Coincident plasmids and antimicrobial resistance in marine bacteria isolated from polluted and unpolluted Atlantic Ocean samples

Anthropogenic impact and antibiotic resistance among the indicator and pathogenic bacteria from several industrial and sewage discharge points along the coast from Pydibhimavaram to Tuni, East Coast of India

Increasing urbanisation and industrialisation of the Visakhapatnam region have brought domestic sewage and industrial wastewater discharge into the coastal ocean. This study examines the indicator and pathogenic bacteria's quantitative abundance and antibiotic susceptibility. This study collected surface and subsurface water samples from ten different regions (147 stations; 294 samples), including 12 industrial discharge points, surrounding stations and two harbours from the coast of Pydibheemavaram to Tuni. Physicochemical parameters like salinity, temperature, fluorescence, pH, total suspended matter, nutrients, chlorophyll-a and dissolved oxygen showed a difference between regions. We noticed the presence of indicator (Escherichia coli and Enterococcus faecalis) and pathogenic (Aeromonas hydrophila, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa, Salmonella and Shigella, Vibrio cholera and Vibrio parahaemolyticus) bacteria among the samples. Waters from the near harbour and Visakhapatnam steel plant showed lower bacterial load with no direct input from industries to the coastal water. Samples collected during the industrial discharge period had a higher bacterial load, including E. coli. Enteric bacteria were found in higher numbers at most stations. Some isolates were resistant to multiple antibiotics with higher antibiotic resistance and multiple antibiotic resistance indexes compared with the other coastal water habitats in the Bay of Bengal. The occurrence of these bacteria above the standard limits and with multiple antibiotic resistance in the study region may pose a potential threat to the local inhabitants. It can create an alarming situation in the coastal waters in the study region.

Community composition and antibiotic resistance of bacteria in bottlenose dolphins Tursiops truncatus - Potential impact of 2010 BP Oil Spill

Aquatic contamination, oil spills in particular, could lead to the accumulation of antibiotic resistance by promoting selection for and/or transfer of resistance genes. However, there have been few studies on antibiotic resistance in marine mammals in relation to environmental disturbances, specifically oil contaminations. Here we initiated a study on antibiotic resistance bacteria in bottlenose dolphins Tursiops truncatus in relation to oil contamination following the 2010 BP Oil Spill in the northern Gulf of Mexico. Bacterial communities and antibiotic resistance prevalence one year after the 2010 BP Oil Spill were compared between Barataria Bay (BB) and Sarasota Bay (SB) by applying the rarefaction curve method, and (generalized) linear mixed models. The results showed that the most common bacteria included Vibrio, Shewanella, Bacillus and Pseudomonas. The prevalence of antibiotic resistance was high in the bacterial isolates at both bays. Though bacterial diversity did not differ significantly among water or dolphin samples, and antibiotic resistance did not differ significantly among water samples between the two bays, antibiotic resistance and multi-drug resistance in dolphin samples was significantly higher in the BB than in the SB, mainly attributed to the resistance to E, CF, FEP and SXT. We also found sulfamethoxazole-trimethoprim-resistant Stenotrophomonas maltophilia the first time in the natural aquatic environment. The higher antibiotic resistance in the dolphins in BB is likely attributed to 2010 BP Oil Spill as we expected SB, a more urbanized bay area, would have had higher antibiotic resistance based on the previous studies. The antibiotic resistance data gathered in this research will fill in the important data gaps and contributes to the broader spatial-scale emerging studies on antibiotic resistance in aquatic environments.

Insertion sequences enrichment in extreme Red sea brine pool vent

Mobile genetic elements are major agents of genome diversification and evolution. Limited studies addressed their characteristics, including abundance, and role in extreme habitats. One of the rare natural habitats exposed to multiple-extreme conditions, including high temperature, salinity and concentration of heavy metals, are the Red Sea brine pools. We assessed the abundance and distribution of different mobile genetic elements in four Red Sea brine pools including the world's largest known multiple-extreme deep-sea environment, the Red Sea Atlantis II Deep. We report a gradient in the abundance of mobile genetic elements, dramatically increasing in the harshest environment of the pool. Additionally, we identified a strong association between the abundance of insertion sequences and extreme conditions, being highest in the harshest and deepest layer of the Red Sea Atlantis II Deep. Our comparative analyses of mobile genetic elements in secluded, extreme and relatively non-extreme environments, suggest that insertion sequences predominantly contribute to polyextremophiles genome plasticity.

Detection of antibiotic-resistant bacteria endowed with antimicrobial activity from a freshwater lake and their phylogenetic affiliation

Antimicrobial resistance poses a serious challenge to global public health. In this study, fifty bacterial strains were isolated from the sediments of a freshwater lake and were screened for antibiotic resistance. Out of fifty isolates, thirty-three isolates showed resistance against at least two of the selected antibiotics. Analysis of 16S rDNA sequencing revealed that the isolates belonged to ten different genera, namely Staphylococcus(n = 8), Bacillus(n = 7), Lysinibacillus(n = 4), Achromobacter(n=3), bacterium(n = 3), Methylobacterium(n = 2), Bosea(n = 2), Aneurinibacillus(n = 2), Azospirillum(n = 1), Novosphingobium(n = 1). Enterobacterial repetitive intergenic consensus (ERIC) and BOX-PCR markers were used to study the genetic relatedness among the antibiotic resistant isolates. Further, the isolates were screened for their antimicrobial activity against bacterial pathogens viz., Staphylococcus aureus(MTCC-96), Pseudomonas aeruginosa(MTCC-2453) and Escherichia coli(MTCC-739), and pathogenic fungi viz., Fusarium proliferatum (MTCC-286), Fusarium oxysporum (CABI-293942) and Fusarium oxy. ciceri (MTCC-2791). In addition, biosynthetic genes (polyketide synthase II (PKS-II) and non-ribosomal peptide synthetase (NRPS)) were detected in six and seven isolates, respectively. This is the first report for the multifunctional analysis of the bacterial isolates from a wetland with biosynthetic potential, which could serve as potential source of useful biologically active metabolites.

Complete nucleotide sequence and analysis of two conjugative broad host range plasmids from a marine microbial biofilm

The complete nucleotide sequence of plasmids pMCBF1 and pMCBF6 was determined and analyzed. pMCBF1 and pMCBF6 form a novel clade within the IncP-1 plasmid family designated IncP-1 ς. The plasmids were exogenously isolated earlier from a marine biofilm. pMCBF1 (62 689 base pairs; bp) and pMCBF6 (66 729 bp) have identical backbones, but differ in their mercury resistance transposons. pMCBF1 carries Tn5053 and pMCBF6 carries Tn5058. Both are flanked by 5 bp direct repeats, typical of replicative transposition. Both insertions are in the vicinity of a resolvase gene in the backbone, supporting the idea that both transposons are “res-site hunters” that preferably insert close to and use external resolvase functions. The similarity of the backbones indicates recent insertion of the two transposons and the ongoing dynamics of plasmid evolution in marine biofilms. Both plasmids also carry the insertion sequence ISPst1, albeit without flanking repeats. ISPs1is located in an unusual site within the control region of the plasmid. In contrast to most known IncP-1 plasmids the pMCBF1/pMCBF6 backbone has no insert between the replication initiation gene (trfA) and the vegetative replication origin (oriV). One pMCBF1/pMCBF6 block of about 2.5 kilo bases (kb) has no similarity with known sequences in the databases. Furthermore, insertion of three genes with similarity to the multidrug efflux pump operon mexEF and a gene from the NodT family of the tripartite multi-drug resistance-nodulation-division (RND) system in Pseudomonas aeruginosa was found. They do not seem to confer antibiotic resistance to the hosts of pMCBF1/pMCBF6, but the presence of RND on promiscuous plasmids may have serious implications for the spread of antibiotic multi-resistance.

Antimicrobial use in aquaculture re-examined: its relevance to antimicrobial resistance and to animal and human health

The worldwide growth of aquaculture has been accompanied by a rapid increase in therapeutic and prophylactic usage of antimicrobials including those important in human therapeutics. Approximately 80% of antimicrobials used in aquaculture enter the environment with their activity intact where they select for bacteria whose resistance arises from mutations or more importantly, from mobile genetic elements containing multiple resistance determinants transmissible to other bacteria. Such selection alters biodiversity in aquatic environments and the normal flora of fish and shellfish. The commonality of the mobilome (the total of all mobile genetic elements in a genome) between aquatic and terrestrial bacteria together with the presence of residual antimicrobials, biofilms, and high concentrations of bacteriophages where the aquatic environment may also be contaminated with pathogens of human and animal origin can stimulate exchange of genetic information between aquatic and terrestrial bacteria. Several recently found genetic elements and resistance determinants for quinolones, tetracyclines, and β-lactamases are shared between aquatic bacteria, fish pathogens, and human pathogens, and appear to have originated in aquatic bacteria. Excessive use of antimicrobials in aquaculture can thus potentially negatively impact animal and human health as well as the aquatic environment and should be better assessed and regulated.

Fitness factors in vibrios: a mini-review

Vibrios are Gram-negative curved bacilli that occur naturally in marine, estuarine, and freshwater systems. Some species include human and animal pathogens, and some vibrios are necessary for natural systems, including the carbon cycle and osmoregulation. Countless in vivo and in vitro studies have examined the interactions between vibrios and their environment, including molecules, cells, whole animals, and abiotic substrates. Many studies have characterized virulence factors, attachment factors, regulatory factors, and antimicrobial resistance factors, and most of these factors impact the organism's fitness regardless of its external environment. This review aims to identify common attributes among factors that increase fitness in various environments, regardless of whether the environment is an oyster, a rabbit, a flask of immortalized mammalian cells, or a planktonic chitin particle. This review aims to summarize findings published thus far to encapsulate some of the basic similarities among the many vibrio fitness factors and how they frame our understanding of vibrio ecology. Factors representing these similarities include hemolysins, capsular polysaccharides, flagella, proteases, attachment factors, type III secretion systems, chitin binding proteins, iron acquisition systems, and colonization factors.

Detection of antibiotic-resistant bacteria and their resistance genes in wastewater, surface water, and drinking water biofilms

Abstract In view of the increasing interest in the possible role played by hospital and municipal wastewater systems in the selection of antibiotic-resistant bacteria, biofilms were investigated using enterococci, staphylococci, Enterobacteriaceae, and heterotrophic bacteria as indicator organisms. In addition to wastewater, biofilms were also investigated in drinking water from river bank filtrate to estimate the occurrence of resistant bacteria and their resistance genes, thus indicating possible transfer from wastewater and surface water to the drinking water distribution network. Vancomycin-resistant enterococci were characterized by antibiograms, and the vanA resistance gene was detected by molecular biology methods, including PCR. The vanA gene was found not only in wastewater biofilms but also in drinking water biofilms in the absence of enterococci, indicating possible gene transfer to autochthonous drinking water bacteria. The mecA gene encoding methicillin resistance in staphylococci was detected in hospital wastewater biofilms but not in any other compartment. Enterobacterial ampC resistance genes encoding beta-lactamase activities were amplified by PCR from wastewater, surface water and drinking water biofilms.

Antibiotic resistant pathogens versus human impacts: a study from three eco-regions of the Chennai coast, southern India

We assessed the occurrence of pollution indicators and antibiotic resistant bacterial isolates from water and sediment samples of three different eco-regions of the Chennai coast between March - May of 2010. Total of 960 bacterial strains belonging to four genera were isolated which show the highest frequencies of resistance to vancomycin (53.6%) and penicillin (52.6%) (except Enterococcus sp., which is highly resistant to erythromycin) and lowest frequencies of resistance to chloramphenicol (3.43%), ciprofloxacin (3.95%), gentamicin (4.68%), and tetracycline (6.97%). The E. coli, Vibrio sp., Salmonella sp. and Enterococcus sp. show high frequency of resistance to 2-5 antibacterials of 60.4%, 45.83%, 69.16% and 46.6%, respectively. High pollution indices (PI - 6.66-14.06) and antibiotic resistance indices (ARI - 0.29-0.343) indicate that the coastal environment is highly exposed to antibiotic sources that suggesting to avoid direct contact.

Horizontal gene exchange in environmental microbiota

Horizontal gene transfer (HGT) plays an important role in the evolution of life on the Earth. This view is supported by numerous occasions of HGT that are recorded in the genomes of all three domains of living organisms. HGT-mediated rapid evolution is especially noticeable among the Bacteria, which demonstrate formidable adaptability in the face of recent environmental changes imposed by human activities, such as the use of antibiotics, industrial contamination, and intensive agriculture. At the heart of the HGT-driven bacterial evolution and adaptation are highly sophisticated natural genetic engineering tools in the form of a variety of mobile genetic elements (MGEs). The main aim of this review is to give a brief account of the occurrence and diversity of MGEs in natural ecosystems and of the environmental factors that may affect MGE-mediated HGT.

Antimicrobial resistance of heterotrophic marine bacteria isolated from seawater and sands of recreational beaches with different organic pollution levels in southeastern Brazil: evidences of resistance dissemination

Antimicrobial resistance of marine heterotrophic bacteria to different antimicrobials agents were evaluated in seawater, dry and wet sands from three marine recreational beaches with different pollution levels. In all studied beaches, the greatest frequencies of resistance were found in relation to penicillin. On Gonzaguinha, the most polluted beach, 72.3% of all isolated strains showed simple resistance, whilst 8.33% had multiple resistance. The values found on Ilha Porchat beach, were 70.8% and 6.9% for simple and multiple resistances, respectively. On Guaraú, the less polluted beach, only 35.3% of isolated strains had simple resistance. Multiple resistance was not observed. While samples from Gonzaguinha and Ilha Porchat beach showed isolated strains resistant to seven and six different antimicrobial agents, respectively, samples from Guaraú beach were resistant only to penicillin and erytromicin. The positive correlations obtained between the degree of seawater contamination and frequency and variability of bacterial resistance indicate that polluted marine recreational waters and sands are sources of resistant bacteria contributing thus, to the dissemination of bacterial resistance.

Genes Responsible for Size Reduction of Marine Vibrios during Starvation Are Located on the Chromosome

In a survey of 21 marine Vibrio spp., all responded to nutrient deprivation by undergoing a reduction in size (dwarfing). However, only 43% of these strains possessed one or more plasmids, suggesting that the genes responsible for dwarfing were located on the chromosome rather than on the plasmids. This conclusion was confirmed by the observation that fragmentation and subsequent size reduction occurred in three strains from which the plasmids had been removed by curing. The cured strains lost certain characteristics, such as resistance to some heavy metals and antibiotics, that were restored when the plasmids were reintroduced by either transformation or electroporation.

Detection of antibiotic resistant bacteria inhabiting the sand of non-recreational marine beach

The present study examined the antibiotic resistance of heterotrophic bacteria, which were isolated from the sand of the beach located in the National Park of the southern Baltic Sea coast. The bacteria demonstrated low levels of antibiotic resistance. These microorganisms were the most resistant to cefaclor and clindamycin and the most sensitive to clarithromycin, doxycycline, gentamycin and oxytetracycline. The majority of bacteria inhabiting the sand of the studied beach were resistant to only one antibiotic out of 18 tested antibiotics in this study. The bacteria inhabiting the middle part of the beach and the dune were more antibiotic resistant than bacteria isolated from the seawater and the shoreline-seawater contact zone. Generally, there was no significant difference in antibiotic resistance between bacteria isolated from the surface and the subsurface sand layers. The bacterial antibiotic resistance level depends on the chemical structure of antibiotics.

Effects of administration mode of antibiotics on antibiotic resistance of Enterococcus faecalis in aquatic ecosystems

In this study we investigated the effects of antibiotic administration mode on development of antibiotic resistance in a freshwater model ecosystem. Mesocosms were established in 2.25 m(3) cement pools containing tap water and yellow soil free of antibiotic contamination. Oxytetracycline (5 mg L(-1)) and ciprofloxacin (2 mg L(-1)) were used as experimental antibiotics and Enterococcus faecalis was used as indicator bacteria. Antibiotics were either administered directly to the pools, or were administered in a feed-antibiotic mixture or feces-antibiotic mixture. Surface sediment samples were collected and analyzed at 0, 3, 7, 14, 21, 30, 60 and 120 d after inoculation. E. faecalis was isolated and identified by polymerase chain reaction (PCR) and a drug sensitivity test was performed using the micro-broth-dilution method. Maximum antibiotic resistance was reached on day 3 with all methods of administration. The effect was significantly higher in the feed-administration group compared with the direct administration and feces-administration groups, and between the latter two groups the effect appeared to be slightly higher in the direct administration group. The minimum inhibitory concentration (MIC) values showed bacterial resistance percent decreased in a time-dependent manner in all groups; however, the decreasing trend was less dramatic in bacteria isolated from the feed-antibiotics group. Overall, the percent and level of resistance to oxytetracycline was higher than to ciprofloxacin, and the sensitivity recovery time was longer for bacteria exposed to oxytetracycline than to ciprofloxacin. Our findings suggest that antibiotics introduced to water via feed can induce high percent of antibiotic-resistant bacteria in aquatic ecosystems.

Potential for horizontal gene transfer in microbial communities of the terrestrial subsurface

The deep terrestrial subsurface is a vast, largely unexplored environment that is oligotrophic, highly heterogeneous, and may contain extremes of both physical and chemical factors. In spite of harsh conditions, subsurface studies at several widely distributed geographic sites have revealed diverse communities of viable organisms, which have provided evidence of low but detectable metabolic activity. Although much of the terrestrial subsurface may be considered to be distant and isolated, the concept of horizontal gene transfer (HGT) in this environment has far-reaching implications for bioremediation efforts and groundwater quality, industrial harvesting of subsurface natural resources such as petroleum, and accurate assessment of the risks associated with DNA release and transport from genetically modified organisms. This chapter will explore what is known about some of the major mechanisms of HGT, and how the information gained from surface organisms might apply to conditions in the terrestrial subsurface. Evidence for the presence of mobile elements in subsurface bacteria and limited retrospective studies examining genetic signatures of potential past gene transfer events will be discussed.

Horizontal gene transfer and mobile genetic elements in marine systems

The pool of mobile genetic elements (MGE) in microbial communities consists of viruses, plasmids, and associated elements (insertion sequences, transposons, and integrons) that are either self-transmissible or use mobile plasmids and viruses as vehicles for their dissemination. This mobilome facilitates the horizontal transfer of genes that promote the evolution and adaptation of microbial communities. Efforts to characterize MGEs from microbial populations resident in a variety of ecological habitats have revealed a surprisingly novel and seemingly untapped biodiversity. To better understand the impact of horizontal gene transfer (HGT), as well as the agents that promote HGT in marine ecosystems and to determine whether or not environmental parameters can effect the composition and structure of the mobilome in marine microbial communities, information on the distribution, diversity, and ecological traits of the marine mobilome is presented. In this chapter we discuss recent insights gained from different methodological approaches used to characterize the biodiversity and ecology of MGE in marine environments and their contributions to HGT. In addition, we present case studies that highlight specific HGT examples in coastal, open-ocean, and deep-sea marine ecosystems.

Antibiotic resistance among bacteria isolated from seawater and penguin fecal samples collected near Palmer Station, AntarcticaThis article is one of a selection of papers in the Special Issue on Polar and Alpine Microbiology

Antibiotic resistance in aquatic bacteria has increased steadily as a consequence of the widespread use of antibiotics, but practice and international treaty should have limited antibiotic contamination in Antarctica. We estimated antibiotic resistance in microorganisms isolated from the Antarctic marine waters and a penguin rookery, for 2 reasons: (i) as a measure of human impact and (ii) as a potential “snapshot” of the preantibiotic world. Samples were taken at 4 established sampling sites near Palmer Station, which is situated at the southern end of the Palmer Archipelago (64°10′S, 61°50′W). Sites were chosen to provide different potentials for human contamination. Forty 50 mL samples of seawater were collected and colony-forming units (CFU)/mL were determined at 6 and 20 °C. For this study, presumed psychrophiles (growth at 6 °C) were assumed to be native to Antarctic waters, whereas presumed mesophiles (growth at 20 °C but not at 6 °C) were taken to represent introduced organisms. The 20–6 °C CFU/mL ratio was used as a measure of the relative impact to the ecosystem of presumably introduced organisms. This ratio was highest at the site nearest to Palmer Station and decreased with distance from it, suggesting that human presence has impacted the natural microbial flora of the site. The frequency of resistance to 5 common antibiotics was determined in each group of isolates. Overall drug resistance was higher among the presumed mesophiles than the presumed psychrophiles and increased with proximity to Palmer Station, with the presumed mesophiles showing higher frequencies of single and multiple drug resistance than the psychrophile population. The frequency of multidrug resistance followed the same pattern. It appears that multidrug resistance is low among native Antarctic bacteria but is increased by human habitation.

Antimicrobial resistance and species composition of Enterococcus spp. isolated from waters and sands of marine recreational beaches in Southeastern Brazil

Density, species composition and antimicrobial resistance in bacteria of the Enterococcus genus were evaluated in seawater and sands from 2 marine recreational beaches with different levels of pollution. The 2 beaches showed predominance of Enterococcus faecalis and Enterococcus faecium, in the water and the sand. Dry sand presented higher densities of Enterococcus sp. and higher frequency of resistant strains than wet sand and seawater. The beach with a higher degree of pollution presented higher percentages of resistant strains (66.7% and 61.5%, in sand and in water, respectively) and resistance to a larger number of antimicrobials compared with the less polluted beach, Ilha Porchat (35.7% and 31.25% of resistant strains in sand and water, respectively). In water samples, the highest frequencies of resistance were obtained against streptomycin (38.5%) and erythromycin (25%), whilst in sand, the highest frequencies were observed in relation to erythromycin and tetracycline (38.1% and 14.3%, respectively). These results show that water and sands from beaches with high indexes of faecal contamination of human origin may be potential sources of contamination by pathogens and contribute to the dissemination of bacterial resistance.

Diverse tetracycline resistant bacteria and resistance genes from coastal waters of Jiaozhou Bay

Environmental microbiology investigation was carried out in Jiaozhou Bay to determine the source and distribution of tetracycline-resistant bacteria and their resistance mechanisms. At least 25 species or the equivalent molecular phylogenetic taxa in 16 genera of resistant bacteria could be identified based on 16S ribosomal deoxyribonucleic acid sequence analysis. Enterobacteriaceae, Pseudomonadaceae, and Vibrionaceae constituted the majority of the typical resistant isolates. Indigenous estuarine and marine Halomonadaceae, Pseudoalteromonadaceae, Rhodobacteraceae, and Shewanellaceae bacteria also harbored tetracycline resistance. All the six resistance determinants screened, tet(A)-(E) and tet(G), could be detected, and the predominant genes were tet(A), tet(B), and tet(G). Both anthropogenic activity-related and indigenous estuarine or coastal bacteria might contribute to the tet gene reservoir, and resistant bacteria and their molecular determinants may serve as bioindicators of coastal environmental quality. Our work probably is the first identification of tet(E) in Proteus, tet(G) in Acinetobacter, tet(C) and tet(D) in Halomonas, tet(D) and tet(G) in Shewanella, and tet(B), tet(C), tet(E), and tet(G) in Roseobacter.

Biology of Pseudomonas stutzeri

Pseudomonas stutzeri is a nonfluorescent denitrifying bacterium widely distributed in the environment, and it has also been isolated as an opportunistic pathogen from humans. Over the past 15 years, much progress has been made in elucidating the taxonomy of this diverse taxonomical group, demonstrating the clonality of its populations. The species has received much attention because of its particular metabolic properties: it has been proposed as a model organism for denitrification studies; many strains have natural transformation properties, making it relevant for study of the transfer of genes in the environment; several strains are able to fix dinitrogen; and others participate in the degradation of pollutants or interact with toxic metals. This review considers the history of the discovery, nomenclatural changes, and early studies, together with the relevant biological and ecological properties, of P. stutzeri.

Identification of environmental plasmid-bearing Vibrio species isolated from polluted and pristine marine reserves of Hong Kong, and resistance to antibiotics and mercury

Fifty environmental isolates of Vibrio species were isolated from water samples of Mai Po Nature Reserve and the Cape d'Aguilar Marine Reserve in Hong Kong and screened for the presence of plasmid. Mai Po is a wastewater-impacted area while the Cape d'Aguilar Marine Reserve is pristine natural marine water. Plasmid was found in Vibrio isolates from both sites at similar frequencies and each site showed distinctive plasmid profiles. These plasmid-bearing Vibrio isolates were identified as different species of the Vibrio genus by both biochemical test and subsequently full-length 16S rRNA sequences. Antibiotic resistance test showed that all these plasmid-bearing Vibrio isolates showed multiple resistance to 21 antibiotics tested. In addition, selective isolates also showed tolerance to 10 microM Hg 2+ in culture medium and they generally harbored large plasmid(s) (>30 kb). Our results show that the high frequency of plasmid in Vibrio species of both polluted and pristine environments may be ecologically important to the survival of these bacteria in the environment. The specific functioning of the cryptic plasmids remains the focus of current investigations.

Characterization of a mercury-reducing Bacillus cereus strain isolated from the Pulicat Lake sediments, south east coast of India

Pulicat Lake sediments are often severely polluted with the toxic heavy metal mercury. Several mercury-resistant strains of Bacillus species were isolated from the sediments and all the isolates exhibited broad spectrum resistance (resistance to both organic and inorganic mercuric compounds). Plasmid curing assay showed that all the isolated Bacillus strains carry chromosomally borne mercury resistance. Polymerase chain reaction and southern hybridization analyses using merA and merB3 gene primers/probes showed that five of the isolated Bacillus strains carry sequences similar to known merA and merB3 genes. Results of multiple sequence alignment revealed 99% similarity with merA and merB3 of TnMERI1 (class II transposons). Other mercury resistant Bacillus species lacking homology to these genes were not able to volatilize mercuric chloride, indicating the presence of other modes of resistance to mercuric compounds.

Carbapenemase-producing Enterobacteriaceae, U.S. rivers

Identification of imipenem-resistant Enterobacter asburiae isolates from distant rivers indicates an environmental reservoir for carbapenemase genes.

Our study was initiated by previous isolation of 30 imipenem-resistant, gram-negative rods from 7 of 16 U.S. rivers sampled from 1999 to 2001. Imipenem hydrolysis was detected in 22 of those isolates identified as Enterobacter asburiae. Random amplified polymorphism DNA analysis showed that these E. asburiae isolates were genetically indistinguishable. An identical clavulanic acid–inhibited β-lactamase IMI-2 was identified from each isolate that shared 99% and 97% amino acid identity with the chromosome-encoded β-lactamases IMI-1 and NmcA, respectively, from E. cloacae clinical isolates. The bla_IMI-2 gene was located on a self-transferable 66-kb plasmid. Sequence analysis of a cloned 5.5-kb DNA fragment obtained from 1 of the imipenem-resistant E. asburiae isolates identified an upstream LysR-type regulator gene that explained inducibility of IMI-2 expression. β-Lactamase IMI-2 is the first inducible and plasmid-encoded carbapenemase. Identification of clonally related E. asburiae isolates from distant rivers indicates an environmental and enterobacterial reservoir for carbapenemase genes.

Metagenomics: application of genomics to uncultured microorganisms

Metagenomics (also referred to as environmental and community genomics) is the genomic analysis of microorganisms by direct extraction and cloning of DNA from an assemblage of microorganisms. The development of metagenomics stemmed from the ineluctable evidence that as-yet-uncultured microorganisms represent the vast majority of organisms in most environments on earth. This evidence was derived from analyses of 16S rRNA gene sequences amplified directly from the environment, an approach that avoided the bias imposed by culturing and led to the discovery of vast new lineages of microbial life. Although the portrait of the microbial world was revolutionized by analysis of 16S rRNA genes, such studies yielded only a phylogenetic description of community membership, providing little insight into the genetics, physiology, and biochemistry of the members. Metagenomics provides a second tier of technical innovation that facilitates study of the physiology and ecology of environmental microorganisms. Novel genes and gene products discovered through metagenomics include the first bacteriorhodopsin of bacterial origin; novel small molecules with antimicrobial activity; and new members of families of known proteins, such as an Na(+)(Li(+))/H(+) antiporter, RecA, DNA polymerase, and antibiotic resistance determinants. Reassembly of multiple genomes has provided insight into energy and nutrient cycling within the community, genome structure, gene function, population genetics and microheterogeneity, and lateral gene transfer among members of an uncultured community. The application of metagenomic sequence information will facilitate the design of better culturing strategies to link genomic analysis with pure culture studies.

Approaches to investigating the ecology of plasmids in marine bacterial communities

To better understand prokaryotic gene flux in marine ecosystems and to determine whether or not environmental parameters can effect the composition and structure of plasmid populations in marine bacterial communities, information on the distribution, diversity, and ecological traits of marine plasmids is necessary. This mini-review highlights recent insights gained into the molecular diversity and ecology of plasmids occurring in marine microbial communities.

Endogenous isolation of replicon probes for assessing plasmid ecology of marine sediment microbial communities

Six functional replication origins (repGA14, repGA33, repGA70, repSD41, repSD164 and repSD172), obtained from endogenously isolated, broad-host-range (BHR) marine plasmids ranging in size from 5 to 60 kb, were used to determine plasmid occurrence in three coastal marine sediment sites (in California, Georgia and South Carolina, USA). The plasmid-specific replicons were isolated from plasmid-bearing marine sediment bacteria belonging to the alpha and gamma subclasses of the Proteobacteria. The plasmid sources of the endogenous replicons were considered to be cryptic due to a lack of identifiable phenotypic traits. The putative Rep proteins from a number of these replicons showed similarity to replicons of two recognized families: RCR group III (repSD164) and the FIA family of theta group A (repSD41, repSD121, repGA33 and repGA14). Plasmids isolated from marine bacteria belonging to the genera Pseudoalteromonas, Shewanella and Vibrio cultivated from geographically different coastal sites exhibited homology to two of the marine plasmid replicons, repSD41 and repGA70, obtained from a Vibrio sp. The repGA33 plasmid origin, obtained from a Shewanella sp. isolated from coastal Georgia, was detected in 7% of the Georgia marine sediment Shewanella sp. isolates. Microbial community DNA extracted from marine sediments was also screened for the presence of the plasmid replication sequences. Community DNA samples amplified by PCR yielded a positive signal for the repSD172 and repGA14 replication sequences. The replication origin of BHR plasmid RK2 (IncP) was also detected in marine Vibrio sp. and microbial community DNA extracted from the three coastal sites. These findings provide molecular evidence that marine sediment bacteria harbour an untapped population of BHR plasmids.

Impact of an urban effluent on antibiotic resistance of riverine Enterobacteriaceae and Aeromonas spp

In order to evaluate the impact of an urban effluent on antibiotic resistance of freshwater bacterial populations, water samples were collected from the Arga river (Spain), upstream and downstream from the wastewater discharge of the city of Pamplona. Strains of Enterobacteriaceae (representative of the human and animal commensal flora) (110 isolates) and Aeromonas (typically waterborne bacteria) (118 isolates) were selected for antibiotic susceptibility testing. Most of the Aeromonas strains (72%) and many of the Enterobacteriaceae (20%) were resistant to nalidixic acid. Singly nalidixic acid-resistant strains were frequent regardless of the sampling site for Aeromonas, whereas they were more common upstream from the discharge for enterobacteria. The most common resistances to antibiotics other than quinolones were to tetracycline (24.3%) and beta-lactams (20.5%) for Enterobacteriaceae and to tetracycline (27.5%) and co-trimoxazole (26.6%) for Aeromonas. The rates of these antibiotic resistances increased downstream from the discharge at similar degrees for the two bacterial groups; it remained at high levels for enterobacteria but decreased along the 30-km study zone for Aeromonas. Genetic analysis of representative strains demonstrated that these resistances were mostly (enterobacteria) or exclusively (Aeromonas) chromosomally mediated. Moreover, a reference strain of Aeromonas caviae (CIP 7616) could not be transformed with conjugative R plasmids of enterobacteria. Thus, the urban effluent resulted in an increase of the rates of resistance to antibiotics other than quinolones in the riverine bacterial populations, despite limited genetic exchanges between enterobacteria and Aeromonas. Quinolone resistance probably was selected by heavy antibiotic discharges of unknown origin upstream from the urban effluent.

Characterization of mercury resistance mechanisms in marine sediment microbial communities

While estuarine sediments are often severely polluted with mercury, few studies have focused on the mechanisms of adaptation to mercury contamination in marine sediment microbial communities. In this study, we report a high frequency of Gram-negative bacterial isolates that are resistant to the heavy metal mercury obtained from the aerobic culturable marine microbial community. We detected a low frequency of genes homologous to mer(Tn21) in isolates from three out of four different estuarine environments. Other mercury resistant culturable bacterial isolates lacking homology to the known mer genes were able to reduce Hg(II) to its volatile Hg(0) form, indicating the presence of divergent mer genes. In addition, a number of mercury resistant isolates, obtained from three of the four marine sites investigated, exhibited decreased resistance to mercury in the presence of the protonophore carbonyl cyanide m-chlorophenylhydrazone. Representative mercury resistant bacterial isolates were identified by phylogenetic analysis as belonging to the alpha and gamma subclasses of the class Proteobacteria.

Association of multiple-antibiotic-resistance profiles with point and nonpoint sources of Escherichia coli in Apalachicola Bay

A total of 765 Escherichia coli isolates from point and nonpoint sources were collected from the Apalachicola National Estuarine Research Reserve, and their multiple-antibiotic-resistance (MAR) profiles were determined with 10 antibiotics. E. coli isolates from point sources showed significantly greater resistance (P < 0.05) to antibiotics and higher MAR indices than isolates from nonpoint sources. Specifically, 65 different resistance patterns were observed among point source isolates, compared to 32 among nonpoint source isolates. Examples of this contrast in MAR profiles included percentages of isolates with resistance to chlortetracycline-sulfathiazole of 33.7% and to chlortetracycline-penicillin G-sulfathiazole of 14.5% for point source isolates versus 15.4 and 1.7%, respectively, for nonpoint source isolates. MAR profile homology, based on coefficient similarity, showed that isolates from point sources were markedly more diverse than isolates from nonpoint sources. Seven clusters were observed among point source isolates, with a coefficient value of approximately 1.8. In contrast, only four clusters were observed among nonpoint source isolates. Covariance matrices of data displayed six very distinct foci representing nonpoint source E. coli isolates. Importantly, E. coli isolates obtained directly from human and animal feces also clustered among point and nonpoint sources, respectively. We conclude that E. coli MAR profiles were associated with point and nonpoint sources of pollution within Apalachicola Bay and that this method may be useful in facilitating management of other estuaries.

Evaluation of tributyltin resistance in marine sediment bacteria

Tributyltin (TBT) resistance of aerobic and anaerobic bacteria isolated from TBT-contaminated coastal sediments in Arcachon Bay, France, was determined and compared with taxonomically similar bacteria originating from diverse non-TBT-contaminated environments. The minimum inhibitory concentrations (MICs) showed that TBT was toxic to most of the bacteria studied at concentrations above 2.1 μM (0.7 mg/L) for clostridia, 76 μM (25 mg/L) for pseudomonads, and 3 mM (1000 mg/L) for enterobacteria. The aerobic or facultative anaerobic Gram-negative bacteria (pseudomonads and enterobacteria) presented the highest TBT tolerance. No difference in TBT resistance was observed between strains originating from the polluted site and strains originating from non-TBT-polluted environments (thermal muds, Hospital of Bordeaux, etc.), suggesting that a TBT-polluted environment did not select for more specific resistant bacteria. It should be noted that the bacteria tested were found to be tolerant to TBT concentrations 1000 times higher than those found in the polluted site. Further, all strains presented the same pattern of metal and pharmaceutical antibiotic sensitivity despite the origin of the environment (TBT-polluted or non-TBT-polluted sediments). Six strains of Pseudomonas stutzeri isolated from Arcachon Harbor and one strain of Pseudomonas aeruginosa originating from the bacterial collection of Bordeaux Hospital have been selected for their TBT resistance. As antibiotic resistance, metal or organometal resistance can be plasmid mediated. However, among these TBT-resistant strains no plasmid was detected.Key words: TBT resistance, coastal environment, clostridia, pseudomonads, enterobacteria.

Characterization of diverse 2,4-dichlorophenoxyacetic acid-degradative plasmids isolated from soil by complementation

The diversity of 2,4-dichlorophenoxyacetic acid (2,4-D)-degradative plasmids in the microbial community of an agricultural soil was examined by complementation. This technique involved mixing a suitable Alcaligenes eutrophus (Rifr) recipient strain with the indigenous microbial populations extracted from soil. After incubation of this mixture, Rifr recipient strains which grow with 2,4-D as the only C source were selected. Two A. eutrophus strains were used as recipients: JMP228 (2,4-D-), which was previously derived from A. eutrophus JMP134 by curing of the 2,4-D-degradative plasmid pJP4, and JMP228 carrying pBH501aE (a plasmid derived from pJP4 by deletion of a large part of the tfdA gene which encodes the first step in the mineralization of 2,4-D). By using agricultural soil that had been treated with 2,4-D for several years, transconjugants were obtained with both recipients. However, when untreated control soil was used, no transconjugants were isolated. The various transconjugants had plasmids with seven different EcoRI restriction patterns. The corresponding plasmids are designated pEMT1 to pEMT7. Unlike pJP4, pEMT1 appeared not to be an IncP1 plasmid, but all the others (pEMT2 to pEMT7) belong to the IncP1 group. Hybridization with individual probes for the tfdA to tfdF genes of pJP4 demonstrated that all plasmids showed high degrees of homology to the tfdA gene. Only pEMT1 showed a high degree of homology to tfdB, tfdC, tfdD, tfdE, and tfdF, while the others showed only moderate degrees of homology to tfdB and low degrees of homology to tfdC.(ABSTRACT TRUNCATED AT 250 WORDS)

Transfer in Marine Sediments of the Naturally Occurring Plasmid pRAS1 Encoding Multiple Antibiotic Resistance

The results of microcosm experiments performed with the fish-pathogenic bacterium Aeromonas salmonicida acting as a donor showed that promiscuous plasmid pRAS1, which encodes tetracycline resistance, is transferred at a high frequency in marine sediments even in the absence of a selective factor. The presence of oxytetracycline resulted in an increase in the transfer frequency compared with that of a microcosm to which no selective factor was added. Transfer frequencies of 3.4 × 10 -1 transconjugant per recipient and 3.6 transconjugants per donor cell were obtained in a microcosm to which oxytetracycline had been added. Hybridization with a DNA probe specific for plasmid pRAS1 revealed that 45.8% of the oxytetracycline-resistant isolates obtained from a microcosm with no selective pressure carried the plasmid, while 86.8% of the isolates obtained from a microcosm to which oxytetracycline had been added carried the plasmid. Phenotypic characterization of the transconjugants revealed that the plasmid had been transferred to a variety of different biotypes in both microcosms. The diversity among the transconjugants isolated from the microcosm to which oxytetracycline had been added was substantially lower than the diversity among the transconjugants isolated from the microcosm to which no selective agent had been added.

Transfer of multiple drug resistance plasmids between bacteria of diverse origins in natural microenvironments

Plasmids harboring multiple antimicrobial-resistance determinants (R plasmids) were transferred in simulated natural microenvironments from various bacterial pathogens of human, animal, or fish origin to susceptible strains isolated from a different ecological niche. R plasmids in a strain of the human pathogen Vibrio cholerae O1 E1 Tor and a bovine Escherichia coli strain were conjugated to a susceptible strain of the fish pathogenic bacterium Aeromonas salmonicida subsp. salmonicida in marine water. Conjugations of R plasmids between a resistant bovine pathogenic E. coli strain and a susceptible E. coli strain of human origin were performed on a hand towel contaminated with milk from a cow with mastitis. A similar conjugation event between a resistant porcine pathogenic E. coli strain of human origin was studied in minced meat on a cutting board. Conjugation of R plasmids between a resistant strain of the fish pathogenic bacterium A. salmonicida subsp. salmonicida and a susceptible E. coli strain of human origin was performed in raw salmon on a cutting board. R plasmids in a strain of A. salmonicida subsp. salmonicida and a human pathogenic E. coli strain were conjugated to a susceptible porcine E. coli strain in porcine feces. Transfer of the different R plasmids was confirmed by plasmid profile analyses and determination of the resistance pattern of the transconjugants. The different R plasmids were transferred equally well under simulated natural conditions and under controlled laboratory conditions, with median conjugation frequencies ranging from 3 x 10(-6) to 8 x 10(-3). The present study demonstrates that conjugation and transfer of R plasmids is a phenomenon that belongs to the environment and can occur between bacterial strains of human, animal, and fish origins that are unrelated either evolutionarily or ecologically even in the absence of antibiotics. Consequently, the contamination of the environment with bacterial pathogens resistant to antimicrobial agents is a real threat not only as a source of disease but also as a source from which R plasmids can easily spread to other pathogens of diverse origins.

Distribution of tetracycline resistance determinants among gram-negative bacteria isolated from polluted and unpolluted marine sediments

Tetracycline-resistant gram-negative bacteria were isolated from four different marine sediments in Scandinavia and analyzed with DNA probes for the determinant classes A to E. Colony hybridizations of 429 isolates revealed that class E is the dominating resistance determinant in these marine sediments. Comparison of fecally polluted and unpolluted sediments showed few determinant classes in unpolluted sediment and a complex composition of several determinant classes in polluted sediment. Total DNA extraction and analysis with DNA probes for determinant classes A to E resulted in no hybridization signal, because of the low number of gram-negative tetracycline-resistant bacteria. Identification of class E isolates revealed that this determinant is present not only in Aeromonas hydrophila, Escherichia coli, and Vibrio salmonicida but also in additional strains.