Heat shock treatment increases the frequency of loss of an erythromycin resistance-encoding transposable element from the chromosome of Lactobacillus crispatus CHCC3692

Detection of Acquired Antibiotic Resistance Genes in Domestic Pig (Sus scrofa) and Common Carp (Cyprinus carpio) Intestinal Samples by Metagenomics Analyses in Hungary

The aim of this study was metagenomics analyses of acquired antibiotic-resistance genes (ARGs) in the intestinal microbiome of two important food-animal species in Hungary from a One Health perspective. Intestinal content samples were collected from 12 domestic pigs (Sus scrofa) and from a common carp (Cyprinus carpio). Shotgun metagenomic sequencing of DNA purified from the intestinal samples was performed on the Illumina platform. The ResFinder database was applied for detecting acquired ARGs in the assembled metagenomic contigs. Altogether, 59 acquired ARG types were identified, 51 genes from domestic pig and 12 genes from the carp intestinal microbiome. ARG types belonged to the antibiotic classes aminoglycosides (27.1%), tetracyclines (25.4%), β-lactams (16.9%), and others. Of the identified ARGs, tet(E), a bla_OXA-_48-like β-lactamase gene, as well as cphA4, ampS, aadA2, qnrS2, and sul1, were identified only in carp but not in swine samples. Several of the detected acquired ARGs have not yet been described from food animals in Hungary. The tet(Q), tet(W), tet(O), and mef(A) genes detected in the intestinal microbiome of domestic pigs had also been identified from free-living wild boars in Hungary, suggesting a possible relationship between the occurrence of acquired ARGs in domestic and wild animal populations.

Minocycline, focus on mechanisms of resistance, antibacterial activity, and clinical effectiveness: Back to the future

OBJECTIVES

The increasing crisis regarding multidrug-resistant (MDR) and extensively drug-resistant microorganisms leads to appealing therapeutic options.

METHODS

During the last 30 years, minocycline, a wide-spectrum antimicrobial agent, has been effective against MDR Gram-positive and Gram-negative bacterial infections. As with other tetracyclines, the mechanism of action of minocycline involves attaching to the bacterial 30S ribosomal subunit and preventing protein synthesis.

RESULTS

This antimicrobial agent has been approved for the treatment of acne vulgaris, some sexually transmitted diseases and rheumatoid arthritis. Although many reports have been published, there remains limited information regarding the prevalence, mechanism of resistance and clinical effectiveness of minocycline.

CONCLUSION

Thus, we summarize here the currently available data concerning pharmacokinetics and pharmacodynamics, mechanism of action and resistance, antibacterial activity and clinical effectiveness of minocycline.

The art of strain improvement of industrial lactic acid bacteria without the use of recombinant DNA technology

The food industry is constantly striving to develop new products to fulfil the ever changing demands of consumers and the strict requirements of regulatory agencies. For foods based on microbial fermentation, this pushes the boundaries of microbial performance and requires the constant development of new starter cultures with novel properties. Since the use of ingredients in the food industry is tightly regulated and under close scrutiny by consumers, the use of recombinant DNA technology to improve microbial performance is currently not an option. As a result, the focus for improving strains for microbial fermentation is on classical strain improvement methods. Here we review the use of these techniques to improve the functionality of lactic acid bacteria starter cultures for application in industrial-scale food production. Methods will be described for improving the bacteriophage resistance of specific strains, improving their texture forming ability, increasing their tolerance to stress and modulating both the amount and identity of acids produced during fermentation. In addition, approaches to eliminating undesirable properties will be described. Techniques include random mutagenesis, directed evolution and dominant selection schemes.

Occurrence and persistence of erythromycin resistance genes (erm) and tetracycline resistance genes (tet) in waste treatment systems on swine farms

Animal manure from modern animal agriculture constitutes the single largest source of antibiotic resistance (AR) owing to the use of large quantities of antibiotics. After animal manure enters the environment, the AR disseminates into the environment and can pose a potentially serious threat to the health and well-being of both humans and animals. In this study, we evaluated the efficiency of three different on-farm waste treatment systems in reducing AR. Three classes of erythromycin resistance genes (erm) genes (B, F, and X) conferring resistances to macrolide-lincosamides-streptogramin B (MLS(B)) and one class of tetracycline resistance genes (tet) gene (G) conferring resistance to tetracyclines were used as models. Real-time polymerase chain reaction assays were used to determine the reservoir sizes of these AR genes present in the entire microbiome. These classes of AR genes varied considerably in abundance, with erm(B) being more predominant than erm(F), erm(X), and tet(G). These AR genes also varied in persistence in different waste treatment systems. Aerobic biofiltration reduced erm(X) more effectively than other AR genes, while mesophilic anaerobic digestion and lagoon storage did not appreciably reduce any of these AR genes. Unlike chemical pollutants, some AR genes could increase after reduction in a preceding stage of the treatment processes. Season might also affect the persistence of AR. These results indicate that AR arising from swine-feeding operations can survive typical swine waste treatment processes and thus treatments that are more effective in destructing AR on farms are required.

Genome sequence of Lactobacillus helveticus, an organism distinguished by selective gene loss and insertion sequence element expansion

Mobile genetic elements are major contributing factors to the generation of genetic diversity in prokaryotic organisms. For example, insertion sequence (IS) elements have been shown to specifically contribute to niche adaptation by promoting a variety of genetic rearrangements. The complete genome sequence of the cheese culture Lactobacillus helveticus DPC 4571 was determined and revealed significant conservation compared to three nondairy gut lactobacilli. Despite originating from significantly different environments, 65 to 75% of the genes were conserved between the commensal and dairy lactobacilli, which allowed key niche-specific gene sets to be described. However, the primary distinguishing feature was 213 IS elements in the DPC 4571 genome, 10 times more than for the other lactobacilli. Moreover, genome alignments revealed an unprecedented level of genome stability between these four Lactobacillus species, considering the number of IS elements in the L. helveticus genome. Comparative analysis also indicated that the IS elements were not the primary agents of niche adaptation for the L. helveticus genome. A clear bias toward the loss of genes reported to be important for gut colonization was observed for the cheese culture, but there was no clear evidence of IS-associated gene deletion and decay for the majority of genes lost. Furthermore, an extraordinary level of sequence diversity exists between copies of certain IS elements in the DPC 4571 genome, indicating they may represent an ancient component of the L. helveticus genome. These data suggest a special unobtrusive relationship between the DPC 4571 genome and its mobile DNA complement.

Antibiotic resistance in non-enterococcal lactic acid bacteria and bifidobacteria

Over the last 50 years, human life expectancy and quality of life have increased dramatically due to improvements in nutrition and the use of antibiotics in the fight against infectious diseases. However, the heyday of antibiotic treatment is on the wane due to the appearance and spread of resistance among harmful microorganisms. At present, there is great concern that commensal bacterial populations from food and the gastrointestinal tract (GIT) of humans and animals, such as lactic acid bacteria (LAB) and bifidobacteria, could act as a reservoir for antibiotic resistance genes. Resistances could ultimately be transferred to human pathogenic and opportunistic bacteria hampering the treatment of infections. LAB species have traditionally been used as starter cultures in the production of fermented feed and foodstuffs. Further, LAB and bifidobacteria are normal inhabitants of the GIT where they are known to exert health-promoting effects, and selected strains are currently been used as probiotics. Antibiotic resistance genes carried by LAB and bifidobacteria can be transferred to human pathogenic bacteria either during food manufacture or during passage through the GIT. The aim of this review is to address well-stated and recent knowledge on antibiotic resistance in typical LAB and bifidobacteria species. Therefore, the commonest antibiotic resistance profiles, the distinction between intrinsic and atypical resistances, and some of the genetic determinants already discovered will all be discussed.

Genetic basis of tetracycline and minocycline resistance in potentially probiotic Lactobacillus plantarum strain CCUG 43738

The potentially probiotic strain Lactobacillus plantarum CCUG 43738, which displayed atypical phenotypic resistance to tetracycline (MIC, 512 microg/ml) and minocycline (MIC, 256 microg/ml), was found to contain a tet(S) gene located on a plasmid of approximately 14 kb. Plasmid curing with novobiocin eliminated this plasmid and restored the tetracycline-susceptible phenotype of the host strain.

Cloacal Lactobacillus isolates from broilers show high prevalence of resistance towards macrolide and lincosamide antibiotics

Eighty-seven Lactobacillus strains isolated from cloacal swabs of broiler chickens derived from 20 different farms in Belgium were identified to species level and tested for susceptibility to macrolide and lincosamide antibiotics. Five different Lactobacillus species were identified as being predominantly present in the cloacae of broilers: Lactobacillus crispatus, Lactobacillus salivarius subsp. salivarius, Lactobacillus amylovorus, Lactobacillus gallinarum and Lactobacillu sreuteri. Acquired resistance prevalence to macrolides and lincosamides was very high in the investigated lactobacilli: 89% of the strains were resistant to either or both lincosamide and macrolide class antibiotics. The vast majority of these resistant strains (96%) displayed constitutive resistance. More than one-half of the macrolide and/or lincosamide resistant strains carried an erm(B), erm(C), mef(A), lnu(A) gene or a combination of these genes.

DNA microarray analysis of anaerobic Methanosarcina barkeri reveals responses to heat shock and air exposure

Methanosarcina barkeri is a methanogenic archaeon that can digest cellulose and other polysaccharides to produce methane. It can only grow under strictly anoxic conditions, but which can survive air exposure. To obtain further knowledge of cellular changes occurring in M. barkeri in response to air exposure and other environmental stresses, we constructed the first oligonucleotide microarray for M. barkeri and used it to investigate the global transcriptomic responses of M. barkeri to air exposure and heat shock at 45 degrees C for 1 h. The results showed that various house-keeping genes, such as genes involved in DNA replication recombination and repair, energy production and conversion, and protein turnover were regulated by environmental stimuli. In response to air exposure, up-regulation of a large number of transposase encoding genes was observed. However, no differential expression of genes encoding superoxide dismutase, catalase, nonspecific peroxidases or thioredoxin reductase was observed in response to air exposure, implying that no significant level of reactive oxygen species has been formed under air exposure. In response to heat shock, both Hsp70 (DnaK-DnaJ-GrpE chaperone system) the Hsp60 (GroEL) systems were up-regulated, suggesting that they may play an important role in protein biogenesis in M. barkeri during heat stress.

Characterization of a mobile clpL gene from Lactobacillus rhamnosus

Two genes encoding ClpL ATPase proteins were identified in a probiotic Lactobacillus rhamnosus strain, E-97800. Sequence analyses revealed that the genes, designated clpL1 and clpL2, share 80% identity. The clpL2 gene showed the highest degree of identity (98.5%) to a clpL gene from Lactobacillus plantarum WCFSI, while it was not detected in three other L. rhamnosus strains studied. According to Northern analyses, the expression of clpL1 and the clpL2 were induced during heat shock by > 20- and 3-fold, respectively. The functional promoter regions were determined by primer extension analyses, and the clpL1 promoter was found to be overlapped by an inverted repeat structure identical to the conserved CIRCE element, indicating that clpL1 belongs to the HrcA regulon in L. rhamnosus. No consensus binding sites for HrcA or CtsR could be identified in the clpL2 promoter region. Interestingly, the clpL2 gene was found to be surrounded by truncated transposase genes and flanked by inverted repeat structures nearly identical to the terminal repeats of the ISLpl1 from L. plantarum HN38. Furthermore, clpL2 was shown to be mobilized during prolonged cultivation at elevated temperature. The presence of a gene almost identical to clpL2 in L. plantarum and its absence in other L. rhamnosus strains suggest that the L. rhamnosus E-97800 has acquired the clpL2 gene via horizontal transfer. No change in the stress tolerance of the ClpL2-deficient derivative of E-97800 compared to the parental strain was observed.