Detection of Tn5-like sequences in kanamycin-resistant stream bacteria and environmental DNA

Crucifer Lesion-Associated Xanthomonas Strains Show Multi-Resistance to Heavy Metals and Antibiotics

Copper resistance in phytopathogens is a major challenge to crop production globally and is known to be driven by excessive use of copper-based pesticides. However, recent studies have shown co-selection of multiple heavy metal and antibiotic resistance genes in bacteria exposed to heavy metal and xenobiotics, which may impact the epidemiology of plant, animal, and human diseases. In this study, multi-resistance to heavy metals and antibiotics were evaluated in local Xanthomonas campestris pv. campestris (Xcc) and co-isolated Xanthomonas melonis (Xmel) strains from infected crucifer plants in Trinidad. Resistance to cobalt, cadmium, zinc, copper, and arsenic (V) was observed in both Xanthomonas species up to 25 mM. Heavy metal resistance (HMR) genes were found on a small plasmid-derived locus with ~ 90% similarity to a Stenotrophomonas spp. chromosomal locus and a X. perforans pLH3.1 plasmid. The co-occurrence of mobile elements in these regions implies their organization on a composite transposon-like structure. HMR genes in Xcc strains showed the lowest similarity to references, and the cus and ars operons appear to be unique among Xanthomonads. Overall, the similarity of HMR genes to Stenotrophomonas sp. chromosomal genomes suggest their origin in this genus or a related organism and subsequent spread through lateral gene transfer events. Further resistome characterization revealed the presence of small multidrug resistance (SMR), multidrug resistance (MDR) efflux pumps, and bla (Xcc) genes for broad biocide resistance in both species. Concurrently, resistance to antibiotics (streptomycin, kanamycin, tetracycline, chloramphenicol, and ampicillin) up to 1000 µg/mL was confirmed.

Study of antibiotic resistance in freshwater ecosystems with low anthropogenic impact

This study aimed to investigate the bacterial diversity and the background level of antibiotic resistance in two freshwater ecosystems with low anthropogenic impact in order to evaluate the presence of natural antimicrobial resistance in these areas and its potential to spread downstream. Water samples from a pre-Alpine and an Apennine river (Variola and Tiber, respectively) were collected in three different sampling campaigns and bacterial diversity was assessed by 16S sequencing, while the presence of bacteria resistant to five antibiotics was screened using a culturable approach. Overall bacterial load was higher in the Tiber River compared with the Variola River. Furthermore, the study revealed the presence of resistant bacteria, especially the Tiber River showed, for each sampling, the presence of resistance to all antibiotics tested, while for the Variola River, the detected resistance was variable, comprising two or more antibiotics. Screening of two resistance genes on a total of one hundred eighteen bacterial isolates from the two rivers showed that bla_TEM, conferring resistance to β-lactam antibiotics, was dominant and present in ~58 % of isolates compared to only ~9 % for mefA/E conferring resistance to macrolides. Moreover, β-lactam resistance was detected in various isolates showing also resistance to additional antibiotics such as macrolides, aminoglycosides and tetracyclines. These observations would suggest the presence of co-resistant bacteria even in non-anthropogenic environments and this resistance may spread from the environment to humans and/or animals.

Antibiotic resistance marker genes as environmental pollutants in GMO-pristine agricultural soils in Austria

Antibiotic resistance genes may be considered as environmental pollutants if anthropogenic emission and manipulations increase their prevalence above usually occurring background levels. The prevalence of aph(3')-IIa/nptII and aph(3')-IIIa/nptIII - frequent marker genes in plant biotechnology conferring resistance to certain aminoglycosides - was determined in Austrian soils from 100 maize and potato fields not yet exposed to but eligible for GMO crop cultivation. Total soil DNA extracts were analysed by nptII/nptIII-specific TaqMan real time PCR. Of all fields 6% were positive for nptII (median: 150 copies/g soil; range: 31-856) and 85% for nptIII (1190 copies/g soil; 13-61600). The copy-number deduced prevalence of nptIII carriers was 14-fold higher compared to nptII. Of the cultivable kanamycin-resistant soil bacteria 1.8% (95% confidence interval: 0-3.3%) were positive for nptIII, none for nptII (0-0.8%). The nptII-load of the studied soils was low rendering nptII a typical candidate as environmental pollutant upon anthropogenic release into these ecosystems.

Involvement of aph(3')-IIa in the formation of mosaic aminoglycoside resistance genes in natural environments

Intragenic recombination leading to mosaic gene formation is known to alter resistance profiles for particular genes and bacterial species. Few studies have examined to what extent aminoglycoside resistance genes undergo intragenic recombination. We screened the GenBank database for mosaic gene formation in homologs of the aph(3')-IIa (nptII) gene. APH(3')-IIa inactivates important aminoglycoside antibiotics. The gene is widely used as a selectable marker in biotechnology and enters the environment via laboratory discharges and the release of transgenic organisms. Such releases may provide opportunities for recombination in competent environmental bacteria. The retrieved GenBank sequences were grouped in three datasets comprising river water samples, duck pathogens and full-length variants from various bacterial genomes and plasmids. Analysis for recombination in these datasets was performed with the Recombination Detection Program (RDP4), and the Genetic Algorithm for Recombination Detection (GARD). From a total of 89 homologous sequences, 83% showed 99-100% sequence identity with aph(3')-IIa originally described as part of transposon Tn5. Fifty one were unique sequence variants eligible for recombination analysis. Only a single recombination event was identified with high confidence and indicated the involvement of aph(3')-IIa in the formation of a mosaic gene located on a plasmid of environmental origin in the multi-resistant isolate Pseudomonas aeruginosa PA96. The available data suggest that aph(3')-IIa is not an archetypical mosaic gene as the divergence between the described sequence variants and the number of detectable recombination events is low. This is in contrast to the numerous mosaic alleles reported for certain penicillin or tetracycline resistance determinants.

Prevalence of the aminoglycoside phosphotransferase genes aph(3')-IIIa and aph(3')-IIa in Escherichia coli, Enterococcus faecalis, Enterococcus faecium, Pseudomonas aeruginosa, Salmonella enterica subsp. enterica and Staphylococcus aureus isolates in Austria

The aminoglycoside phosphotransferase aph(3')-IIa primarily inactivates kanamycin and neomycin, whilst aph(3')-IIIa also inactivates amikacin. The aim of this study was to determine the frequency of both resistance genes in major human pathogens to obtain their baseline prevalence in the gene pool of these bacterial populations in Austria. In total, 10 541 Escherichia coli, Enterococcus faecalis, Enterococcus faecium, Pseudomonas aeruginosa, Salmonella enterica subsp. enterica and Staphylococcus aureus isolates were collected representatively without selection bias between 2008 and 2011. Isolates were analysed by aph(3')-IIIa/nptIII- and aph(3')-IIa/nptII-specific TaqMan real-time PCR. For positive strains, MICs using Etests were performed and resistance gene sequences were determined. The overall prevalence of aph(3')-IIIa/nptIII was 1.62 % (95 % confidence interval: 1.38-1.88 %). In Escherichia coli, enterococci, Staphylococcus aureus, P. aeruginosa and Salmonella spp., the aph(3')-IIIa/nptIII prevalence was 0.47 % (0-1.47 %), 37.53 % (32.84-42.40 %), 2.90 % (1.51-5.02 %), 0 % (0-0.32 %) and 0 % (0-0.037 %), respectively. Eleven of a total of 169 carriers showed single-nucleotide polymorphisms in the resistance allele. The overall prevalence of aph(3')-IIa/nptII was 0.0096 % (0-0.046 %). Escherichia coli (0-0.70 %), enterococci (0-0.75 %), Staphylococcus aureus (0-0.73 %) and P. aeruginosa (0-0.32 %) did not carry aph(3')-IIa. A single Salmonella isolate was positive, resulting in an aph(3')-IIa prevalence of 0.013 % (0-0.058 %). aph(3')-IIIa/nptIII carriers were moderately prevalent in the strains tested except for in enterococci, which appeared to be an important reservoir for aph(3')-IIIa. aph(3')-IIa/nptII genes were detected at clinically irrelevant frequencies and played no significant role in the aminoglycoside resistance gene pool during the observation period.

Metabolic Characterization of cold active Pseudomonas, Arthrobacter, Bacillus, and Flavobacterium spp. from Western Himalayas

Himalayan soils undergo dramatic temporal changes in their microclimatic properties. The soil habitats in the high altitude cold habitats of Himalayas are little explored with respect to bacterial diversity and metabolic potentials of the bacterial species. Soil habitat in Western Himalayas is dominated by the genera of Pseudomonas, Arthrobacter, Bacillus, and Flavobacterium. Strains were found to be diverse in their metabolic potentials to utilize different carbon sources by growing them on media containing 114 different sole carbon sources. Bacillus sp. STL9 was supported by the lowest number (12.3%) of the carbon sources while growth was observed in 73.7% of the carbon sources tested for the Pseudomonas sp. SPS2. Carbohydrates appeared to be preferred carbon sources for these Himalayan isolates followed by amino acids and proteins. These microbes also produced various extra-cellular hydrolytic enzymes having biotechnological potentials, lipase being the one secreted by most strains (85.7%) followed by β-galactosidase (42.8%). Antibiotic resistance profiling for 85 different antibiotics has also been described.

ELECTRONIC SUPPLEMENTARY MATERIAL

The online version of this article (doi:10.1007/s12088-011-0092-7) contains supplementary material, which is available to authorized users.

Occurrence and distribution of steroids, hormones and selected pharmaceuticals in South Florida coastal environments

The common occurrence of human derived contaminants like pharmaceuticals, steroids and hormones in surface waters has raised the awareness of the role played by the release of treated or untreated sewage in the water quality along sensitive coastal ecosystems. South Florida is home of many important protected environments ranging from wetlands to coral reefs which are in close proximity to large metropolitan cities. Because, large portions of South Florida and most of the Florida Keys population are not served by modern sewage treatment plants and rely heavily on the use of septic systems, a comprehensive survey of selected human waste contamination markers was conducted in three areas to assess water quality with respect to non-traditional micro-constituents. This study documents the occurrence and distribution of fifteen hormones and steroids and five commonly detected pharmaceuticals in surface water samples collected from different near shore environments along South Florida between 2004 and 2006. The compounds most frequently detected were: cholesterol, caffeine, estrone, DEET, coprostanol, biphenol-A, beta-estradiol, and triclosan. The concentration detected for estrone and beta-estradiol were up to 5.2 and 1.8 ng/L, respectively. Concentrations of caffeine (5.5-68 ng/L) and DEET (4.8-49 ng/L) were generally higher and more prevalent than were the steroids. Distribution of microconstituents was site specific likely reflecting a diversity of sources. In addition to chemical analysis, the yeast estrogen screen assay was used to screen the samples for estrogen equivalency. Overall, the results show that water collected from inland canals and restricted circulation water bodies adjacent to heavily populated areas had high concentrations of multiple steroids, pharmaceuticals, and personal care products while open bay waters were largely devoid of the target analytes.

Biosynthesis of aminocyclitol-aminoglycoside antibiotics and related compounds

This review covers the biosynthesis of aminocyclitol-aminoglycoside antibiotics and related compounds, particularly from the molecular genetic perspectives. 195 references are cited.

A global perspective on the use, sales, exposure pathways, occurrence, fate and effects of veterinary antibiotics (VAs) in the environment

Veterinary antibiotics (VAs) are widely used in many countries worldwide to treat disease and protect the health of animals. They are also incorporated into animal feed to improve growth rate and feed efficiency. As antibiotics are poorly adsorbed in the gut of the animals, the majority is excreted unchanged in faeces and urine. Given that land application of animal waste as a supplement to fertilizer is often a common practice in many countries, there is a growing international concern about the potential impact of antibiotic residues on the environment. Frequent use of antibiotics has also raised concerns about increased antibiotic resistance of microorganisms. We have attempted in this paper to summarize the latest information available in the literature on the use, sales, exposure pathways, environmental occurrence, fate and effects of veterinary antibiotics in animal agriculture. The review has focused on four important groups of antibiotics (tylosin, tetracycline, sulfonamides and, to a lesser extent, bacitracin) giving a background on their chemical nature, fate processes, occurrence, and effects on plants, soil organisms and bacterial community. Recognising the importance and the growing debate, the issue of antibiotic resistance due to the frequent use of antibiotics in food-producing animals is also briefly covered. The final section highlights some unresolved questions and presents a way forward on issues requiring urgent attention.

Household disposal of pharmaceuticals as a pathway for aquatic contamination in the United kingdom

Pharmaceuticals are produced and used in increasingly large volumes every year. With this growth comes concern about the fate and effects of these compounds in the environment. The discovery of pharmaceuticals in the aquatic environment has stimulated research in the last decade. A wide range of pharmaceuticals has been found in fresh and marine waters, and it has recently been shown that even in small quantities, some of these compounds have the potential to cause harm to aquatic life. The primary pathway into the environment is the use and disposal of medicines; although much of the research in the area currently focuses on the removal of pharmaceuticals during sewage treatment processes, disposal via household waste might be a significant pathway requiring further research. To investigate the household disposal of unused and expired pharmaceuticals as a source of pharmaceutical compounds in the environment, we carried out a survey and interviewed members of 400 households, predominantly from southeastern England. We used the information on when and how they disposed of unfinished pharmaceuticals to construct a conceptual model to assess the pathways of human pharmaceuticals into the environment. The model demonstrated that disposal of unused pharmaceuticals, either by household waste or via the sink or toilet, may be a prominent route that requires greater attention.

Pharmaceuticals in the aquatic environment--a comparison of risk assessment strategies

The growing concern over the release of pharmaceutically active compounds and personal care products into the environment has prompted the introduction of risk assessment guidelines in both the European Union by the European Medicines Evaluation Agency (EMEA) and in the United States by the Food and Drug Administration (FDA), details of which are presented herein. Both employ a similar tiered system that compares the predicted environmental concentrations (PEC) with the worst-case no effect concentrations estimated from standard toxicity assays. These approaches are compared and contrasted. Results demonstrate room for improvement in areas such as the use of threshold values to trigger investigations, chronic and mechanism specific toxicity screening and mixture toxicity for which possible solutions are proposed.

Detection and distribution of insertion sequence 1 (IS1)-containing bacteria in the freshwater environment(1)

The distribution of insertion sequence 1 (IS1)-containing bacteria was investigated in Windermere (Cumbria, UK), a freshwater body impacted by treated sewage discharge and run-off from the surrounding catchment. Culturable IS1-containing bacteria were recovered from the water column at three depths in Windermere North Basin (WNB) and South Basin (WSB), and from sediment at both sites (at the sediment surface in WSB and to a depth of 12-13 cm in WNB). Polymerase chain reaction amplification of IS1 and the Escherichia coli/Shigella sp. specific gene uidA, from community DNA from shallow sediments, extended the detection limit beyond that of culture at both sites. This detection was extended further into deep sediment extracted from WNB as IS1 and uidA were detected in sub-samples to a depth of 4.7 and 2.3 m, respectively. Analysis of a representative subset of 90 IS1-carrying isolates recovered from water and sediment at both sites demonstrated 21 heterogeneous IS1 profiles with estimated copy numbers ranging from 1 to 16. Identification of the host bacteria showed that the element was confined mainly to Enterobacter spp. However, this study showed IS1 to be present in Citrobacter freundii for the first time. Plasmids were carried by 75.3% of enterobacterial isolates and four plasmids (2.6%) carried IS1. DNA sequence analysis of five IS1 clones demonstrated that IS1 isoforms from this study were similar (>89% nucleotide identity) to known IS1 isoforms. Two isoforms of IS1 from a single Enterobacter cloacae isolate differed by 6.7% at the nucleotide level suggesting that they had been acquired independently.

Spatial patterns in antibiotic resistance among stream bacteria: effects of industrial pollution

The spatial distribution of antibiotic resistance to streptomycin and kanamycin was examined in natural bacterial communities of two streams. The proportion of resistant bacteria was substantially higher (P < 0.05) in the midreaches of an industrially perturbed stream, but no such pattern was apparent in an undisturbed reference stream. The highest relative frequency of resistance was found at the confluence of a tributary draining a nuclear reactor and industrial complex. Antibiotic resistance increased with distance upstream from the confluence and was positively correlated (r(2) = 0. 54, P = 0.023) with mercury concentrations in the sediments. When the data for two years were compared, this pattern was stable for streptomycin resistance (paired t test, P < 0.05) but not for kanamycin resistance (P > 0.05). Our results imply that heavy metal pollution may contribute to increased antibiotic resistance through indirect selection.

Structures of homologous composite transposons carrying cbaABC genes from Europe and North America

IS1071 is a class II transposable element carrying a tnpA gene related to the transposase genes of the Tn3 family. Copies of IS1071 that are conserved with more than 99% nucleotide sequence identity have been found as direct repeats flanking a remarkable variety of catabolic gene sequences worldwide. The sequences of chlorobenzoate catabolic transposons found on pBRC60 (Tn5271) in Niagara Falls, N.Y., and on pCPE3 in Bologna, Italy, show that these transposons were formed from highly homologous IS1071 and cbaABC components (levels of identity, > 99.5 and > 99.3%, respectively). Nevertheless, the junction sequences between the IS1071L and IS1071R elements and the internal DNA differ by 41 and 927 bp, respectively, suggesting that these transposons were assembled independently on the two plasmids. The formation of the right junction in both transposons truncated an open reading frame for a putative aryl-coenzyme A ligase with sequence similarity to benzoate- and p-hydroxybenzoate-coenzyme A ligases of Rhodopseudomonas palustris.

Occurrence, fate and effects of pharmaceutical substances in the environment--a review

Medical substances (pharmaceuticals) are a group of substances that until recently have been exposed to the environment with very little attention. The reason why they may be interesting as environmental micropollutants, is that medical substances are developed with the intention of performing a biological effect. Especially antibiotics used as growth promoters, as feed additives in fish farms are anticipated to end up in the environment. Very little is known about the exposure routes of the medical substances to the environment. Only few investigations have reported findings of medical substances in other field samples than sediment or treated waste water samples. Several substances seem to be persistent in the environment. This paper outlines the different anticipated exposure routes to the environment, summarises the legislation on the subject and gives an outline of present knowledge of occurrence, fate and effect on both the aquatic and terrestrial environments of medical substances. Present knowledge does not reveal if regular therapeutic use may be the source of a substance carried by sewage effluent into the aquatic system, even though clofibrate, a lipid lowering agent, has been identified in ground and tap water samples from Berlin. Further research would be necessary to assess the environmental risk involved in exposing medical substances and metabolites to the environment.

Distribution of the streptomycin-resistance transposon Tn5393 among phylloplane and soil bacteria from managed agricultural habitats

The distribution of the strA-strB streptomycin-resistance (Smr) genes associated with Tn5393 was examined in bacteria isolated from the phylloplane and soil of ornamental pear and tomato. Two ornamental pear nurseries received previous foliar applications of streptomycin, whereas the tomato fields had no prior exposure to streptomycin bactericides. Although the recovery of culturable Smr bacteria was generally higher from soil, the highest occurrence of Smr was observed in phylloplane bacteria of an ornamental pear nursery that received 15 annual applications of streptomycin during the previous 2 years. Twenty-two and 12% of 143 Gram-negative phylloplane and 163 Gram-negative soil isolates, respectively, contained sequences that hybridized to probes specific for the strA-strB Smr genes and for the transposase and resolvase genes of Tn5393. These sequences were located on large plasmids (> 60 kb) in 74% of the isolates. The 77 Smr Gram-positive bacteria isolated in the present study showed no homology to the Tn5393-derived probes. Although the repeated use of a single antibiotic in clinical situations is known to favor the development of strains with resistance to other antibiotics, we found no evidence that intensive streptomycin usage in agricultural habitats favors the development of resistance to tetracycline, an antibiotic also registered for disease control on plants. The detection of Tn5393 in bacteria with no prior exposure to streptomycin suggests that this transposon is indigenous to both phylloplane and soil microbial communities.

Abundance of Tn3, Tn21, and Tn501 transposase (tnpA) sequences in bacterial community DNA from marine environments

The occurrence of the tnpA genes of the transposons Tn3, Tn21, and Tn501 was assessed in total bacterial community DNA isolated from different marine environments. The PCR technique was employed, together with most probable number statistics, to determine the abundance of the target tnpA genes. All three genes could be detected, and the Tn21 tnpA sequences predominated in all samples. The smallest amount of total community DNA in which the Tn21 tnpA sequence could be detected was 0.037 ng, and on the basis of our results, we estimated that this sequence was present in 1 of 1,000 to 10,000 bacteria. Hybridization of the PCR products with the respective tnpA probes verified the Tn21 and Tn501 tnpA sequences but only some of the Tn3 tnpA amplification products. The distribution and dissemination of transposons in natural bacterial communities are discussed.

Detection of polychlorinated biphenyl degradation genes in polluted sediments by direct DNA extraction and polymerase chain reaction

It was the aim of this study to specifically detect the DNA sequences for the bphC gene, the meta-cleavage enzyme of the aerobic catabolic pathway for biphenyl and polychlorinated biphenyl degradation, in aquatic sediments without prior cultivation of microorganisms by using extraction of total DNA, PCR amplification of bphC sequences, and detection with specific gene probes. The direct DNA extraction protocol used was modified to enhance lysis efficiency. Crude extracts of DNA were further purified by gel filtration, which yielded DNA that could be used for the PCR. PCR primers were designed for conserved regions of the bphC gene from a sequence alignment of five known sequences. The specificity of PCR amplification was verified by using digoxigenin-labeled DNA probes which were located internal to the amplified gene sequence. The detection limit for the bphC gene of Pseudomonas paucimobilis Q1 and Pseudomonas sp. strain LB400 was 100 cells per g (wet weight) or approximately five copies of the target sequence per PCR reaction mixture. In total-DNA extracts of aerobic top layers of sediment samples obtained from three different sampling sites along the Elbe River, which has a long history of anthropogenic pollution, Pseudomonas sp. strain LB 400-like sequences for the bphC gene were detected, but P. paucimobilis Q1 sequences were not detected. No bphC sequences were detected in an unpolluted lake sediment. A restriction analysis did not reveal any heterogeneity in the PCR product, and the possibility that sequences highly related to the bphC gene (namely, nahC and todE) were present was excluded.(ABSTRACT TRUNCATED AT 250 WORDS)