Characterisation of colistin resistance in Gram-negative microbiota of pregnant women and neonates in Nigeria.

A mobile colistin resistance gene mcr was first reported in 2016 in China and has since been found with increasing prevalence across South-East Asia. Here we survey the presence of mcr genes in 4907 rectal swabs from mothers and neonates from three hospital sites across Nigeria; a country with limited availability or history of colistin use clinically. Forty mother and seven neonatal swabs carried mcr genes in a range of bacterial species: 46 Enterobacter spp. and single isolates of; Shigella, E. coli and Klebsiella quasipneumoniae. Ninety percent of the genes were mcr-10 (n = 45) we also found mcr-1 (n = 3) and mcr-9 (n = 1). While the prevalence during this collection (2015-2016) was low, the widespread diversity of mcr-gene type and range of bacterial species in this sentinel population sampling is concerning. It suggests that agricultural colistin use was likely encouraging sustainment of mcr-positive isolates in the community and implementation of medical colistin use will rapidly select and expand resistant isolates.

Atomistic simulations of calcium aluminosilicate interfaced with liquid water.

The dissolution behavior of calcium aluminosilicate based glass fibers, such as stone wool fibers, is an important consideration in mineral wool applications for both the longevity of the mineral wool products in humid environments and limiting the health impacts of released and inhaled fibers from the mineral wool product. Balancing these factors requires a molecular-level understanding of calcium aluminosilicate glass dissolution mechanisms, details that are challenging to resolve with experiment alone. Molecular dynamics simulations are a powerful tool capable of providing complementary atomistic insights regarding dissolution; however, they require force fields capable of describing not-only the calcium aluminosilicate surface structure but also the interactions relevant to dissolution phenomena. Here, a new force field capable of describing amorphous calcium aluminosilicate surfaces interfaced with liquid water is developed by fitting parameters to experimental and first principles simulation data of the relevant oxide-water interfaces, including ab initio molecular dynamics simulations performed for this work for the wüstite and periclase interfaces. Simulations of a calcium aluminosilicate surface interfaced with liquid water were used to test this new force field, suggesting moderate ingress of water into the porous glass interface. This design of the force field opens a new avenue for the further study of calcium and network-modifier dissolution phenomena in calcium aluminosilicate glasses and stone wool fibers at liquid water interfaces.

Incidence and sociodemographic, living environment and maternal health associations with stillbirth in a tertiary healthcare setting in Kano, Northern Nigeria.

BACKGROUND: Almost two million stillbirths occur annually, most occurring in low- and middle-income countries. Nigeria is reported to have one of the highest stillbirth rates on the African continent. The aim was to identify sociodemographic, living environment, and health status factors associated with stillbirth and determine the associations between pregnancy and birth factors and stillbirth in the Murtala Mohammed Specialist Hospital, Kano, Nigeria. METHODS: A three-month single-site prospective observational feasibility study. Demographic and clinical data were collected. We fitted bivariable and multivariable models for stillbirth (yes/no) and three-category livebirth/macerated stillbirth/non-macerated stillbirth outcomes to explore their association with demographic and clinical factors. FINDINGS: 1,998 neonates and 1,926 mothers were enrolled. Higher odds of stillbirth were associated with low-levels of maternal education, a further distance to travel to the hospital, living in a shack, maternal hypertension, previous stillbirth, birthing complications, increased duration of labour, antepartum haemorrhage, prolonged or obstructed labour, vaginal breech delivery, emergency caesarean-section, and signs of trauma to the neonate following birth. INTERPRETATION: This work has obtained data on some factors influencing stillbirth. This in turn will facilitate the development of improved public health interventions to reduce preventable deaths and to progress maternal health within this site.

Antibiotic resistance genes in the gut microbiota of mothers and linked neonates with or without sepsis from low- and middle-income countries.

Early development of the microbiome has been shown to affect general health and physical development of the infant and, although some studies have been undertaken in high-income countries, there are few studies from low- and middle-income countries. As part of the BARNARDS study, we examined the rectal microbiota of 2,931 neonates (term used up to 60 d) with clinical signs of sepsis and of 15,217 mothers screening for blaCTX-M-15, blaNDM, blaKPC and blaOXA-48-like genes, which were detected in 56.1%, 18.5%, 0% and 4.1% of neonates' rectal swabs and 47.1%, 4.6%, 0% and 1.6% of mothers' rectal swabs, respectively. Carbapenemase-positive bacteria were identified by MALDI-TOF MS and showed a high diversity of bacterial species (57 distinct species/genera) which exhibited resistance to most of the antibiotics tested. Escherichia coli, Klebsiella pneumoniae and Enterobacter cloacae/E. cloacae complex, the most commonly found isolates, were subjected to whole-genome sequencing analysis and revealed close relationships between isolates from different samples, suggesting transmission of bacteria between neonates, and between neonates and mothers. Associations between the carriage of antimicrobial resistance genes (ARGs) and healthcare/environmental factors were identified, and the presence of ARGs was a predictor of neonatal sepsis and adverse birth outcomes.

Prevalence and risk factors for intestinal carriage of CTX-M-type ESBLs in Enterobacteriaceae from a Thai community.

The incidence of infections caused by antimicrobial-resistant Enterobacteriaceae in Thailand is increasing and human intestinal flora is an important reservoir for these organisms. This study was carried out to determine the intestinal carriage of bla CTX-M extended spectrum ß-lactamase-positive Enterobacteriaceae (ESBL + E) and AmpC-positive Enterobacteriaceae in a community setting in Northern Thailand, and to identify potential risk factors for carriage. A total of 307 fecal samples were collected from healthy volunteers in Phitsanulok province, and cefotaxime-resistant Enterobacteriaceae (CtxRE) were isolated using selective media. Polymerase chain reaction (PCR) was used to detect ESBL and AmpC genes. Risk factors were analyzed using multiple logistic regression. Genotyping was performed by multilocus sequence typing (MLST) analysis. Two hundred ninety-one CtxRE isolates were obtained and Escherichia coli was the predominant organism (66.3%). The intestinal carriage rates of bla CTX-M ESBL + E and AmpC-positive Enterobacteriaceae were 52.1% and 6.2%, respectively. Comparative levels of bla CTX-M group 1 and bla CTX-M group 9 were found while bla CMY-2 was the predominant genotype among AmpC genes. Co-existence of two ß-lactamase genes in a single isolate was found in 6.5% of isolates. Consumption of undercooked meat was strongly associated with intestinal carriage of bla CTX-M ESBL + E (p = 0.003, OR = 2.133, 95% CI = 1.289-3.530). Phylogenetic grouping and MLST analysis of E. coli isolates revealed the presence of E. coli B2-ST131 (n = 8). Of these, seven carried bla CTX-M-group 9 and 1 carried bla CMY-2. Our results suggest that residents in Thailand are at high risk for developing endogenous infections caused by antibiotic-resistant Enterobacteriaceae.

Organic-Silica Interactions in Saline: Elucidating the Structural Influence of Calcium in Low-Salinity Enhanced Oil Recovery.

Enhanced oil recovery using low-salinity solutions to sweep sandstone reservoirs is a widely-practiced strategy. The mechanisms governing this remain unresolved. Here, we elucidate the role of Ca2+ by combining chemical force microscopy (CFM) and molecular dynamics (MD) simulations. We probe the influence of electrolyte composition and concentration on the adsorption of a representative molecule, positively-charged alkylammonium, at the aqueous electrolyte/silica interface, for four electrolytes: NaCl, KCl, MgCl2, and CaCl2. CFM reveals stronger adhesion on silica in CaCl2 compared with the other electrolytes, and shows a concentration-dependent adhesion not observed for the other electrolytes. Using MD simulations, we model the electrolytes at a negatively-charged amorphous silica substrate and predict the adsorption of methylammonium. Our simulations reveal four classes of surface adsorption site, where the prevalence of these sites depends only on CaCl2 concentration. The sites relevant to strong adhesion feature the O- silica site and Ca2+ in the presence of associated Cl-, which gain prevalence at higher CaCl2 concentration. Our simulations also predict the adhesion force profile to be distinct for CaCl2 compared with the other electrolytes. Together, these analyses explain our experimental data. Our findings indicate in general how silica wettability may be manipulated by electrolyte concentration.

Genetic & virulence profiling of ESBL-positive E. coli from nosocomial & veterinary sources.

CTX-M genes are the most prevalent ESBL globally, infiltrating nosocomial, community and environmental settings. Wild and domesticated animals may act as effective vectors for the dissemination of CTX-producing Enterobacteriaceae. This study aimed to contextualise blaCTX-M-14-positive, cephalosporin-resistant Enterobacteriaceae human infections and compared resistance and pathogenicity markers with veterinary isolates. Epidemiologically related human (n=18) and veterinary (n=4) blaCTX-M-14-positive E. coli were fully characterised. All were typed by XbaI pulsed field gel electrophoresis and ST. Chromosomal/plasmidic locations of blaCTX-M-14 were deduced by S1-nuclease digestion, and association with ISEcp1 was investigated by sequencing. Conjugation experiments assessed transmissibility of plasmids carrying blaCTX-M-14. Presence of virulence determinants was screened by PCR assay and pathogenicity potential was determined by in vitro Galleria mellonella infection models. 84% of clinical E. coli originated from community patients. blaCTX-M-14 was found ubiquitously downstream of ISEcp1 upon conjugative plasmids (25-150 kb). blaCTX-M-14 was also found upon the chromosome of eight E. coli isolates. CTX-M-14-producing E. coli were found at multiple hospital sites. Clonal commonality between patient, hospitals and livestock microbial populations was found. In vivo model survival rates from clinical isolates (30%) and veterinary isolates (0%) were significantly different (p<0.05). Co-transfer of blaCTX-M-14 and virulence determinants was demonstrated. There is evidence of clonal spread of blaCTX-M-14-positive E. coli involving community patients and farm livestock. blaCTX-M-14 positive human clinical isolates carry a lower intrinsic pathogenic potential than veterinary E. coli highlighting the need for greater veterinary practices in preventing dissemination of MDR E. coli among livestock.

Ductile thermoset polymers via controlling network flexibility.

We report the design and synthesis of a polymer structure from a cross-linkable epoxy-ionic liquid system which behaves like a hard and brittle epoxy thermoset, perfectly ductile thermoplastic and an elastomer, all depending on controllable network compositions.

blaNDM-1 is a chimera likely constructed in Acinetobacter baumannii.

Alignment of DNA sequences found upstream of aphA6 and all bla(NDM-1) genes displays 100% identity. This identity continues 19 bp into the bla(NDM-1) gene such that the first 6 amino acids of aphA6 and bla(NDM-1) are the same. Furthermore, the percent GC content (GC%) of aphA6 is considerably lower than that of bla(NDM-1) and the GC% within the bla(NDM-1) structural gene changes dramatically after the first 19 bp. This is unequivocal evidence that bla(NDM-1) is a chimera.

Characterization of IncA/C conjugative plasmid harboring bla TEM-52 and bla CTX-M-15 extended-spectrum ß-lactamases in clinical isolates of Escherichia coli in Tunisia.

To characterize the extended-spectrum ß-lactamases (ESBLs) as well as their genetic environment in different isolates of Escherichia coli from patients with repeated urinary tract infections, large multidrug resistance (MDR) plasmids have been found. Definitive evidence for the presence of an A/C incompatibility complex (IncA/C) plasmid in the MDR isolates was provided by the probing of plasmids extracted from the clinical isolates. Conjugation experiments showed that bla genes were transferred by conjugation from the ten E. coli clinical isolates to E. coli XL1-Blue recipient. A comparative restriction fragment length polymorphism (RFLP) analysis of these plasmids showed that they are genetically similar, while the overall similarity of these plasmids supports the likelihood of recent movements among these E. coli isolates. Polymerase chain reaction (PCR) amplification and sequencing of the amplicons showed that the IncA/C plasmids harbor two ESBLs, identified as TEM-52 and CTX-M-15. Analysis of the plasmid DNA surrounding the bla (CTX-M-15) gene in the clinical isolates under study revealed a partially truncated fragment of ISEcp1 tnpA transposase. This result indicates the variety of genetic events that have enabled associations between ISEcp1 sequences and bla (CTX-M-15) genes in these clinical isolates.

Association of bla(DHA-1) and qnrB genes carried by broad-host-range plasmids among isolates of Enterobacteriaceae at a Spanish hospital.

A collection of 30 DHA-1-Enterobacteriaceae producers was examined for the presence of qnr genes. PCR-based replicon typing, plasmid profile and Southern hybridisation analyses revealed that all isolates co-harboured bla(DHA-1) and qnrB genes on the same plasmid. All but one of these plasmids belonged to the L/M group. Genetic organization analyses of a randomly selected isolate revealed the co-localization of both genes on an IS26-composite transposon. As plasmids carrying both genes seem to have a high prevalence and a worldwide distribution, care should be taken when quinolones are used to treat infections caused by DHA-1 producers.

Molecular characterization of VIM-producing Klebsiella pneumoniae from Scandinavia reveals genetic relatedness with international clonal complexes encoding transferable multidrug resistance.

VIM-producing Klebsiella pneumoniae (VPKP) has been identified as a source of hospital outbreaks and is prevalent particularly in the Mediterranean region. In this study we have characterized eight VPKP isolates identified in Scandinavia during 2005-2008. With the exception of one isolate, all were from patients with recent history of hospitalization abroad (Greece, n = 6; Turkey, n = 1). Multilocus sequence typing (MLST) resulted in five sequence types (STs), ST36 (n = 1), ST147 (n = 4), ST272 (n = 1), ST273 (n = 1) and ST383 (n = 1), which except for ST272 were part of putative international clonal complexes. All were multidrug resistant due to the presence of other resistance determinants, including extended-spectrum ß-lactamases (CTX-M-3, SHV-5 and SHV-12), 16S rRNA methylases (ArmA) and plasmid-mediated quinolone resistance determinants (QnrS). One isolate harboured a novel VIM-variant (VIM-26) while VIM-1 and VIM-19 were detected in six and one isolate, respectively. Two different genetic structures surrounding the bla(VIM) gene were identified in four isolates. In two isolates bla(VIM-1) and bla(VIM-26) were located in an integron similar to In-e541 (intI1;bla(VIM-1/-26);aacA7; dhfrI;aadA1;3'CS) while in the other two isolates bla(VIM-1) was located in an integron lacking 3'CS but with an IS26 element in the 3'end (intI1;bla(VIM-1);aac(6')-Ib;IS26), as identified in the IncN plasmid pKOX105. The bla(VIM) -genes were located on transferable plasmids ranging from ∼40 to ∼240 kb and associated with Tn21 in four isolates. PCR-based replicon typing indicated association of bla(VIM) with IncN (n = 3) and A/C (n = 1) broad-host-range plasmids but also with unknown replicons (n = 4). In conclusion, Scandinavian VPKP is associated with importation and genetically related to international clones encoding transferable plasmid-mediated multidrug resistance.

Probing the structures of gas-phase rhodium cluster cations by far-infrared spectroscopy.

The geometric structures of small cationic rhodium clusters Rh(n)(+) (n = 6-12) are investigated by comparison of experimental far-infrared multiple photon dissociation spectra with spectra calculated using density functional theory. The clusters are found to favor structures based on octahedral and tetrahedral motifs for most of the sizes considered, in contrast to previous theoretical predictions that rhodium clusters should favor cubic motifs. Our findings highlight the need for further development of theoretical and computational methods to treat these high-spin transition metal clusters.

Probing diameter-selective solubilisation of carbon nanotubes by reversible cyclic peptides using molecular dynamics simulations.

Molecular dynamics simulations are used to explore the encapsulation behaviour of reversible cyclic peptides when adsorbed onto single-walled carbon nanotubes (CNTs) in aqueous solution. Our findings suggest that CNT encapsulation via cyclisation of a single peptide chain is relatively less likely, compared with encapsulation via two-chain complexes. These two-chain complexes comprise pairings of the motifs identified for single-chain adsorption. Our simulation data are compared with existing experimental findings [A. Ortiz-Acevedo et al., J. Am. Chem. Soc., 2005, 127, 9512], for relevant CNT diameters, and are found to be consistent with the experimental results. Our data help to explain the limited diameter selectivity reported by Ortiz-Acevedo et al. These findings should help in the optimisation and future design of peptides capable of enhanced selectivity for specific CNT diameters.

Investigation of the influence of surface defects on peptide adsorption onto carbon nanotubes.

The number of possible applications that interface carbon nanotubes with biological systems is rapidly growing, and with these advances comes a need for characterisation of such interfaces. Molecular simulation is one such approach, and many recent examples exist where simulation has been used to investigate the atomic-scale details of the interface between biomolecules and carbon nanotubes (CNTs). However, these studies have been confined to the realm of pristine CNTs. Here, we build on our previous work and use molecular simulation to consider the adsorption on to defective CNTs of peptide sequences known to bind to the CNT surface [Wang et al., Nat. Mater., 2003, 2, 196]. Two types of idealised chemical defects are considered, along with two different distributions of these defects on the CNT surface. We find that the densely-packed defect distribution yields relatively little engagement with the peptides. Spreading the defects out along the nanotube increases the degree of contact with the peptide, without affecting the binding strength of the peptide-CNT interface in most cases. Both types of defect tend to act more as physical barriers to peptide mobility than as a source of attractive interactions. The resulting physical confinement of the peptide did not affect all sequences in the same way; two of the four sequences were found to be more sensitive to the presence of defects. This study has implications for the practical usage of CNTs in a wide range of biological contexts, where well-dispersed, functionalised nanotubes are required.

Communications: The structure of Rh(8) (+) in the gas phase.

The geometric structure of the Rh(8) (+) cation is investigated using a combination of far-infrared multiple photon dissociation spectroscopy and density functional theory (DFT) calculations. The energetic ordering of the different structural motifs is found to depend sensitively on the choice of pure or hybrid exchange functionals. Comparison of experimental and calculated spectra suggests the cluster to have a close-packed, bicapped octahedral structure, in contrast to recent predictions of a cubic structure for the neutral cluster. Our findings demonstrate the importance of including some exact exchange contributions in the DFT calculations, via hybrid functionals, when applied to rhodium clusters, and cast doubt on the application of pure functionals for late transition metal clusters in general.

A multipole-based water potential with implicit polarization for biomolecular simulations.

A new water potential, DMIP (distributed multipoles, implicit polarization), is constructed using distributed multipoles to describe the electrostatic interactions, while accounting for polarization implicitly. In this procedure, small clusters are randomly sampled from atomistic simulations of bulk water using the AMOEBA (Ren and Ponder, J Comput Chem 2002, 23, 1497) potential. The multipole moments of the central water in each cluster are obtained from ab initio densities for each cluster, and the moments are then averaged over all clusters. Properties of bulk water calculated using DMIP compare favorably with existing data from AMOEBA simulations and experiment, with a conservative estimate of reduction in compute time of roughly 40%. The implicit force-field is also shown to work compatibly with existing polarizable multipole-based force-fields for biomolecules.

Oxides of small Rhodium clusters: Theoretical investigation of experimental reactivities.

Density functional theory is used to investigate the structures of cationic rhodium cluster oxides, Rh(6)O(m) (+) (m=1,4). On the monoxide and dioxide, the oxygen atoms occupy bridge sites, while on trioxide and tetroxide clusters, high-coordination sites are favored. A range of spin multiplicities are investigated for each cluster, with high spin multiplicities found to be less favored for the oxides compared with the naked metal clusters. The dissociation of nitric oxide on low-energy isomers of Rh(6)O(4) (+) is investigated and found to be unfavorable compared to molecular adsorption due to a combination of thermodynamic and kinetic factors. These calculations are consistent with, and help to account for, the experimentally observed reactivity of rhodium and rhodium oxide clusters with nitric oxide [M. S. Ford et al., Phys. Chem. Chem. Phys. 7, 975 (2005)].