Persulfate-based ISCO for field-scale remediation of NAPL-contaminated soil: Column experiments and modeling.

An experimental and computational investigation of in situ chemical oxidation (ISCO) of weathered diesel fuel in soil columns was undertaken to validate a reactive-transport model capable of predicting contaminant mass reduction from a residual source zone. Reactivity tests with contaminated groundwater in batch reactors were used to estimate a priori the kinetic parameters of a phenomenological model of the oxidation of petroleum hydrocarbon (PHC) mixture fractions. The transport model, which incorporated groundwater flow, dissolution of main PHC fractions, and homogeneous reaction in the aqueous phase, was subsequently validated against experimental data of ISCO in soil columns using repetitive treatments with unactivated and alkaline-activated persulfate. No significant effect of the initial concentration of persulfate on the remediation performance was observed in the batch system, but alkaline activation significantly improved performance. The alkaline-activated persulfate treatment achieved ∼80% removal of the initial NAPL mass in soil columns. The combination of models and experiments described herein should enable the rational design of field-scale advanced oxidation strategies for the removal of weathered petroleum hydrocarbons. This expectation was supported by a comprehensive demonstration study at a historical site contaminated by weathered diesel fuel present as a residual source within the soil and dissolved within groundwater.

Correction: Isolation of five Enterobacteriaceae species harbouring blaNDM-1 and mcr-1 plasmids from a single paediatric patient.

[This corrects the article DOI: 10.1371/journal.pone.0221960.].

Isolation of five Enterobacteriaceae species harbouring blaNDM-1 and mcr-1 plasmids from a single paediatric patient.

In Argentina, NDM metallo-ß-lactamase was first reported in 2013. By now, it has disseminated throughout the country in diverse Gram negative bacteria. Here, we report the case of a paediatric patient that underwent a 1-year hospitalisation due to erythrodermic psoriasis in 2014 and received multiple antimicrobial treatments. During his stay, five isolates were obtained from rectal swabs (rs) or blood culture (bc) suspicious of carbapenemase production: a K. quasipneumoniae subsp. quasipneumoniae (rs), Citrobacter freundii (rs), Escherichia coli (bc), Enterobacter cloacae (rs), and a Serratia marcescens (bc). The isolates were studied with broth microdilution, biparental conjugation and plasmid and whole genome sequencing (Illumina). All isolates harboured an 138,998-bp type 1 IncC plasmid that carried blaNDM-1, bleMBL, blaCMY-6, rmtC, aac(6')-Ib, and sul1 resistance genes. Additionally, the blaNDM-plasmids contained ISKpn8 an insertion sequence previously described as associated only to blaKPC. One isolate, a colistin-resistant E. coli, also carried a mcr-1-containing an IncI2 plasmid, which did not harbour additional resistance. The whole genome of K. quasipneumoniae subsp. quasipneumoniae isolate was fully sequenced. This isolate harboured, additionally to blaNDM, three plasmid-mediated quinolone resistance genes: qnrB4, qnrB52 and aac(6')-Ib-cr1. The E. cloacae isolate also harboured qnrA1. These findings alert to the underestimated horizontal dissemination of multidrug-resistant plasmids limiting treatment options with last resort antimicrobials.

Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity.

BACKGROUND: Chlamydia trachomatis (Ct) is the most common infectious cause of blindness and bacterial sexually transmitted infection worldwide. Ct strain-specific differences in clinical trachoma suggest that genetic polymorphisms in Ct may contribute to the observed variability in severity of clinical disease. METHODS: Using Ct whole genome sequences obtained directly from conjunctival swabs, we studied Ct genomic diversity and associations between Ct genetic polymorphisms with ocular localization and disease severity in a treatment-naïve trachoma-endemic population in Guinea-Bissau, West Africa. RESULTS: All Ct sequences fall within the T2 ocular clade phylogenetically. This is consistent with the presence of the characteristic deletion in trpA resulting in a truncated non-functional protein and the ocular tyrosine repeat regions present in tarP associated with ocular tissue localization. We have identified 21 Ct non-synonymous single nucleotide polymorphisms (SNPs) associated with ocular localization, including SNPs within pmpD (odds ratio, OR = 4.07, p* = 0.001) and tarP (OR = 0.34, p* = 0.009). Eight synonymous SNPs associated with disease severity were found in yjfH (rlmB) (OR = 0.13, p* = 0.037), CTA0273 (OR = 0.12, p* = 0.027), trmD (OR = 0.12, p* = 0.032), CTA0744 (OR = 0.12, p* = 0.041), glgA (OR = 0.10, p* = 0.026), alaS (OR = 0.10, p* = 0.032), pmpE (OR = 0.08, p* = 0.001) and the intergenic region CTA0744-CTA0745 (OR = 0.13, p* = 0.043). CONCLUSIONS: This study demonstrates the extent of genomic diversity within a naturally circulating population of ocular Ct and is the first to describe novel genomic associations with disease severity. These findings direct investigation of host-pathogen interactions that may be important in ocular Ct pathogenesis and disease transmission.

European Chlamydia abortus livestock isolate genomes reveal unusual stability and limited diversity, reflected in geographical signatures.

BACKGROUND: Chlamydia abortus (formerly Chlamydophila abortus) is an economically important livestock pathogen, causing ovine enzootic abortion (OEA), and can also cause zoonotic infections in humans affecting pregnancy outcome. Large-scale genomic studies on other chlamydial species are giving insights into the biology of these organisms but have not yet been performed on C. abortus. Our aim was to investigate a broad collection of European isolates of C. abortus, using next generation sequencing methods, looking at diversity, geographic distribution and genome dynamics. RESULTS: Whole genome sequencing was performed on our collection of 57 C. abortus isolates originating primarily from the UK, Germany, France and Greece, but also from Tunisia, Namibia and the USA. Phylogenetic analysis of a total of 64 genomes shows a deep structural division within the C. abortus species with a major clade displaying limited diversity, in addition to a branch carrying two more distantly related Greek isolates, LLG and POS. Within the major clade, seven further phylogenetic groups can be identified, demonstrating geographical associations. The number of variable nucleotide positions across the sampled isolates is significantly lower than those published for C. trachomatis and C. psittaci. No recombination was identified within C. abortus, and no plasmid was found. Analysis of pseudogenes showed lineage specific loss of some functions, notably with several Pmp and TMH/Inc proteins predicted to be inactivated in many of the isolates studied. CONCLUSIONS: The diversity within C. abortus appears to be much lower compared to other species within the genus. There are strong geographical signatures within the phylogeny, indicating clonal expansion within areas of limited livestock transport. No recombination has been identified within this species, showing that different species of Chlamydia may demonstrate different evolutionary dynamics, and that the genome of C. abortus is highly stable.

Whole genome sequencing of Shigella sonnei through PulseNet Latin America and Caribbean: advancing global surveillance of foodborne illnesses.

OBJECTIVES: Shigella sonnei is a globally important diarrhoeal pathogen tracked through the surveillance network PulseNet Latin America and Caribbean (PNLA&C), which participates in PulseNet International. PNLA&C laboratories use common molecular techniques to track pathogens causing foodborne illness. We aimed to demonstrate the possibility and advantages of transitioning to whole genome sequencing (WGS) for surveillance within existing networks across a continent where S. sonnei is endemic. METHODS: We applied WGS to representative archive isolates of S. sonnei (n = 323) from laboratories in nine PNLA&C countries to generate a regional phylogenomic reference for S. sonnei and put this in the global context. We used this reference to contextualise 16 S. sonnei from three Argentinian outbreaks, using locally generated sequence data. Assembled genome sequences were used to predict antimicrobial resistance (AMR) phenotypes and identify AMR determinants. RESULTS: S. sonnei isolates clustered in five Latin American sublineages in the global phylogeny, with many (46%, 149 of 323) belonging to previously undescribed sublineages. Predicted multidrug resistance was common (77%, 249 of 323), and clinically relevant differences in AMR were found among sublineages. The regional overview showed that Argentinian outbreak isolates belonged to distinct sublineages and had different epidemiologic origins. CONCLUSIONS: Latin America contains novel genetic diversity of S. sonnei that is relevant on a global scale and commonly exhibits multidrug resistance. Retrospective passive surveillance with WGS has utility for informing treatment, identifying regionally epidemic sublineages and providing a framework for interpretation of prospective, locally sequenced outbreaks.

Plasmid CDS5 influences infectivity and virulence in a mouse model of Chlamydia trachomatis urogenital infection.

The native plasmid of both Chlamydia muridarum and Chlamydia trachomatis has been shown to control virulence and infectivity in mice and in lower primates. We recently described the development of a plasmid-based genetic transformation protocol for Chlamydia trachomatis that for the first time provides a platform for the molecular dissection of the function of the chlamydial plasmid and its individual genes or coding sequences (CDS). In the present study, we transformed a plasmid-free lymphogranuloma venereum isolate of C. trachomatis, serovar L2, with either the original shuttle vector (pGFP::SW2) or a derivative of pGFP::SW2 carrying a deletion of the plasmid CDS5 gene (pCDS5KO). Female mice were inoculated with these strains either intravaginally or transcervically. We found that transformation of the plasmid-free isolate with the intact pGFP::SW2 vector significantly enhanced infectivity and induction of host inflammatory responses compared to the plasmid-free parental isolate. Transformation with pCDS5KO resulted in infection courses and inflammatory responses not significantly different from those observed in mice infected with the plasmid-free isolate. These results indicate a critical role of plasmid CDS5 in in vivo fitness and in induction of inflammatory responses. To our knowledge, these are the first in vivo observations ascribing infectivity and virulence to a specific plasmid gene.

Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts.

The global epidemic of multidrug-resistant Salmonella Typhimurium DT104 provides an important example, both in terms of the agent and its resistance, of a widely disseminated zoonotic pathogen. Here, with an unprecedented national collection of isolates collected contemporaneously from humans and animals and including a sample of internationally derived isolates, we have used whole-genome sequencing to dissect the phylogenetic associations of the bacterium and its antimicrobial resistance genes through the course of an epidemic. Contrary to current tenets supporting a single homogeneous epidemic, we demonstrate that the bacterium and its resistance genes were largely maintained within animal and human populations separately and that there was limited transmission, in either direction. We also show considerable variation in the resistance profiles, in contrast to the largely stable bacterial core genome, which emphasizes the critical importance of integrated genotypic data sets in understanding the ecology of bacterial zoonoses and antimicrobial resistance.

Chlamydia trachomatis clinical isolates identified as tetracycline resistant do not exhibit resistance in vitro: whole-genome sequencing reveals a mutation in porB but no evidence for tetracycline resistance genes.

Chlamydia trachomatis is the most common bacterial sexually transmitted infection worldwide and the leading cause of preventable blindness in developing countries. Tetracycline is commonly the drug of choice for treating C. trachomatis infections, but cases of antibiotic resistance in clinical isolates have previously been reported. Here, we used antibiotic resistance assays and whole-genome sequencing to interrogate the hypothesis that two clinical isolates (IU824 and IU888) have acquired mechanisms of antibiotic resistance. Immunofluorescence staining was used to identify C. trachomatis inclusions in cell cultures grown in the presence of tetracycline; however, only antibiotic-free control cultures yielded the strong fluorescence associated with the presence of chlamydial inclusions. Infectivity was lost upon passage of harvested cultures grown in the presence of tetracycline into antibiotic-free medium, so we conclude that these isolates were phenotypically sensitive to tetracycline. Comparisons of the genome and plasmid sequences for the two isolates with tetracycline-sensitive strains did not identify regions of low sequence identity that could accommodate horizontally acquired resistance genes, and the tetracycline binding region of the 16S rRNA gene was identical to that of the sensitive control strains. The porB gene of strain IU824, however, was found to contain a premature stop codon not previously identified, which is noteworthy but unlikely to be related to tetracycline resistance. In conclusion, we found no evidence of tetracycline resistance in the two strains investigated, and it seems most likely that the small, aberrant inclusions previously identified resulted from the high chlamydial load used in the original antibiotic resistance assays.

Retrospective analysis of whole genome sequencing compared to prospective typing data in further informing the epidemiological investigation of an outbreak of Shigella sonnei in the UK.

The aim of this study was to retrospectively assess the value of whole genome sequencing (WGS) compared to conventional typing methods in the investigation and control of an outbreak of Shigella sonnei in the Orthodox Jewish (OJ) community in the UK. The genome sequence analysis showed that the strains implicated in the outbreak formed three phylogenetically distinct clusters. One cluster represented cases associated with recent exposure to a single strain, whereas the other two clusters represented related but distinct strains of S. sonnei circulating in the OJ community across the UK. The WGS data challenged the conclusions drawn during the initial outbreak investigation and allowed cases of dysentery to be implicated or ruled out of the outbreak that were previously misclassified. This study showed that the resolution achieved using WGS would have clearly defined the outbreak, thus facilitating the promotion of infection control measures within local schools and the dissemination of a stronger public health message to the community.

Applications and implications of direct groundwater velocity measurement at the centimetre scale.

Three projects involving point velocity probes (PVPs) illustrate the advantages of direct groundwater velocity measurements. In the first, a glacial till and outwash aquifer was characterized using conventional methods and multilevel PVPs for designing a bioremediation program. The PVPs revealed a highly conductive zone that dominated the transport of injected substances. These findings were later confirmed with a natural gradient tracer test. In the second, PVPs were used to map a groundwater velocity field around a dipole recirculation well. The PVPs showed higher than expected velocities near the well, assuming homogeneity in the aquifer, leading to improved representations of the aquifer heterogeneity in a 3D flow model, and an improved match between the modelled and experimental tracer breakthrough curves. In the third study, PVPs detected subtle changes in aquifer permeability downgradient of a biostimulation experiment. The changes were apparently reversible once the oxygen source was depleted, but in locations where the oxygen source lingered, velocities remained low. PVPs can be a useful addition to the hydrogeologist's toolbox, because they can be constructed inexpensively, they provide data in support of models, and they can provide information on flow in unprecedented detail.

High-pressure injection of dissolved oxygen for hydrocarbon remediation in a fractured dolostone aquifer.

A field experiment was completed at a fractured dolomite aquifer in southwestern Ontario, Canada, to assess the delivery of supersaturated dissolved oxygen (supersaturated with respect to ambient conditions) for enhanced bioremediation of petroleum hydrocarbons in groundwater. The injection lasted for 1.5h using iTi's gPro® oxygen injection technology at pressures of up to 450 kPa and at concentrations of up to 34 mg O2/L. A three-dimensional numerical model for advective-dispersive transport of dissolved oxygen within a discretely-fractured porous medium was calibrated to the observed field conditions under a conservative (no-consumption) scenario. The simulation demonstrated that oxygen rapidly filled the local intersecting fractures as well as the porous matrix surrounding the injection well. Following injection, the local fractures were rapidly flushed by the natural groundwater flow system but slow back-diffusion ensured a relatively longer residence time in the matrix. A sensitivity analysis showed significant changes in behaviour with varying fracture apertures and hydraulic gradients. Applying the calibrated model to a 7-day continuous injection scenario showed oxygen residence times (at the 3mg/L limit), within a radius of 2-4m from the injection well, of up to 100 days. This study has demonstrated that supersaturated dissolved oxygen can be effectively delivered to this type of a fractured and porous bedrock system at concentrations and residence times potentially sufficient for enhanced aerobic biodegradation.

Characterization of a broad-host-range flagellum-dependent phage that mediates high-efficiency generalized transduction in, and between, Serratia and Pantoea.

A phage (PhiOT8) isolated on Serratia sp. ATCC 39006 was shown to be flagellum-dependent, and to mediate generalized transduction with high efficiency (up to 10(-4) transductants per p.f.u.). PhiOT8 was shown to have a broad host range because it also infected a strain of Pantoea agglomerans isolated from the rhizosphere. Transduction of plasmid-borne antibiotic resistance between the two bacterial genera was demonstrated, consistent with purported ecological roles of phages in dissemination of genes between bacterial genera. Serratia sp. ATCC 39006 and P. agglomerans produce a number of interesting secondary metabolites that have potential applications in cancer therapy and biocontrol of fungal infections. PhiOT8 has utility as a powerful functional genomics tool in these bacteria.

Rebound of a coal tar creosote plume following partial source zone treatment with permanganate.

The long-term management of dissolved plumes originating from a coal tar creosote source is a technical challenge. For some sites stabilization of the source may be the best practical solution to decrease the contaminant mass loading to the plume and associated off-site migration. At the bench-scale, the deposition of manganese oxides, a permanganate reaction byproduct, has been shown to cause pore plugging and the formation of a manganese oxide layer adjacent to the non-aqueous phase liquid creosote which reduces post-treatment mass transfer and hence mass loading from the source. The objective of this study was to investigate the potential of partial permanganate treatment to reduce the ability of a coal tar creosote source zone to generate a multi-component plume at the pilot-scale over both the short-term (weeks to months) and the long-term (years) at a site where there is >10 years of comprehensive synoptic plume baseline data available. A series of preliminary bench-scale experiments were conducted to support this pilot-scale investigation. The results from the bench-scale experiments indicated that if sufficient mass removal of the reactive compounds is achieved then the effective solubility, aqueous concentration and rate of mass removal of the more abundant non-reactive coal tar creosote compounds such as biphenyl and dibenzofuran can be increased. Manganese oxide formation and deposition caused an order-of-magnitude decrease in hydraulic conductivity. Approximately 125 kg of permanganate were delivered into the pilot-scale source zone over 35 days, and based on mass balance estimates <10% of the initial reactive coal tar creosote mass in the source zone was oxidized. Mass discharge estimated at a down-gradient fence line indicated >35% reduction for all monitored compounds except for biphenyl, dibenzofuran and fluoranthene 150 days after treatment, which is consistent with the bench-scale experimental results. Pre- and post-treatment soil core data indicated a highly variable and random spatial distribution of mass within the source zone and provided no insight into the mass removed of any of the monitored species. The down-gradient plume was monitored approximately 1, 2 and 4 years following treatment. The data collected at 1 and 2 years post-treatment showed a decrease in mass discharge (10 to 60%) and/or total plume mass (0 to 55%); however, by 4 years post-treatment there was a rebound in both mass discharge and total plume mass for all monitored compounds to pre-treatment values or higher. The variability of the data collected was too large to resolve subtle changes in plume morphology, particularly near the source zone, that would provide insight into the impact of the formation and deposition of manganese oxides that occurred during treatment on mass transfer and/or flow by-passing. Overall, the results from this pilot-scale investigation indicate that there was a significant but short-term (months) reduction of mass emanating from the source zone as a result of permanganate treatment but there was no long-term (years) impact on the ability of this coal tar creosote source zone to generate a multi-component plume.

Mass removal of chlorinated ethenes from rough-walled fractures using permanganate.

In situ chemical oxidation (ISCO) employing permanganate is an emerging technology that has been successful at enhancing mass removal from DNAPL source zones in unconsolidated media at the pilot-scale. The focus of this study was to evaluate the applicability of flushing a permanganate solution across two single vertical fractures in a laboratory environment to remove free phase DNAPL. The fracture experiments were designed to represent a portion of a larger fractured aquifer system impacted by a near-surface DNAPL spill over a shallow fractured rock aquifer. Each fracture was characterized by hydraulic and tracer tests, and the aperture field for one of the fractures was mapped using a co-ordinate measurement machine. Following DNAPL emplacement, a series of water and permanganate flushes were performed. To support observations from the fracture experiments, a set of batch experiments was conducted. The data from both fracture experiments showed that the post-oxidation effluent concentration was not impacted by the oxidant flush; however, changes in the aperture distribution, flow field, and flow rate were observed. These changes resulted in a significant decrease to the mass loading from the fractures, and were attributed to the build-up of oxidation by-products (manganese oxides and carbon dioxide) within the fracture which was corroborated by the batch experiment data and visual examination of the walls of one fracture. These results provide insight into the potential impact that a permanganate solution and oxidation by-products can have on the aperture distribution within a fracture and on DNAPL mass transfer rates. A permanganate flush or injection completed within a fractured rock aquifer may lead to the development of an insoluble product adjacent to the DNAPL which results in the reduction or complete elimination of advective regions near the DNAPL and reduces mass transfer rates. This outcome would have significant implications on the plume generating potential of the remaining DNAPL.

Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors.

The bacterial family Enterobacteriaceae is notable for its well studied human pathogens, including Salmonella, Yersinia, Shigella, and Escherichia spp. However, it also contains several plant pathogens. We report the genome sequence of a plant pathogenic enterobacterium, Erwinia carotovora subsp. atroseptica (Eca) strain SCRI1043, the causative agent of soft rot and blackleg potato diseases. Approximately 33% of Eca genes are not shared with sequenced enterobacterial human pathogens, including some predicted to facilitate unexpected metabolic traits, such as nitrogen fixation and opine catabolism. This proportion of genes also contains an overrepresentation of pathogenicity determinants, including possible horizontally acquired gene clusters for putative type IV secretion and polyketide phytotoxin synthesis. To investigate whether these gene clusters play a role in the disease process, an arrayed set of insertional mutants was generated, and mutations were identified. Plant bioassays showed that these mutants were significantly reduced in virulence, demonstrating both the presence of novel pathogenicity determinants in Eca, and the impact of functional genomics in expanding our understanding of phytopathogenicity in the Enterobacteriaceae.

The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129.

Corynebacterium diphtheriae is a Gram-positive, non-spore forming, non-motile, pleomorphic rod belonging to the genus Corynebacterium and the actinomycete group of organisms. The organism produces a potent bacteriophage-encoded protein exotoxin, diphtheria toxin (DT), which causes the symptoms of diphtheria. This potentially fatal infectious disease is controlled in many developed countries by an effective immunisation programme. However, the disease has made a dramatic return in recent years, in particular within the Eastern European region. The largest, and still on-going, outbreak since the advent of mass immunisation started within Russia and the newly independent states of the former Soviet Union in the 1990s. We have sequenced the genome of a UK clinical isolate (biotype gravis strain NCTC13129), representative of the clone responsible for this outbreak. The genome consists of a single circular chromosome of 2 488 635 bp, with no plasmids. It provides evidence that recent acquisition of pathogenicity factors goes beyond the toxin itself, and includes iron-uptake systems, adhesins and fimbrial proteins. This is in contrast to Corynebacterium's nearest sequenced pathogenic relative, Mycobacterium tuberculosis, where there is little evidence of recent horizontal DNA acquisition. The genome itself shows an unusually extreme large-scale compositional bias, being noticeably higher in G+C near the origin than at the terminus.

Air distribution in the Borden aquifer during in situ air sparging.

A field experiment was conducted at Canadian Forces Base Borden (CFB Borden) to assess the air distribution from a single in situ air sparging injection point. This aquifer consists of fine to medium sand deposited in horizontal layers. The permeability at the study location varied from 10(-10) to 10(-14) m2 and distinct low permeability horizons were present at approximately 1.2, 2.0, and 2.9 m below the water table. Prior to air injection, a 15x15-m portion of the vadose zone was excavated to the water table (approximately 1 m below ground surface) in order to visually observe air release distribution at the water table. The water table was actively maintained 5 cm above the excavated surface. The sparging system operated for a period of 7 days with an injection flow rate of 200 m3/days (5 scfm). The resulting subsurface air distribution was assessed using a variety of techniques including neutron logging, borehole and surface ground penetrating radar, piezometric head measurements, surface visualization, and hydraulic testing. Through this combination of tests, it was demonstrated that variations in permeability and, hence, capillary pressure at the site were sufficient to cause the injected air to spread laterally, forming stratigraphically trapped air pockets beneath the low permeability horizons. The formation of these air pockets eventually resulted in a buildup of capillary pressure that exceeded the air entry pressure and allowed some air to migrate up through the lower permeability layers. Each of the assessment techniques employed generated information at different spatial scales that prevented a direct comparison of the results from the various techniques; however, the results from all techniques proved to be critical in the interpretation of the experimental data. As a consequence, the different assessment techniques should not be viewed as alternatives, but rather as complimentary techniques.