Impacts of Domestication and Veterinary Treatment on Mobile Genetic Elements and Resistance Genes in Equine Fecal Bacteria.

Antimicrobial resistance in bacteria is a threat to both human and animal health. We aimed to understand the impact of domestication and antimicrobial treatment on the types and numbers of resistant bacteria, antibiotic resistance genes (ARGs), and class 1 integrons (C1I) in the equine gut microbiome. Antibiotic-resistant fecal bacteria were isolated from wild horses, healthy farm horses, and horses undergoing veterinary treatment, and isolates (9,083 colonies) were screened by PCR for C1I; these were found at frequencies of 9.8% (vet horses), 0.31% (farm horses), and 0.05% (wild horses). A collection of 71 unique C1I+ isolates (17 Actinobacteria and 54 Proteobacteria) was subjected to resistance profiling and genome sequencing. Farm horses yielded mostly C1I+ Actinobacteria (Rhodococcus, Micrococcus, Microbacterium, Arthrobacter, Glutamicibacter, Kocuria), while vet horses primarily yielded C1I+ Proteobacteria (Escherichia, Klebsiella, Enterobacter, Pantoea, Acinetobacter, Leclercia, Ochrobactrum); the vet isolates had more extensive resistance and stronger PC promoters in the C1Is. All integrons in Actinobacteria were flanked by copies of IS6100, except in Micrococcus, where a novel IS5 family element (ISMcte1) was implicated in mobilization. In the Proteobacteria, C1Is were predominantly associated with IS26 and also IS1, Tn21, Tn1721, Tn512, and a putative formaldehyde-resistance transposon (Tn7489). Several large C1I-containing plasmid contigs were retrieved; two of these (plasmid types Y and F) also had extensive sets of metal resistance genes, including a novel copper-resistance transposon (Tn7519). Both veterinary treatment and domestication increase the frequency of C1Is in equine gut microflora, and each of these anthropogenic factors selects for a distinct group of integron-containing bacteria. IMPORTANCE There is increasing acknowledgment that a "one health" approach is required to tackle the growing problem of antimicrobial resistance. This requires that the issue is examined from not only the perspective of human medicine but also includes consideration of the roles of antimicrobials in veterinary medicine and agriculture and recognizes the importance of other ecological compartments in the dissemination of ARGs and mobile genetic elements such as C1I. We have shown that domestication and veterinary treatment increase the frequency of occurrence of C1Is in the equine gut microflora and that, in healthy farm horses, the C1I are unexpectedly found in Actinobacteria, while in horses receiving antimicrobial veterinary treatments, a taxonomic shift occurs, and the more typical integron-containing Proteobacteria are found. We identified several new mobile genetic elements (plasmids, insertion sequences [IS], and transposons) on genomic contigs from the integron-containing equine bacteria.

Early infection is an independent risk factor for increased mortality in patients with culture-confirmed infected pancreatic necrosis.

BACKGROUND: Mortality in infected pancreatic necrosis (IPN) is dynamic over the course of the disease, with type and timing of interventions as well as persistent organ failure being key determinants. The timing of infection onset and how it pertains to mortality is not well defined. OBJECTIVES: To determine the association between mortality and the development of early IPN. METHODS: International multicenter retrospective cohort study of patients with IPN, confirmed by a positive microbial culture from (peri) pancreatic collections. The association between timing of infection onset, timing of interventions and mortality were assessed using Cox regression analyses. RESULTS: A total of 743 patients from 19 centers across 3 continents with culture-confirmed IPN from 2000 to 2016 were evaluated, mortality rate was 20.9% (155/734). Early infection was associated with a higher mortality, when early infection occurred within the first 4 weeks from presentation with acute pancreatitis. After adjusting for comorbidity, advanced age, organ failure, enteral nutrition and parenteral nutrition, early infection (≤4 weeks) and early open surgery (≤4 weeks) were associated with increased mortality [HR: 2.45 (95% CI: 1.63-3.67), p < 0.001 and HR: 4.88 (95% CI: 1.70-13.98), p = 0.003, respectively]. There was no association between late open surgery, early or late minimally invasive surgery, early or late percutaneous drainage with mortality (p > 0.05). CONCLUSION: Early infection was associated with increased mortality, independent of interventions. Early surgery remains a strong predictor of excess mortality.

Endoscopic ultrasound-directed transgastric ERCP (EDGE): a systematic review describing the outcomes, adverse events, and knowledge gaps.

BACKGROUND : Endoscopic ultrasound-directed transgastric endoscopic retrograde cholangiopancreatography (EDGE) has emerged as a viable completely endoscopic method for performing pancreaticobiliary interventions in patients with Roux-en-Y gastric bypass anatomy. The aims of this systematic review were: (1) to describe the indications, outcomes, and complications of EDGE; and (2) to identify deficiencies in our knowledge of important technical approaches and clinical outcomes. METHODS : A systematic review was conducted via comprehensive searches of Medline, Scopus, CINAHL, and Cochrane to identify studies focusing on EDGE outcomes. Simple descriptive statistics were derived from case series only. Case reports were only included to qualitatively describe additional indications, techniques, and adverse events. RESULTS : The initial search identified 2143 abstracts. Nine case series and eight case reports were included. In the nine case series, 169 patients underwent EDGE. The technical success rate was 99 % (168 /169) for gastrogastrostomy/jejunogastrostomy creation and 98 % (166 /169) for subsequent ERCP. Minor adverse events specifically related to EDGE occurred in 18 % (31/169) and included intraprocedural stent migration/malposition (n = 27) and abdominal pain (n = 4). Moderate adverse events specific to EDGE occurred in 5 % (9/169): including bleeding (2 %), persistent fistula (1 %), and perforation (1 %). Severe adverse events occurred in one patient with a perforation requiring surgery. Deficiency in reporting on the clinical significance of adverse events was identified. CONCLUSION : Based on limited observational data, in expert hands, EDGE has a high rate of technical success and an acceptable rate of adverse events. As a novel procedure, many knowledge gaps need to be addressed to inform the design of meaningful comparative studies and guide informed consent.

Zenker's peroral endoscopic myotomy, or flexible or rigid septotomy for Zenker's diverticulum: a multicenter retrospective comparison.

BACKGROUND: Treatment of Zenker's diverticulum has evolved from open surgery to endoscopic techniques, including flexible and rigid endoscopic septotomy, and more recently, peroral endoscopic myotomy (Z-POEM). This study compared the effectiveness of flexible and rigid endoscopic septotomy with that of Z-POEM. METHODS: Consecutive patients who underwent endoscopic septotomy (flexible/rigid) or Z-POEM for Zenker's diverticulum between 1/2016 and 9/2019 were included. Primary outcomes were clinical success (decrease in Dakkak and Bennett dysphagia score to ≤ 1), clinical failure, and clinical recurrence. Secondary outcomes included technical success and rate/severity of adverse events. RESULTS: 245 patients (110 females, mean age 72.63 years, standard deviation [SD] 12.37 years) from 12 centers were included. Z-POEM was the most common management modality (n = 119), followed by flexible (n = 86) and rigid (n = 40) endoscopic septotomy. Clinical success was 92.7 % for Z-POEM, 89.2 % for rigid septotomy, and 86.7 % for flexible septotomy (P = 0.26). Symptoms recurred in 24 patients (15 Z-POEM during a mean follow-up of 282.04 [SD 300.48] days, 6 flexible, 3 rigid [P = 0.47]). Adverse events occurred in 30.0 % rigid septotomy patients, 16.8 % Z-POEM patients, and 2.3 % flexible septotomy patients (P < 0.05). CONCLUSIONS: There was no difference in outcomes between the three treatment approaches for symptomatic Zenker's diverticulum. Rigid endoscopic septotomy was associated with the highest rate of complications, while flexible endoscopic septotomy appeared to be the safest. Recurrence following Z-POEM was similar to flexible and rigid endoscopic septotomy. Prospective studies with long-term follow-up are required.

Comparison of Urologist- vs Gastroenterologist-Directed Extracorporeal Shock Wave Lithotripsy for Pancreaticolithiasis.

BACKGROUND & AIMS: Extracorporeal shock wave lithotripsy (ESWL) for pancreaticolithiasis is most commonly performed by urologists. We investigated the effects of transitioning from urologist- to gastroenterologist-directed ESWL on case complexity, process measures, and duct clearance. METHODS: We performed a retrospective study of patients who underwent ESWL for pancreaticolithiasis from 2014 through 2019 at a single center. We collected demographic, clinical, radiographic, and procedural data in duplicate and compared case complexity and process measures between the periods the procedure was performed by urologists (January 2014 through February 2017; 18 patients, 0.47 patients/month) vs gastroenterologists (March 2017 through December 2019; 61 patients; 1.79 patients/month). We also compared data on pancreatic duct stone characteristics and technical success (duct clearance, determined by imaging analysis). RESULTS: There were no differences in patient demographics, comorbidities, pancreatic stone morphology, or time from referral to ESWL during the period the procedure was performed by urologists vs gastroenterologists. Patients received a higher mean number of ESWL shocks per session during the gastroenterology period (4341) than during the urology period (3117) (P < .001). A higher proportion of patients underwent same-session endoscopic retrograde cholangiopancreatography during the gastroenterology time period (66%) than the urology time period (6%) (P < .001). A higher proportion of patients had partial or complete duct clearance during the gastroenterology period (71%) than during the urology period (44%) (P = .04). During the urology period, a higher proportion of patients were hospitalized following ESWL, although there was no difference in captured adverse events between the periods. CONCLUSIONS: Transition from urologist- to gastroenterologist-directed ESWL did not affect case complexity or wait times for ESWL. However, the transition did result in increased procedure volume, more shocks per ESWL session, and improved duct clearance.

Direct Endoscopic Necrosectomy With and Without Hydrogen Peroxide for Walled-off Pancreatic Necrosis: A Multicenter Comparative Study.

INTRODUCTION: Endoscopic necrosectomy has emerged as the preferred treatment modality for walled-off pancreatic necrosis. This study was designed to evaluate the safety and efficacy of direct endoscopic necrosectomy with and without hydrogen peroxide (H2O2) lavage. METHODS: Retrospective chart reviews were performed for all patients undergoing endoscopic transmural management of walled-off pancreatic necrosis at 9 major medical centers from November 2011 to August 2018. Clinical success was defined as the resolution of the collection by imaging within 6 months, without requiring non-endoscopic procedures or surgery. RESULTS: Of 293 patients, 204 met the inclusion criteria. Technical and clinical success rates were 100% (204/204) and 81% (166/189), respectively. For patients, 122 (59.8%) patients had at least one H2O2 necrosectomy (H2O2 group) and 82 (40.2%) patients had standard endoscopic necrosectomy. Clinical success was higher in the H2O2 group: 106/113 (93.8%) vs 60/76 (78.9%), P = 0.002. On a multivariate analysis, the use of H2O2 was associated with higher clinical success rate (odds ratio 3.30, P = 0.033) and earlier resolution (odds ratio 2.27, P < 0.001). During a mean follow-up of 274 days, 27 complications occurred. Comparing procedures performed with and without H2O2 (n = 250 vs 183), there was no difference in post-procedure bleeding (7 vs 9, P = 0.25), perforation (2 vs 3, P = 0.66), infection (1 vs 2, P = 0.58), or overall complication rate (n = 13 [5.2%] vs 14 [7.7%], P = 0.30). DISCUSSION: H2O2-assisted endoscopic necrosectomy had a higher clinical success rate and a shorter time to resolution with equivalent complication rates relative to standard necrosectomy.See the visual abstract at http://links.lww.com/AJG/B714.(Equation is included in full-text article.).

Acquisition of a genomic resistance island (AbGRI5) from global clone 2 through homologous recombination in a clinical Acinetobacter baumannii isolate.

OBJECTIVES: To reconstruct the evolutionary history of the clinical Acinetobacter baumannii XH1056, which lacks the Oxford scheme allele gdhB. METHODS: Susceptibility testing was performed using broth microdilution and agar dilution. The whole-genome sequence of XH1056 was determined using the Illumina and Oxford Nanopore platforms. MLST was performed using the Pasteur scheme and the Oxford scheme. Antibiotic resistance genes were identified using ABRicate. RESULTS: XH1056 was resistant to all antibiotics tested, apart from colistin, tigecycline and eravacycline. MLST using the Pasteur scheme assigned XH1056 to ST256. However, XH1056 could not be typed with the Oxford MLST scheme as gdhB is not present. Comparative analyses revealed that XH1056 contains a 52 933 bp region acquired from a global clone 2 (GC2) isolate, but is otherwise closely related to the ST23 A. baumannii XH858. The acquired region in XH1056 also contains a 34 932 bp resistance island that resembles AbGRI3 and contains the armA, msrE-mphE, sul1, blaPER-1, aadA1, cmlA1, aadA2, blaCARB-2 and ere(B) resistance genes. Comparison of the XH1056 chromosome to that of GC2 isolate XH859 revealed that the island in XH1056 is in the same chromosomal region as that in XH859. As this island is not in the standard AbGRI3 position, it was named AbGRI5. CONCLUSIONS: XH1056 is a hybrid isolate generated by the acquisition of a chromosomal segment from a GC2 isolate that contains a resistance island in a new location-AbGRI5. As well as generating ST256, it appears likely that a single recombination event is also responsible for the acquisition of AbGRI5 and its associated antibiotic resistance genes.

Transferable Acinetobacter baumannii plasmid pDETAB2 encodes OXA-58 and NDM-1 and represents a new class of antibiotic resistance plasmids.

OBJECTIVES: To characterize a blaOXA-58- and blaNDM-1-containing MDR plasmid from a rare Acinetobacter baumannii lineage and compare it with related plasmids to explore the distribution and evolution of a new plasmid group. METHODS: A. baumannii DETAB-P2 was isolated from a rectal swab of an intensive care patient. Antibiotic susceptibility was determined using broth microdilution. DETAB-P2 was mated with A. baumannii ATCC 17978 and putative transconjugants were characterized by S1/PFGE and Southern hybridization. WGS was performed on the Illumina and Oxford Nanopore platforms. MLST was performed with the Pasteur and Oxford schemes. Antibiotic resistance genes were identified with ABRicate. Plasmid sequence annotation was performed manually. Complete plasmids in GenBank with the same rep gene were used for comparative analyses. RESULTS: A. baumannii DETAB-P2 was ST138 by the Pasteur scheme and a novel Oxford type, ST2209. It transferred blaOXA-58 and blaNDM-1 to ATCC 17978 in the 100 072 bp plasmid pDETAB2 that also carried bleMBL, sul2, aacC2d, tet(39), msr(E)-mph(E) and putative mercury resistance and RND efflux system determinants. pDETAB2 represents a new plasmid type, GR34, and contained 16 pdif sites and several novel dif modules. Only a 10 kbp core sequence is shared amongst pDETAB2 and 18 further GR34 plasmids in GenBank, with diverse accessory regions comprised of various dif modules. CONCLUSIONS: GR34 plasmids are found in several Acinetobacter species from diverse environments. They display considerable variation in accessory content owing to the presence of pdif sites and an array of dif modules, some of which contain antibiotic resistance genes.

Evolution and dissemination of L and M plasmid lineages carrying antibiotic resistance genes in diverse Gram-negative bacteria.

Conjugative, broad host-range plasmids of the L/M complex have been associated with antibiotic resistance since the 1970s. They are found in Gram-negative bacterial genera that cause human infections and persist in hospital environments. It is crucial that these plasmids are typed accurately so that their clinical and global dissemination can be traced in epidemiological studies. The L/M complex has previously been divided into L, M1 and M2 subtypes. However, those types do not encompass all diversity seen in the group. Here, we have examined 148 complete L/M plasmid sequences in order to understand the diversity of the complex and trace the evolution of distinct lineages. The backbone sequence of each plasmid was determined by removing translocatable genetic elements and reversing their effects in silico. The sequence identities of replication regions and complete backbones were then considered for typing. This supported the distinction of L and M plasmids and revealed that there are five L and eight M types, where each type is comprised of further sub-lineages that are distinguished by variation in their backbone and translocatable element content. Regions containing antibiotic resistance genes in L and M sub-lineages have often formed by initial rare insertion events, followed by insertion of other translocatable elements within the inceptive element. As such, islands evolve in situ to contain genes conferring resistance to multiple antibiotics. In some cases, different plasmid sub-lineages have acquired the same or related resistance genes independently. This highlights the importance of these plasmids in acting as vehicles for the dissemination of emerging resistance genes. Materials are provided here for typing plasmids of the L/M complex from complete sequences or draft genomes. This should enable rapid identification of novel types and facilitate tracking the evolution of existing lineages.

Impedance planimetry values for predicting clinical response following peroral endoscopic myotomy.

BACKGROUND: There is growing interest in developing impedance planimetry as a tool to enhance the clinical outcomes for endoscopic and surgical management of achalasia. The primary aim of this study was to determine whether impedance planimetry measurements can predict clinical response and reflux following peroral endoscopic myotomy (POEM). METHODS: A multicenter cohort study of patients with achalasia undergoing POEM was established from prospective databases and retrospective chart reviews. Patients who underwent impedance planimetry before and after POEM were included. Clinical response was defined as an Eckardt score of ≤ 3. Tenfold cross-validated area under curve (AUC) values were established for the different impedance planimetry measurements associated with clinical response and reflux development. RESULTS: Of the 290 patients included, 91.7 % (266/290) had a clinical response and 39.4 % (108/274) developed reflux following POEM. The most predictive impedance planimetry measurements for a clinical response were: percent change in cross-sectional area (%ΔCSA) and percent change in distensibility index (%ΔDI), with AUCs of 0.75 and 0.73, respectively. Optimal cutoff values for %ΔCSA and %ΔDI to determine a clinical response were a change of 360 % and 272 %, respectively. Impedance planimetry values were much poorer at predicting post-POEM reflux, with AUCs ranging from 0.40 to 0.62. CONCLUSION: Percent change in CSA and distensibility index were the most predictive measures of a clinical response, with a moderate predictive ability. Impedance planimetry values for predicting reflux following POEM showed weak predictive capacity.

Exploring cation disorder in mixed-metal pyrochlore ceramics using 17 O NMR spectroscopy and first-principles calculations.

Characterising the local structures (e.g., the cation distribution) of mixed-metal ceramics by NMR spectroscopy is often challenging owing to the unfavourable properties (low γ, large quadrupole moment and/or low abundance) of many metal nuclei. 17 O is an attractive option owing to the prevalence of oxygen within ceramics. The moderate γ and small quadrupole moment of 17 O mean that the greatest barrier to accessing the information available from this nucleus is isotopic enrichment. We explore the challenges of ensuring uniform isotopic enrichment with 17 O2 (g) for the pyrochlore solid solutions, Y2 Snx Ti2-x O7 , La2 Snx Zr2-x O7 and La2 Snx Hf2-x O7 , demonstrating that high enrichment temperatures (900 °C for 12 hr) are required. In addition, for sites with very high symmetry (such as the tetrahedral OY4 and OLa4 sites with CQ ≈ 0 present here), we demonstrate that quantitative 17 O NMR spectra require correction for the differing contributions from the centreband of the satellite transitions, which can be as high as a factor of ~3.89. It is common to use first-principles calculations to aid in interpreting NMR spectra of disordered solids. Here, we use an ensemble modelling approach to ensure that all possible cation arrangements are modelled in the minimum possible number of calculations. By combining uniform isotopic enrichment, quantitative NMR spectroscopy and a comprehensive computational approach, we are able to show that the cation distribution in Y2 Snx Ti2-x O7 is essentially random, whereas in La2 Snx Zr2-x O7 and La2 Snx Hf2-x O7 , OLa2SnZr and OLa2SnHf sites are slightly energetically disfavoured, leading to a weak preference for clustering of like cations.

Evolution of IS26-bounded pseudo-compound transposons carrying the tet(C) tetracycline resistance determinant.

A large plasmid, pCERC14, found in an antibiotic resistant commensal Escherichia coli isolate recovered from a healthy adult was sequenced. pCERC14 was 162,926 bp and carried FII-18 and FIB-1 replicons and an F-like transfer region as well as several virulence determinants, some of which are involved in the uptake of iron which would be advantageous for the commensal lifestyle. The plasmid backbone is interrupted in 11 places by complete IS (IS1 (4 copies), IS2 (2), IS629 (2) and single IS100, IS186, ISEc33) and in three places by partial IS copies. The antibiotic resistance genes were found in two IS26-bounded pseudo-compound transposons (PCT). One contained a remnant of a class 1 integron that includes a dfrA5 gene cassette and the sul1 gene conferring resistance to trimethoprim and sulphonamides, respectively. The second, named PTntet(C)-var, contained a 4828 bp DNA segment that includes the tet(C) tetracycline resistance determinant. As tet(C) is relatively rare in E. coli and other Gram-negative bacterial isolates, the structure and evolution of tet(C)-containing PCT in available sequences was examined. The largest identified was PTntet(C), a close relative of PTntet(C)-var, and a potential progenitor for these PCT. Most PCT shared one internal boundary with PTntet(C) but the length of the central tet(C)-containing segment was shorter due to IS26-mediated deletions. The most abundant variant form, previously named Tn6309, was widely distributed and, in a derivative of it, most of the tetA(C) gene has been replaced by the tetA(A) gene presumably by homologous recombination.

Ensemble-Based Modeling of the NMR Spectra of Solid Solutions: Cation Disorder in Y2(Sn,Ti)2O7.

The sensitivity of NMR to the local environment, without the need for any long-range order, makes it an ideal tool for the characterization of disordered materials. Computational prediction of NMR parameters can be of considerable help in the interpretation and assignment of NMR spectra of solids, but the statistical representation of all possible chemical environments for a solid solution is challenging. Here, we illustrate the use of a symmetry-adapted configurational ensemble in the simulation of NMR spectra, in combination with solid-state NMR experiments. We show that for interpretation of the complex and overlapped lineshapes that are typically observed, it is important to go beyond a single-configuration representation or a simple enumeration of local environments. The ensemble method leads to excellent agreement between simulated and experimental spectra for Y2(Sn,Ti)2O7 pyrochlore ceramics, where the overlap of signals from different local environments prevents a simple decomposition of the experimental spectral lineshapes. The inclusion of a Boltzmann weighting confirms that the best agreement with experiment is obtained at higher temperatures, in the limit of full disorder. We also show that to improve agreement with experiment, in particular at low dopant concentrations, larger supercells are needed, which might require alternative simulation approaches as the complexity of the system increases. It is clear that ensemble-based modeling approaches in conjunction with NMR spectroscopy offer great potential for understanding configurational disorder, ultimately aiding the future design of functional materials.

A Picture of Disorder in Hydrous Wadsleyite-Under the Combined Microscope of Solid-State NMR Spectroscopy and Ab Initio Random Structure Searching.

The Earth's transition zone, at depths of 410-660 km, while being composed of nominally anhydrous magnesium silicate minerals, may be subject to significant hydration. Little is known about the mechanism of hydration, despite the vital role this plays in the physical and chemical properties of the mantle, leading to a need for improved structural characterization. Here we present an ab initio random structure searching (AIRSS) investigation of semihydrous (1.65 wt % H2O) and fully hydrous (3.3 wt % H2O) wadsleyite. Following the AIRSS process, k-means clustering was used to select sets of structures with duplicates removed, which were then subjected to further geometry optimization with tighter constraints prior to NMR calculations. Semihydrous models identify a ground-state structure (Mg3 vacancies, O1-H hydroxyls) that aligns with a number of previous experimental observations. However, predicted NMR parameters fail to reproduce low-intensity signals observed in solid-state NMR spectra. In contrast, the fully hydrous models produced by AIRSS, which enable both isolated and clustered defects, are able to explain observed NMR signals via just four low-enthalpy structures: (i) a ground state, with isolated Mg3 vacancies and O1-H hydroxyls; (ii/iii) edge-sharing Mg3 vacancies with O1-H and O3-H species; and (iv) edge-sharing Mg1 and Mg3 vacancies with O1-H, O3-H, and O4-H hydroxyls. Thus, the combination of advanced structure searching approaches and solid-state NMR spectroscopy is able to provide new and detailed insight into the structure of this important mantle mineral.

B/O plasmid R16 from 1956 carries an In1-like class 1 integron embedded in a complex region containing parts of the Acinetobacter baumannii AbaR resistance island.

The IncB/O multiresistance plasmid R16, recovered in 1956 and used in experimental studies of B/O plasmid features, was sequenced. The resistance genes are all within a class 1 integron closely related to In1 containing the cassette array oxa2-aadA1-oxa2-orfD and the sul1 gene in the 3'-conserved segment (3'-CS), with Tn10, containing tetA(B), inserted just inside the 3'-CS. The integron is part of a 25,144 bp region inserted in the plasmid backbone, bounded on only one side by a truncated Tn6018 and flanked by a 4 bp duplication. Most of the 82,026 bp R16 backbone is almost identical to that of the B/O plasmid R805a. However, two short regions containing genes of unknown function are <95% identical to the corresponding regions of R805a, and were likely acquired from a related plasmid. The insertion in R16 is related to one in the I1 plasmid pSE69-3861-1, which is embedded at the same position in an almost 11 kb segment of R16 backbone. In pSE69-3861-1, Tn6018 is complete, and two regions previously seen only in AbaR type islands of GC1 Acinetobacter baumannii are present. One contains a top topoisomerase gene and the second contains a resX resolvase gene. These regions are identical to the corresponding parts of AbaR islands. Thus, the complete sequence of R16 sheds light on the role of homologous recombination in the evolution of plasmid backbones and the acquisition of antibiotic resistance genes by I-complex plasmids, as well as on the formation of the AbaR islands of GC1 A. baumannii.

pBuzz: A cryptic rolling-circle plasmid from a commensal Escherichia coli has two inversely oriented oriTs and is mobilised by a B/O plasmid.

Ampicillin, streptomycin and sulphamethoxazole resistant commensal E. coli 838-3B contains five plasmids that range in size from >90 kb to <2 kb. The resistance genes blaTEM (ampicillin), strA (streptomycin) and sul2 (sulphamethoxazole) transferred along with a B/O plasmid named p838B-R. However, three plasmids smaller than 7 kb were also found in transconjugants, suggesting that they could be mobilised by the B/O plasmid. The complete sequences of p838B-R and pBuzz, a small plasmid mobilised by p838B-R with 70% efficiency, were determined. p838B-R is 94,803 bp and contains an 8400 bp resistance island that includes the three antibiotic resistance genes. The p838B-R backbone contains a complete conjugative transfer region, including an oriT site upstream of nikAB that resembles the experimentally-defined oriT of R64. The 1982 bp pBuzz contains a rep gene and sites associated with replication that resemble those of pC194/pUB110 family rolling-circle plasmids. It also contains two, inversely oriented copies of an 84 bp sequence that differs from the oriT region in p838B-R at just 6 positions. These oriT-like sites likely explain the ability of pBuzz to co-transfer with the B/O plasmid using the NikB relaxase and NikA accessory protein encoded by p838B-R, i.e. pBuzz utilises relaxase-in trans mobilisation. Several rolling-circle plasmids related to pBuzz were found in the GenBank non-redundant nucleotide database. They contain diverse potential oriTs, including sequences similar to known oriTs found in conjugative plasmids of I-complex (I1, B/O, K, Z and I2), L or M types.

Analysis of two B/O plasmids, R805a from 1972 and pCERC6 from 2008, reveals extensive mosaicism in B/O plasmid backbones.

Two B/O plasmids were sequenced. The kanamycin resistance plasmid R805a was found in a Salmonella Typhi strain from a 1972 typhoid fever outbreak in Mexico City. pCERC6, which confers resistance to ampicillin, streptomycin and sulphamethoxazole, was found in a commensal E. coli isolated from a healthy adult in Sydney in 2008. Both plasmids contain the same gene for RNAI, the incompatibility determinant, as the reference B/O plasmid pMU707 and the recently reported plasmid p838B-R, which came from a commensal E. coli isolated in Sydney in 2004. However, three different repA alleles are associated with the IncB/O rnaI. Whereas the repA gene of p838B-R is identical to that of pMU707, R805a and pCERC6 each carry a different repA. Comparison of the plasmid backbones revealed that R805a has a different oriT-nikAB region to that in pCERC6 and p838B-R, encoding different NikA relaxosome accessory factors and NikB relaxases. The different nikA genes were associated with oriT sites that differed in the sequences of their long, imperfect inverted repeats. A further 11 publicly available complete plasmid sequences contain the same B/O rnaI, with either the repA of pMU707/p838B-R or of R805a, and the oriT-nikAB region of p838B-R/pCERC6 or of R805a. All four possible combinations were seen. Extensive variation was also observed in the traY-excA entry exclusion region, and in the locations of mobile elements, including ones carrying antibiotic resistance genes. Plasmids that contain the same rnaI gene would be considered the same by a number of typing methods, but this study has unveiled previously unnoticed mosaicism in the backbones of one such group. This highlights the importance of considering entire plasmid backbones for the typing and tracking of specific lineages.

An improved plasmid size standard, 39R861.

The four plasmids in E. coli 39R861 have been used as size standards for closed-circular plasmid DNA since the 1980s. However, their sizes had only been estimated. Here, the complete sequence of the 61.3 kb cryptic FII plasmid p39R861-3 is reported, and the sizes of p39R861-4, pSa and NTP168 were determined to be 155.8, 40.1 and 6.8 kb, respectively. An improved size standard, 39R861+, was created by adding two sequenced, compatible plasmids to 39R861 via conjugation. The 94.8 kb conjugative B/O plasmid p838B-R mobilised the cryptic, 2.0 kb pBuzz. The six plasmids in 39R861+ are all stably maintained.

Is the 31 P chemical shift anisotropy of aluminophosphates a useful parameter for NMR crystallography?

The 31 P chemical shift anisotropy (CSA) offers a potential source of new information to help determine the structures of aluminophosphate (AlPO) framework materials. We investigate how to measure the CSAs, which are small (span of ~20-30 ppm) for AlPOs, demonstrating the need for CSA-amplification experiments (often in conjunction with 27 Al and/or 1 H decoupling) at high magnetic field (20.0 T) to obtain accurate values. We show that the most shielded component of the chemical shift tensor, δ33 , is related to the length of the shortest P─O bond, whereas the more deshielded components, δ11 and δ22 can be related more readily to the mean P─O bond lengths and P─O─Al angles. Using the case of Mg-doped STA-2 as an example, the CSA is shown to be much larger for P(OAl)4-n (OMg)n environments, primarily owing to a much shorter P─O(Mg) bond affecting δ33 , however, because the mean P─O bond lengths and P─O─T (T = Al, Mg) bond angles do not change significantly between P(OAl)4 and P(OAl)4-n (OMg)n sites, the isotropic chemical shifts for these species are similar, leading to overlapped spectral lines. When the CSA information is included, spectral assignment becomes unambiguous, therefore, although the specialist conditions required might preclude the routine measurement of 31 P CSAs in AlPOs, in some cases (particularly doped materials), the experiments can still provide valuable additional information for spectral assignment.

Endoscopic treatment of pain in chronic pancreatitis.

PURPOSE OF REVIEW: Pain is the most common symptom of chronic pancreatitis, having a profound effect on patients and a broad socioeconomic impact. Endoscopy is guideline recommended as first-line management for chronic pancreatitis pain in certain clinical scenarios. Herein, we provide an evidence-based review of the endoscopic treatment of pain due to chronic pancreatitis while highlighting some important confounders in the measurement of this outcome in clinical practice and research. RECENT FINDINGS: Multiple recent studies have reported on the efficacy of current endoscopic therapies for chronic pancreatitis pain. Despite the high technical success rates of these procedures, pain outcomes remain disappointing. Complex mechanisms beyond ductal hypertension, such as central sensitization, visceral hypersensitivity and inflammatory neuritis account for some of the discordance observed between the rates of technical and clinical success. In addition, the sham effect is increasingly recognized as a confounder when interpreting the procedural benefit. Nevertheless, there are multiple promising innovations in the field of pancreatic endoscopy that are aimed to improve technical and clinical outcomes, but rigorous investigation is necessary to establish their role in clinical practice. SUMMARY: Endoscopic therapy for chronic pancreatitis pain appears to be safe and effective in certain contexts and recent innovations in the field will hopefully further improve outcomes. In addition to evaluating the technical success of endotherapy in chronic pancreatitis, methodologically rigorous research focusing on patient-centered outcomes and accounting for the sham effect is necessary to advance this field.