Acinetobacter baumannii from grass: novel but non-resistant clones.

Acinetobacter baumannii is one the most worrisome nosocomial pathogens, which has long been considered almost mainly as a hospital-associated bacterium. There have been some studies about animal and environmental isolates over the last decade. However, little effort has been made to determine if this pathogen dwells in the grass. Here, we aim to determine the evolutionary relationships and antibiotic resistance of clones of A. baumannii sampled from grass to the major human international clones and animal clones. Two hundred and forty genomes were considered in total from four different sources for this study. Our core and accessory genomic epidemiology analyses showed that grass isolates cluster in seven groups well differentiated from one another and from the major human and animal isolates. Furthermore, we found new sequence types under both multilocus sequence typing schemes: two under the Pasteur scheme and seven for the Oxford scheme. The grass isolates contained fewer antibiotic-resistance genes and were not resistant to the antibiotics tested. Our results demonstrate that these novel clones appear to have limited antibiotic resistance potential. Given our findings, we propose that genomic epidemiology and surveillance of A. baumannii should go beyond the hospital settings and consider the environment in an explicit One Health approach.

The Acinetobacter baumannii website (Ab-web): a multidisciplinary knowledge hub, communication platform, and workspace.

Acinetobacter baumannii is a Gram-negative bacterium increasingly implicated in hospital-acquired infections and outbreaks. Effective prevention and control of such infections are commonly challenged by the frequent emergence of multidrug-resistant strains. Here we introduce Ab-web (https://www.acinetobacterbaumannii.no), the first online platform for sharing expertise on A. baumannii. Ab-web is a species-centric knowledge hub, initially with 10 articles organized into two main sections, 'Overview' and 'Topics', and three themes, 'epidemiology', 'antibiotic resistance', and 'virulence'. The 'workspace' section provides a spot for colleagues to collaborate, build, and manage joint projects. Ab-web is a community-driven initiative amenable to constructive feedback and new ideas.

Knowledge, attitudes and behaviour of Egyptians towards antibiotic use in the community: can we do better?

BACKGROUND: Infectious diseases are among the leading causes of death worldwide. This is concerning because of the increasing capacity of the pathogens to develop antibiotic resistance. Antibiotic overuse and misuse remain the main drivers of resistance development. In the USA and Europe, annual campaigns raise awareness of antibiotic misuse hazards and promote their judicial use. Similar efforts are lacking in Egypt. This study assessed the knowledge of the public in Alexandria, Egypt of antibiotic misuse risks and their habits towards antibiotic use, in addition to conducting a campaign to increase awareness of the safe use of antibiotics. METHODS: A questionnaire assessing knowledge, attitudes and behaviour towards antibiotics was used to collect responses from study participants at various sports clubs in Alexandria in 2019. An awareness campaign to correct misconceptions and a post awareness survey followed. RESULTS: Most of the participants were well-educated (85%), in their middle age (51%) and took antibiotics last year (80%). 22% would take an antibiotic for common cold. This dropped to 7% following the awareness. There was a 1.6 time increase in participants who would start an antibiotic on a healthcare professional's advice following the campaign. A 1.3 time increase in participants who would finish an antibiotic regimen was also observed. The campaign made all participants recognize that unwise antibiotic use is harmful to them or others; and 1.5 more participants would spread the word about antibiotic resistance. Despite learning of the risks of antibiotic use, there was no change in how often participants thought they should take antibiotics. CONCLUSIONS: Although awareness of antibiotic resistance is rising, some wrong perceptions hold fast. This highlights the need for patient and healthcare-tailored awareness sessions as part of a structured and national public health program directed to the Egyptian population.

OXA-66 structure and oligomerisation of OXAAb enzymes.

The OXA ß-lactamases are responsible for hydrolysing ß-lactam antibiotics and contribute to the multidrug-resistant phenotype of several major human pathogens. The OXAAb enzymes are intrinsic to Acinetobacter baumannii and can confer resistance to carbapenem antibiotics. Here we determined the structure of the most prevalent OXAAb enzyme, OXA-66. The structure of OXA-66 was solved at a resolution of 2.1 Å and found to be very similar to the structure of OXA-51, the only other OXAAb enzyme that has had its structure solved. Our data contained one molecule per asymmetric unit, and analysis of positions responsible for dimer formation in other OXA enzymes suggest that OXA-66 likely exists as a monomer.

Acinetobacter baumannii Sampled from Cattle and Pigs Represent Novel Clones.

Acinetobacter baumannii is a very important human pathogen. Nonetheless, we know very little about nonhuman isolates of A. baumannii. Here, we determine the genomic identity of 15 Scottish cattle and pig isolates, as well as their antibiotic and virulence genetic determinants, and compare them with 148 genomes from the main human clinical international clones. Our results demonstrate that cattle and pig isolates represent novel clones well separated from the major international clones. Furthermore, these new clones showed fewer antibiotic resistance genes and may have fewer virulence genes than human clinical isolates. IMPORTANCE Over the last decades, huge amounts of information have been obtained for clinical isolates of A. baumannii and the clones they belong to. In contrast, very little is known about the genomic identity and the genomic basis for virulence and resistance of animal isolates. To fulfil this gap, we conducted a genomic epidemiology study of 15 Scottish cattle and pig isolates in the context of almost 150 genomes belonging to the main international clones of A. baumannii. Our findings show that these animal isolates represent novel clones clearly different from the major international clones. Furthermore, these new clones are distinct in nature considering both antibiotic resistance and virulence when compared with their human clinical counterparts.

Diversity of carbapenem-resistant Acinetobacter baumannii and bacteriophage-mediated spread of the Oxa23 carbapenemase.

Carbapenem-resistant Acinetobacter baumannii are prevalent in low- and middle-income countries such as Egypt, but little is known about the molecular epidemiology and mechanisms of resistance in these settings. Here, we characterize carbapenem-resistant A. baumannii from Alexandria, Egypt, and place it in a regional context. Fifty-four carbapenem-resistant isolates from Alexandria Main University Hospital (AMUH), Alexandria, Egypt, collected between 2010 and 2015 were genome sequenced using Illumina technology. Genomes were de novo assembled and annotated. Genomes for 36 isolates from the Middle East region were downloaded from GenBank. The core-gene compliment was determined using Roary, and analyses of recombination were performed in Gubbins. Multilocus sequence typing (MLST) sequence type (ST) and antibiotic-resistance genes were identified. The majority of Egyptian isolates belonged to one of three major clades, corresponding to Pasteur MLST clonal complex (CCPAS) 1, CCPAS2 and STPAS158. Strains belonging to STPAS158 have been reported almost exclusively from North Africa, the Middle East and Pakistan, and may represent a region-specific lineage. All isolates carried an oxa23 gene, six carried blaNDM-1 and one carried blaNDM-2. The oxa23 gene was located on a variety of different mobile elements, with Tn2006 predominant in CCPAS2 strains, and Tn2008 predominant in other lineages. Of particular concern, in 8 of the 13 CCPAS1 strains, the oxa23 gene was located in a temperate bacteriophage phiOXA, previously identified only once before in a CCPAS1 clone from the USA military. The carbapenem-resistant A. baumannii population in AMUH is very diverse, and indicates an endemic circulating population, including a region-specific lineage. A major mechanism for oxa23 dissemination in CCPAS1 isolates appears to be a bacteriophage, presenting new concerns about the ability of these carbapenemases to spread throughout the bacterial population.

Soft Capsule Magnetic Millirobots for Region-Specific Drug Delivery in the Central Nervous System.

Small soft robotic systems are being explored for myriad applications in medicine. Specifically, magnetically actuated microrobots capable of remote manipulation hold significant potential for the targeted delivery of therapeutics and biologicals. Much of previous efforts on microrobotics have been dedicated to locomotion in aqueous environments and hard surfaces. However, our human bodies are made of dense biological tissues, requiring researchers to develop new microrobotics that can locomote atop tissue surfaces. Tumbling microrobots are a sub-category of these devices capable of walking on surfaces guided by rotating magnetic fields. Using microrobots to deliver payloads to specific regions of sensitive tissues is a primary goal of medical microrobots. Central nervous system (CNS) tissues are a prime candidate given their delicate structure and highly region-specific function. Here we demonstrate surface walking of soft alginate capsules capable of moving on top of a rat cortex and mouse spinal cord ex vivo, demonstrating multi-location small molecule delivery to up to six different locations on each type of tissue with high spatial specificity. The softness of alginate gel prevents injuries that may arise from friction with CNS tissues during millirobot locomotion. Development of this technology may be useful in clinical and preclinical applications such as drug delivery, neural stimulation, and diagnostic imaging.

Reconfigurable Magnetic Origami Actuators with On-Board Sensing for Guided Assembly.

Origami utilizes orchestrated transformation of soft 2D structures into complex 3D architectures, mimicking shapes and functions found in nature. In contrast to origami in nature, synthetic origami lacks the ability to monitor the environment and correspondingly adjust its behavior. Here, magnetic origami actuators with capabilities to sense their orientation and displacement as well as detect their own magnetization state and readiness for supervised folding are designed, fabricated, and demonstrated. These origami actuators integrate photothermal heating and magnetic actuation by using composite thin films (≈60 µm thick) of shape-memory polymers with embedded magnetic NdFeB microparticles. Mechanically compliant magnetic field sensors, known as magnetosensitive electronic skins, are laminated on the surface of the soft actuators. These ultrathin actuators accomplish sequential folding and recovery, with hinge locations programmed on the fly. Endowing mechanically active smart materials with cognition is an important step toward realizing intelligent, stimuli-responsive structures.

Variability in carbapenemase activity of intrinsic OxaAb (OXA-51-like) ß-lactamase enzymes in Acinetobacter baumannii.

OBJECTIVES: To measure the variability in carbapenem susceptibility conferred by different OxaAb variants, characterize the molecular evolution of oxaAb and elucidate the contribution of OxaAb and other possible carbapenem resistance factors in the clinical isolates using WGS and LC-MS/MS. METHODS: Antimicrobial susceptibility tests were performed on 10 clinical Acinetobacter baumannii isolates. Carbapenem MICs were evaluated for all oxaAb variants cloned into A. baumannii CIP70.10 and BM4547, with and without their natural promoters. Molecular evolution analysis of the oxaAb variants was performed using FastTree and SplitsTree4. Resistance determinants were studied in the clinical isolates using WGS and LC-MS/MS. RESULTS: Only the OxaAb variants with I129L and L167V substitutions, OxaAb(82), OxaAb(83), OxaAb(107) and OxaAb(110) increased carbapenem MICs when expressed in susceptible A. baumannii backgrounds without an upstream IS element. Carbapenem resistance was conferred with the addition of their natural upstream ISAba1 promoter. LC-MS/MS analysis on the original clinical isolates confirmed overexpression of the four I129L and L167V variants. No other differences in expression levels of proteins commonly associated with carbapenem resistance were detected. CONCLUSIONS: Elevated carbapenem MICs were observed by expression of OxaAb variants carrying clinically prevalent substitutions I129L and L167V. To drive carbapenem resistance, these variants required overexpression by their upstream ISAba1 promoter. This study clearly demonstrates that a combination of IS-driven overexpression of oxaAb and the presence of particular amino acid substitutions in the active site to improve carbapenem capture is key in conferring carbapenem resistance in A. baumannii and other mechanisms are not required.

Microevolution in the major outer membrane protein OmpA of Acinetobacter baumannii.

Acinetobacter baumannii is nowadays a relevant nosocomial pathogen characterized by multidrug resistance (MDR) and concomitant difficulties to treat infections. OmpA is the most abundant A. baumannii outer membrane (OM) protein, and is involved in virulence, host-cell recognition, biofilm formation, regulation of OM stability, permeability and antibiotic resistance. OmpA members are two-domain proteins with an N-terminal eight-stranded ß-barrel domain with four external loops (ELs) interacting with the environment, and a C-terminal periplasmic domain binding non-covalently to the peptidoglycan. Here, we combined data from genome sequencing, phylogenetic and multilocus sequence analyses from 975 strains/isolates of the Acinetobacter calcoaceticus/Acinetobacter baumannii complex (ACB), 946 from A. baumannii, to explore ompA microevolutionary divergence. Five major ompA variant groups were identified (V1 to V5) in A. baumannii, encompassing 52 different alleles coding for 23 different proteins. Polymorphisms were concentrated in five regions corresponding to the four ELs and the C-terminal end, and provided evidence for intra-genic recombination. ompA variants were not randomly distributed across the A. baumannii phylogeny, with the most frequent V1(lct)a1 allele found in most clonal complex 2 (CC2) strains and the second most frequent V2(lct)a1 allele in the majority of CC1 strains. Evidence was found for assortative exchanges of ompA alleles not only between separate A. baumannii lineages, but also different ACB species. The overall results have implications for A. baumannii evolution, epidemiology, virulence and vaccine design.

Origin of OXA-23 Variant OXA-239 from a Recently Emerged Lineage of Acinetobacter baumannii International Clone V.

Over the last few decades, carbapenemase-producing Acinetobacter baumannii has become a major cause of nosocomial infections all over the world. However, the genome identity of lineages of this species in Latin America has not been studied as much as in developed countries. Here, through a population genomics approach considering the whole genomes of 148 isolates (almost 40 from Mexico and Honduras), we describe the recent emergence of the lineage sequence type 758 (ST758), which belongs to the international clone V and has spread out to Canada, Mexico, Honduras, and Colombia. Notably, this lineage was found to coexist with other A. baumannii lineages in hospitals in Mexico and Honduras. Isolates from this lineage show considerable variation in antibiotic resistance profiles, but most of them are resistant to carbapenems. Moreover, we found a variety of acquired oxacillinase (OXA) families within this lineage and tracked the very recent inception, and subsequent horizontal transmission, of the OXA-239 carbapenemase. This work highlights the urgent need to investigate recently emerged lineages of this species in Latin America and elsewhere, as these might harbor novel antibiotic resistance genes.IMPORTANCEA. baumannii is a major cause of nosocomial infections all over the world. Although many isolates from developed countries have been studied in terms of their genome sequence, isolates from Latin America have been much less studied. In this study, using a population genomics approach considering the whole genomes of 148 isolates, we describe the recent emergence of the lineage ST758 endemic to Latin America and the inception of the OXA-239 carbapenemase. Our study highlights the urgent need to investigate recently emerged lineages of this species in Latin America and elsewhere, as these might harbor novel antibiotic resistance genes.

Photothermally and magnetically controlled reconfiguration of polymer composites for soft robotics.

New materials are advancing the field of soft robotics. Composite films of magnetic iron microparticles dispersed in a shape memory polymer matrix are demonstrated for reconfigurable, remotely actuated soft robots. The composite films simultaneously respond to magnetic fields and light. Temporary shapes obtained through combined magnetic actuation and photothermal heating can be locked by switching off the light and magnetic field. Subsequent illumination in the absence of the magnetic field drives recovery of the permanent shape. In cantilevers and flowers, multiple cycles of locking and unlocking are demonstrated. Scrolls show that the permanent shape of the film can be programmed, and they can be frozen in intermediate configurations. Bistable snappers can be magnetically and optically actuated, as well as biased, by controlling the permanent shape. Grabbers can pick up and release objects repeatedly. Simulations of combined photothermal heating and magnetic actuation are useful for guiding the design of new devices.

Magnetically Aligned Nanorods in Alginate Capsules (MANiACs): Soft Matter Tumbling Robots for Manipulation and Drug Delivery.

Soft, untethered microrobots composed of biocompatible materials for completing micromanipulation and drug delivery tasks in lab-on-a-chip and medical scenarios are currently being developed. Alginate holds significant potential in medical microrobotics due to its biocompatibility, biodegradability, and drug encapsulation capabilities. Here, we describe the synthesis of MANiACs-Magnetically Aligned Nanorods in Alginate Capsules-for use as untethered microrobotic surface tumblers, demonstrating magnetically guided lateral tumbling via rotating magnetic fields. MANiAC translation is demonstrated on tissue surfaces as well as inclined slopes. These alginate microrobots are capable of manipulating objects over millimeter-scale distances. Finally, we demonstrate payload release capabilities of MANiACs during translational tumbling motion.

Automatic diagnosis of tuberculosis disease based on Plasmonic ELISA and color-based image classification.

Tuberculosis (TB) remains one of the most devastating infectious diseases and its treatment efficiency is majorly influenced by the stage at which infection with the TB bacterium is diagnosed. The available methods for TB diagnosis are either time consuming, costly or not efficient. This study employs a signal generation mechanism for biosensing, known as Plasmonic ELISA, and computational intelligence to facilitate automatic diagnosis of TB. Plasmonic ELISA enables the detection of a few molecules of analyte by the incorporation of smart nanomaterials for better sensitivity of the developed detection system. The computational system uses k-means clustering and thresholding for image segmentation. This paper presents the results of the classification performance of the Plasmonic ELISA imaging data by using various types of classifiers. The five-fold cross-validation results show high accuracy rate (>97%) in classifying TB images using the entire data set. Future work will focus on developing an intelligent mobile-enabled expert system to diagnose TB in real-time. The intelligent system will be clinically validated and tested in collaboration with healthcare providers in Malaysia.

Pherotype Polymorphism in Streptococcus pneumoniae Has No Obvious Effects on Population Structure and Recombination.

Natural transformation in the Gram-positive pathogen Streptococcus pneumoniae occurs when cells become "competent," a state that is induced in response to high extracellular concentrations of a secreted peptide signal called competence stimulating peptide (CSP) encoded by the comC locus. Two main CSP signal types (pherotypes) are known to dominate the pherotype diversity across strains. Using 4,089 fully sequenced pneumococcal genomes, we confirm that pneumococcal populations are highly genetically structured and that there is significant variation among diverged populations in pherotype frequencies; most carry only a single pherotype. Moreover, we find that the relative frequencies of the two dominant pherotypes significantly vary within a small range across geographical sites. It has been variously proposed that pherotypes either promote genetic exchange among cells expressing the same pherotype, or conversely that they promote recombination between strains bearing different pherotypes. We attempt to distinguish these hypotheses using a bioinformatics approach by estimating recombination frequencies within and between pherotypes across 4,089 full genomes. Despite underlying population structure, we observe extensive recombination between populations; additionally, we found significantly higher (although marginal) rates of genetic exchange between strains expressing different pherotypes than among isolates carrying the same pherotype. Our results indicate that pherotypes do not restrict, and may even slightly facilitate, recombination between strains; however, these marginal effects suggest the more likely possibility that the cause of CSP polymorphism lies outside of its effects on transformation. Our results suggest that the CSP balanced polymorphism does not causally underlie population differentiation. Therefore, when strains carrying different pherotypes encounter one another during cocolonization, genetic exchange can occur without restriction.

Chained Iron Microparticles for Directionally Controlled Actuation of Soft Robots.

Magnetic field-directed self-assembly of magnetic particles in chains is useful for developing directionally responsive materials for applications in soft robotics. Using materials with greater complexity allows advanced functions, while still using simple device architectures. Elastomer films containing chained magnetic microparticles were prepared through solvent casting and formed into magnetically actuated lifters, accordions, valves, and pumps. Chaining both enhances actuation and imparts a directional response. Cantilevers used as lifters were able to lift up to 50 times the mass of the polymer film. We introduce the "specific torque", the torque per field per mass of magnetic particles, as a figure of merit for assessing and comparing the performance of lifters and related devices. Devices in this work generated specific torques of 68 Nm/kgT, which is significantly higher than in previously reported actuators. Applying magnetic fields to folded accordion structures caused extension and compression, depending on the accordion's orientation. In peristaltic pumps comprised of composite tubes containing embedded chains, magnetic fields caused a section of the tube to pinch closed where the field was applied. These results will facilitate both the further development of soft robots based on chained magnetic particles and efforts to engineer materials with higher specific torque.

Magnetically Responsive Negative Acoustic Contrast Microparticles for Bioanalytical Applications.

Smart colloidal particles are routinely used as carriers for biological molecules, fluorescent reporters, cells, and other analytes for the purposes of sample preparation and detection. However, such particles are typically engineered to respond to a single type of stimulus (e.g., commercial magnetic beads to magnetic fields). Here, we demonstrate a unique class of particles that display both positive magnetic contrast and negative acoustic contrast in water. This dual functionality allows for fine spatiotemporal control, enabling multiple separation modalities and increasing the utility of the particles in various chemical and biological assays.