high for ciprofloxacin-sensitive and ciprofloxacin-resistant strains. The patterns of intracellular killing of ciprofloxacin-sensitive and ciprofloxacin-resistant strains by PMNs underline that PMNs alone were able to kill lactobacilli. The addition of ciprofloxacin to PMNs did not result in a significant increase in the bacterial uptake by phagocytes. On the contrary, ciprofloxacin had a marked effect on PMN intracellular killing, resulting in increased numbers of killed ciprofloxacin-sensitive bacteria in comparison with antibiotic-free controls. Our data show that by itself, the profile of antibiotic resistance does not constitute an intrinsic factor of greater or lesser pathogenicity toward the host. The ability of PMNs to kill a diverse array of bacterial pathogens is essential for human innate host defense, primarily in immunocompromised patients.

Antibiotic susceptibility and heterogeneity in technological traits of lactobacilli isolated from Algerian goat's milk

The objective of this study was to identify and study the heterogeneity of technological traits of lactobacilli from goat's milk of Algeria and to evaluate in vitro their safety aspect. Using API50 CHL system and 16S rDNA sequencing, 51 % of strains were assigned as Lactobacillus plantarum, 34 % as L. pentosus, 7 % as L. rhamnosus and 8 % as L. fermentum. A large variability was noted for the acidifying capacity in skim milk after 6, 12 and 24 h of incubation. All strains expressed aminopeptidase activity against alanine-ρ-NA and leucine-ρ-NA at different levels. All strains were resistant to vancomycin and most of strains showed more susceptibility to β-lactam antibiotic. High susceptibility toward the inhibitors of protein synthesis was also observed. Minimum inhibitory concentrations data obtained revealed that isolates were susceptible to penicillin and chloramphenicol, and resistant to gentamicin and vancomycin. Minimum inhibitory concentrations distribution of other antibiotics showed variability. The analysis of graphical representation of principal component analysis of technological properties of L. plantarum and L. pentosus strains showed diversity among the isolates. Finally, eight L. plantarum (LAM1, LAM3, LAM21, LAM25, LAM35, LF15, LAM34, and LAM35), four L. pentosus (LAM38, LAM39, LF9 and LF16) and two L. rhamnosus (LF3 and LF10) strains, could be good candidates as adjunct culture in dairy product in Algeria.

Identification and characterization of tetracycline resistance in Lactococcus lactis isolated from Polish raw milk and fermented artisanal products

To assess the occurrence of antibiotic-resistant Lactic Acid Bacteria (LAB) in Polish raw milk and fermented artisanal products, a collection comprising 500 isolates from these products was screened. Among these isolates, six strains (IBB28, IBB160, IBB161, IBB224, IBB477 and IBB487) resistant to tetracycline were identified. The strains showing atypical tetracycline resistance were classified as Lactococcus lactis: three of them were identified as L. lactis subsp. cremoris (IBB224, IBB477 and IBB487) and the other three (IBB28, IBB160, IBB161) were identified as L. lactis subsp. lactis. The mechanism involving Ribosomal Protection Proteins (RPP) was identified as responsible for tetracycline resistance. Three of the tested strains (IBB28, IBB160 and IBB224) had genes encoding the TetS protein, whereas the remaining three (IBB161, IBB477 and IBB487) expressed TetM. The results also demonstrated that the genes encoding these proteins were located on genetic mobile elements. The tet(S) gene was found to be located on plasmids, whereas tet(M) was found within the Tn916 transposon.

Identification and Antimicrobial Resistance of Bacteria Isolated from Probiotic Products Used in Shrimp Culture

Probiotics are increasingly used in aquaculture to control diseases and improve feed digestion and pond water quality; however, little is known about the antimicrobial resistance properties of such probiotic bacteria and to what extent they may contribute to the development of bacterial resistance in aquaculture ponds. Concerns have been raised that the declared information on probiotic product labels are incorrect and information on bacterial composition are often missing. We therefore evaluated seven probiotics commonly used in Vietnamese shrimp culture for their bacterial species content, phenotypic antimicrobial resistance and associated transferable resistance genes. The bacterial species was established by 16S rRNA sequence analysis of 125 representative bacterial isolates. MIC testing was done for a range of antimicrobials and whole genome sequencing of six multiple antimicrobial resistant Bacillus spp. used to identify resistance genes and genetic elements associated with horizontal gene transfer. Thirteen bacterial species declared on the probiotic products could not be identified and 11 non-declared Bacillus spp. were identified. Although our culture-based isolation and identification may have missed a few bacterial species present in the tested products this would represent minor bias, but future studies may apply culture independent identification methods like pyro sequencing. Only 6/60 isolates were resistant to more than four antimicrobials and whole genome sequencing showed that they contained macrolide (ermD), tetracycline (tetL), phenicol (fexA) and trimethoprim (dfrD, dfrG and dfrK) resistance genes, but not known structures associated with horizontal gene transfer. Probiotic bacterial strains used in Vietnamese shrimp culture seem to contribute with very limited types and numbers of resistance genes compared to the naturally occurring bacterial species in aquaculture environments. Approval procedures of probiotic products must be strengthened through scientific-based efficacy trials and product labels should allow identification of individual bacterial strains and inform the farmer on specific purpose, dosage and correct application measures.

Antibiotic susceptibility of Lactobacillus strains isolated from domestic geese

The aim of this study was to determine the antibiotic susceptibility of 93 Lactobacillus strains isolated from domestic geese raised on Polish farms. The minimal inhibitory concentration (MIC) of 13 antimicrobial substances was determined by the broth microdilution method. All strains were sensitive to the cell wall inhibitors ampicillin and amoxicillin (MIC ≤ 8 μg/ml). Resistance to inhibitors of protein synthesis and to fluoroquinolone inhibitors of replication was found in 44.1% and 60.2% of isolates, respectively; 26.9% strains were resistant to neomycin (MIC ≥ 64 μg/ml), 23.6% to tetracycline (MIC ≥ 32 μg/ml), 15% to lincomycin (MIC ≥ 64 μg/ml), 18.3% to doxycycline (MIC ≥ 32 μg/ml), 9.7% to tylosin (MIC ≥ 32 μg/ml), 56% to flumequine (MIC ≥ 256 μg/ml) and 22.6% to enrofloxacin (MIC ≥ 64 μg/ml). Bimodal distribution of MICs indicative of acquired resistance and unimodal distribution of the high MIC values indicative of intrinsic resistance were correlated with Lactobacillus species. Eleven (11.8%) strains displayed multiple resistance for at least three classes of antibiotics. Data derived from this study can be used as a basis for reviewing current microbiological breakpoints for categorisation of susceptible and resistant strains of Lactobacillus genus and help to assess the hazards associated with the occurrence of drug resistance among natural intestinal microflora.

Antibiotic resistance of lactic acid bacteria isolated from dry-fermented sausages

Dry-fermented sausages are meat products highly valued by many consumers. Manufacturing process involves fermentation driven by natural microbiota or intentionally added starter cultures and further drying. The most relevant fermentative microbiota is lactic acid bacteria (LAB) such as Lactobacillus, Pediococcus and Enterococcus, producing mainly lactate and contributing to product preservation. The great diversity of LAB in dry-fermented sausages is linked to manufacturing practices. Indigenous starters development is considered to be a very promising field, because it allows for high sanitary and sensorial quality of sausage production. LAB have a long history of safe use in fermented food, however, since they are present in human gastrointestinal tract, and are also intentionally added to the diet, concerns have been raised about the antimicrobial resistance in these beneficial bacteria. In fact, the food chain has been recognized as one of the key routes of antimicrobial resistance transmission from animal to human bacterial populations. The World Health Organization 2014 report on global surveillance of antimicrobial resistance reveals that this issue is no longer a future prediction, since evidences establish a link between the antimicrobial drugs use in food-producing animals and the emergence of resistance among common pathogens. This poses a risk to the treatment of nosocomial and community-acquired infections. This review describes the possible sources and transmission routes of antibiotic resistant LAB of dry-fermented sausages, presenting LAB antibiotic resistance profile and related genetic determinants. Whenever LAB are used as starters in dry-fermented sausages processing, safety concerns regarding antimicrobial resistance should be addressed since antibiotic resistant genes could be mobilized and transferred to other bacteria.

Lactococcus hircilactis sp. nov. and Lactococcus laudensis sp. nov., isolated from milk

Two strains of lactic acid bacteria, designated 117(T) and 4195(T), were isolated from goat milk in Valtellina, Italy and from cow milk in Valle Trompia, Italy, respectively, and characterized taxonomically by a polyphasic approach. The strains were Gram-stain-positive, coccoid, non-spore-forming and catalase-negative bacteria. Morphological, physiological and phylogenetic data indicated that these isolates belonged to the genus Lactococcus. Strain 117(T) was closely related to Lactococcus fujiensis, Lactococcus lactis subsp. lactis, L. lactis subsp. cremoris, L. lactis subsp. hordniae, L. lactis subsp. tructae and Lactococcus taiwanensis, showing 93-94% and 82-89% 16S rRNA and rpoB gene sequence similarities, respectively. Strain 4195(T) was closely related to Lactococcus chungangensis, Lactococcus raffinolactis, Lactococcus plantarum and Lactococcus piscium, showing 92-98% and 86-99% 16S rRNA and rpoB gene sequence similarities, respectively. Based on this evidence and the data obtained in the present study, the milk isolates represent two novel species of the genus Lactococcus, for which the names Lactococcushircilactis sp. nov., and Lactococcuslaudensis sp. nov. are proposed. The respective type strains are 117(T) ( = LMG 28352(T) = DSM 28960(T)) and 4195(T )( = LMG 28353(T) = DSM 28961(T)).