SEARCH · Search bioRxiv

Results for “Microbiology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 289 records · Page 16Linked to original sources

bioRxiv2020

Biofilm development on urinary catheters promotes the appearance of viable but non-culturable (VBNC) bacteria

Catheter-associated urinary tract infections have serious consequences, both for patients and in impacting on healthcare resources. Much work has been carried out to develop an antimicrobial catheter. Although such developments have shown promise under laboratory conditions, none have demonstrated a clear advantage in clinical trials. Using a range of microbiological and advanced microscopy techniques, a detailed laboratory study comparing biofilm development on silicone, hydrogel latex and silver alloy coated hydrogel latex catheters was carried out. Biofilm development by Escherichia coli, Pseudomonas aeruginosa and Proteus mirabilis on three commercially available catheters was tracked over time. Samples were examined with episcopic differential interference contrast (EDIC) microscopy, culture analysis and staining techniques to quantify viable but non-culturable (VBNC) bacteria. Both qualitative and quantitative assessment found biofilms to develop rapidly on all three materials. EDIC microscopy revealed the rough surface topography of the materials. Differences between culture counts and quantification of total and dead cells demonstrated the presence of VBNC populations, where bacteria retain viability but are not metabolically active. The use of non-culture based techniques showed the development of widespread VBNC populations. These VBNC populations were more evident on silver alloy coated hydrogel latex catheters, indicating a bacteriostatic effect at best. The laboratory tests reported here, that detect VBNC bacteria, allow more rigorous assessment of antimicrobial catheters offering an explanation for why there is often minimal benefit to patients. IMPORTANCESeveral antimicrobial urinary catheter materials have been developed but, although laboratory studies may show a benefit, none have significantly improved clinical outcomes. The use of poorly designed laboratory testing and lack of consideration to the impact of VBNC populations may be responsible. While the presence of VBNC populations is becoming more widely reported, there remains a lack of understanding of the clinical impact or influence of exposure to antimicrobial products. This is the first study to investigate the impact of antimicrobial surface materials and the appearance of VBNC populations. This demonstrates how improved testing is needed prior to clinical trials uptake.

microbiology↗

bioRxiv2020

Genetic and phylogenetic analysis of dissimilatory iodate-reducing bacteria identifies potential niches across the world's oceans

Iodine is oxidized and reduced as part of a biogeochemical cycle that is especially pronounced in the oceans, where the element naturally concentrates. The use of oxidized iodine in the form of iodate (IO3-) as an electron acceptor by microorganisms is poorly understood. Here, we outline genetic, physiological, and ecological models for dissimilatory IO3- reduction to iodide (I-) by a novel estuarine bacterium, Denitromonas iodocrescerans strain IR-12, sp. nov. Our results show that dissimilatory iodate reduction (DIR) by strain IR-12 is molybdenum-dependent and requires an IO3- reductase (idrA) and likely other genes in a mobile cluster with a conserved association across known and predicted DIR microorganisms (DIRM). Based on genetic and physiological data, IO3- is likely reduced to hypoiodous acid (HIO), which rapidly disproportionates into IO3- and iodide (I-), in a respiratory pathway that provides an energy yield equivalent to that of nitrate or perchlorate respiration. Consistent with the ecological niche expected of such a metabolism, idrA is enriched in the metagenome sequence databases of marine sites with a specific biogeochemical signature and diminished oxygen. Taken together, these data suggest that DIRM help explain the disequilibrium of the IO3-:I- concentration ratio above oxygen minimum zones and support a widespread iodine redox cycle mediated by microbiology.

microbiology↗

bioRxiv2021

Genomic insights of high-risk clones of ESBL-producing Escherichia coli isolated from community infections and commercial meat in Southern Brazil

During a microbiological and genomic surveillance study to investigate the molecular epidemiology of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli from community-acquired urinary tract infections (UTI) and commercial meat samples, in a Brazilian city with a high occurrence of infections by ESBL-producing bacteria, we have identified the presence of CTX-M (-55, -27, -24, -15, -14 and -2)-producing E. coli belonging to the international clones ST354, ST131, ST117, and ST38. The ST131 was more prevalent in human samples, and worryingly the high-risk ST131-C1-M27 was identified in human infections for the first time. We also detected CTX-M-55-producing E. coli ST117 isolates from meat samples (i.e., chicken and pork) and human infections. Moreover, we have identified the important clone CTX-M-24-positive E. coli ST354 from human samples in Brazil for the first time. In brief, our results suggest a potential of commercialized meat as a reservoir of high-priority E. coli lineages in the community. In contrast, the identification of E. coli ST131-C1-M27 indicates that novel pandemic clones have emerged in Brazil, constituting a public health issue.

microbiology↗

bioRxiv2021

Incidence and Characteristics of Co-infection and Secondary Infection in Patients with COVID-19

ObjectiveThe etiology and epidemiology of co-infection and secondary infection in COVID-19 patients remain unknown. The study aims to investigate the occurrence and characteristics of co-infection and secondary infection in COVID-19 patients, mainly focusing on Streptococcus pneumoniae co-infections. MethodsThis study was a prospective, observational cohort study of the inpatients diagnosed with COVID-19 in two designated hospitals in south China enrolled between Jan 11 and Feb 22, 2020. The urine specimen was collected on admission and applied for pneumococcal urinary antigen tests (PUATs). Demographic, clinical and microbiological data of patients were recorded simultaneously. ResultA total of 146 patients with a confirm diagnosis of COVID-19 at the median age of 50.0 years (IQR 36.0-61.0) were enrolled, in which, 16 (11.0%) were classified as severe cases and 130 (89.0%) as non-severe cases. Of the enrolled patients, only 3 (2.1%) were considered to present the co-infection, in which 1 was co-infected with S.pneumoniae, 1 with B. Ovatus infection and the other one with Influenza A virus infection. Secondary infection occurred in 16 patients, with S. maltophilia as the most commonly isolated pathogen (43.8%), followed by P. aeruginosa (25.0%), E. aerogenes (25.0%), C. parapsilosis (25.0%) and A. fumigates (18.8%). ConclusionPatients with confirmed COVID-19 were rarely co-infected with Streptococcus pneumoniae or other pathogens, indicating that the application of antibiotics against CAP on admission may not be necessary in the treatment of COVID-19 cases.

microbiology↗

bioRxiv2021

Influence of Fara-darmani Consciousness Field on Bacterial Population Growth

The treatment of bacterial infections and the rising challenges of antibiotics resistance are global concerns and the primary topics in basic science and clinical microbiology. In the present study, the effectiveness of treatment of selected populations of bacteria using an immaterial and non-energetic method called Fara-darmani Consciousness Field treatment is investigated. Population growth was assessed by turbidimetry, colony counting and tetrazolium chloride reduction assays in non-treated control and Fara-darmani-treated groups. Our results suggest effectiveness of the Fara-darmani Consciousness Field on reducing various types of bacterial strain growth rates (up to 46%). In addition, along with a decrease in bacterial population, evidence of increased survival can be seen in the larger healthy population (up to about 60%). Thus, in this study, we confirm the effects of the Consciousness Field on bacterial population survival. This study also warrants additional research.

microbiology↗

bioRxiv2021

Towards a mathematical understanding of colonization resistance

Microbial community composition and dynamics are key to health and disease. Explaining the forces generating and shaping diversity in the microbial consortia making up our bodys defenses is a major aim of current research in microbiology. For this, tractable models are needed, that bridge the gap between observations of patterns and underlying mechanisms. While most microbial dynamics models are based on the Lotka-Volterra framework, we still do not have an analytic quantity for colonization resistance, by which a microbial systems fitness as a whole can be understood. Here, inspired by an epidemiological perspective, we propose a rather general modeling framework whereby colonization resistance can be clearly mathematically defined and studied. In our model, N similar species interact with each other through a co-colonization interaction network encompassing pairwise competition and cooperation, abstractly mirroring how organisms effectively modify their micro-scale environment in relation to others. This formulation relies on a generic notion of shared resources between members of a consortium, yielding explicit frequency-dependent dynamics among N species, in the form of a replicator equation, and offering a precise definition of colonization resistance. We demonstrate that colonization resistance arises and evolves naturally in a multispecies system as a collective quadratic term in a replicator equation, describing dynamic mean invasion fitness. Each pairwise invasion growth rate between two ecological partners, [Formula], is derived explicitly from species asymmetries and mean traits. This makes the systemic colonization resistance [Formula] also an emergent function of global mean-field parameters and trait variation architecture, weighted by the evolving relative abundances among species. In particular, if the underlying invasion fitness matrix {Lambda} displays species-specific invasiveness or invasibility structure, colonization resistance will be insensitive to mean micro-scale cooperation or competition. However, in general, colonization resistance depends on and may undergo critical transitions with changes in mean environment, e.g. cooperation and growth level in a community. We illustrate several key links between our proposed measure of colonization resistance and invader success, including sensitivity to timing, and to the intrinsic pairwise invasion architecture of the resident community. Our simulations reveal that symmetric and invader-driven mutual invasion among resident species tend to maximize systemic colonization resistance to outsiders, when compared to resident-driven, anti-symmetric, almost anti-symmetric and random {Lambda} structures. We contend this modeling approach is a powerful new avenue to study, test and validate interaction networks and invasion topologies in diverse microbial consortia, and quantify analytically their role in colonization resistance, system function, and invasibility.

microbiology↗

bioRxiv2021

Evaluation of the rapidBACpro(R) II kit for the rapid identification of microorganisms directly from blood cultures using MALDI-TOF MS

ObjectivesIdentification of microorganisms directly from blood cultures (BCs) using MALDI-TOF MS has shown to be the application with most impact in this methodology. In this study, a novel commercial method, the rapidBACpro(R) II, was evaluated in four clinical microbiology laboratories. MethodsPositive blood culture samples (n=801) were processed using the rapidBACpro(R) II kit and then compared with routine gold standard. A subset of monomicrobial BCs (n=560) were analyzed in parallel with the Sepsityper(R) kit (Bruker Daltonics, Bremen, Germany) and compared with the rapidBACpro(R) II kit. In addition, the rapidBACpro(R) II kit was also compared with two different in-house methods. ResultsOverall, 80.0% of the monomicrobial isolates (609/761) were correctly identified by the rapidBACpro(R) II kit at the species level (92.3% of the Gram negative and 72.4% of the Gram positive bacteria). The comparison with the Sepsityper(R) kit yielded higher rates of correct species-level identification provided by the rapidBACpro(R) II kit for all categories (p>0.0001) except for yeasts identified with score values >1.7. It also proved superior to the ammonium chloride method (p>0.0001) but the differential centrifugation method allowed higher rates of correct identification for Gram negative bacteria (p>0.1). ConclusionsThe rapidBACpro(R) II kit allowed a high rate of microorganisms correctly identified. The percentage of accurate species-level identification of Gram positive bacteria was particularly noteworthy in comparison with other commercial and in-house methods. This fact was especially interesting in the case of Staphylococcus sp. and Streptococcus sp. in order to elucidate their clinical impact, for example in device-associated bacteremia.

microbiology↗

bioRxiv2021

Speciation of the Mycobacterium tuberculosis complex using mass spectrometry: a proof-of-concept.

Mycobacteria that form the Mycobacterium tuberculosis complex are responsible for deadly tuberculosis in animals and patients. Identification of these pathogens at the species level is of primary importance for treatment and source tracing, and currently relies on DNA analysis, including whole genome sequencing (WGS), which takes a whole day. In this study, we report on the unprecedented identification of the M. tuberculosis complex species using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS), with WGS as the comparative gold standard. In a first step, an optimised peptide extraction applied to 24 isolates otherwise identified in three of the 11 M. tuberculosis complex species by WGS, yielded 94 MALDI-TOF spectra which clustered according to WGS identification. In a second step, 70/74 (95%) other isolates were correctly identified at the species level by this clustering method. This study is the first to report a MALDI-TOF-MS method of identification of M. tuberculosis complex mycobacteria at the species level and is easily implantable in clinical microbiology laboratories.

microbiology↗

bioRxiv2021

Seasonal Dynamics in the Number and Composition of Coliform Bacteria in Drinking Water Reservoirs

Worldwide, surface waters like lakes and reservoirs are one of the major sources for drinking water production, especially in regions with water scarcity. In the last decades, they have undergone significant changes due to climate change. This includes not only an increase of the water temperature but also microbiological changes. In recent years, increased numbers of coliform bacteria have been observed in these surface waters. In our monitoring study we analyzed two drinking water reservoirs (Klingenberg and Kleine Kinzig Reservoir) over a two-year period in 2018 and 2019. We detected high numbers of coliform bacteria up to 2.4 x 104 bacteria per 100 ml during summer months, representing an increase of four orders of magnitude compared to winter. Diversity decreased to one or two species that dominated the entire water body, namely Enterobacter asburiae and Lelliottia spp., depending on the reservoir. Interestingly, the same, very closely related strains have been found in several reservoirs from different regions. Fecal indicator bacteria Escherichia coli and enterococci could only be detected in low concentrations. Furthermore, fecal marker genes were not detected in the reservoir, indicating that high concentrations of coliform bacteria were not due to fecal contamination. Microbial community revealed Frankiales and Burkholderiales as dominant orders. Enterobacterales, however, only had a frequency of 0.04% within the microbial community, which is not significantly affected by the extreme change in coliform bacteria number. Redundancy analysis revealed water temperature, oxygen as well as nutrients and metals (phosphate, manganese) as factors affecting the dominant species. We conclude that this sudden increase of coliform bacteria is an autochthonic process that can be considered as a mass proliferation or "coliform bloom" within the reservoir. It is correlated to higher water temperatures in summer and is therefore expected to occur more frequently in the near future, challenging drinking water production. HighlightsO_LIColiform bacteria proliferate in drinking water reservoirs to values above 104 per 100 ml C_LIO_LIThe genera Lelliottia and Enterobacter can form these "coliform blooms" C_LIO_LIMass proliferation is an autochthonic process, not related to fecal contaminations C_LIO_LIIt is related to water temperature and appears mainly in summer C_LIO_LIIt is expected to occur more often in future due to climate change C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=75 SRC="FIGDIR/small/428560v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@7f63a0org.highwire.dtl.DTLVardef@1659ea7org.highwire.dtl.DTLVardef@932434org.highwire.dtl.DTLVardef@2e12d7_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

Mapping Twenty Years of Antimicrobial Resistance Research Trends

BackgroundAntimicrobial resistance (AMR) is a global threat to health and healthcare. In response to the growing AMR burden, research funding also increased. However, a comprehensive overview of the research output, including conceptual, temporal, and geographical trends, is missing. Therefore, this study uses topic modelling, a machine learning approach, to reveal the scientific evolution of AMR research and its trends, and provides an interactive user interface for further analyses. MethodsStructural topic modelling (STM) was applied on a text corpus resulting from a PubMed query comprising AMR articles (1999-2018). A topic network was established and topic trends were analysed by frequency, proportion, and importance over time and space. FindingsIn total, 88 topics were identified in 158616 articles from 166 countries. AMR publications increased by 450% between 1999 and 2018, emphasizing the vibrancy of the field. Prominent topics in 2018 were Strategies for emerging resistances and diseases, Nanoparticles, and Stewardship. Emerging topics included Water and environment, and Sequencing. Geographical trends showed prominence of Multidrug-resistant tuberculosis (MDR-TB) in the WHO African Region, corresponding with the MDR-TB burden. China and India were growing contributors in recent years, following the United States of America as overall lead contributor. InterpretationThis study provides a comprehensive overview of the AMR research output thereby revealing the AMR research response to the increased AMR burden. Both the results and the publicly available interactive database serve as a base to inform and optimise future research. FundingINTERREG-VA EurHealth-1Health (202085); European Commission Horizon 2020 Framework Research in contextO_ST_ABSEvidence before this studyC_ST_ABSPrior to this study, PubMed, Web of Science, Scopus, and IEEE Xplore were queried to find studies providing a conceptual overview of antimicrobial resistance (AMR) research over time and space. The search string included keywords ("antimicrobial" OR antibiotic*) AND (resistan*) AND ("science mapping" OR bibliometric OR scientometric) in the title and abstract and focused on articles published before 2019 without language restrictions. Few studies were found relying on scientometric and bibliometric methods to assess either subfields of AMR research (e.g., AMR among uropathogens) or AMR-related fields (e.g., microbiology). No studies were found that focus on the entire AMR field. Therefore, this science mapping study using topic modelling was performed to provide an overview of the AMR field by identifying and assessing topics, trends, and geographical differences over time. Added value of this studyTo the best of our knowledge, this study is the first to use a science mapping approach to provide a comprehensive overview of the entire AMR research field, covering over 150 thousand articles published between 1999 and 2018. Our findings revealed important (e.g., Strategies for emerging resistances and diseases, Nanoparticles, and Stewardship) and emerging (e.g., Water and environment, and Sequencing) topics in AMR research. Lastly, this study resulted in an interactive user interface where all data are presented for further analyses. Implications of all the available evidenceOur comprehensive overview of the AMR field, including its conceptual structure, and temporal and geographical trends revealed the response of the research community to the AMR burden. The results and the openly available supporting data provide the base to guide future funding and research directions to tackle AMR.

microbiology↗

bioRxiv2021

Microbial composition, diversity, and activity varies across different types of basal ice

Glaciers and ice sheets possess layers of basal ice characterized by high amounts of entrained debris that can serve as sources of nutrients and organic matter, providing habitat for microorganisms adapted to the frozen conditions. Basal ice forms through various mechanisms and is classified based on its ice and debris content; however, little is known about variation in microbial composition, diversity, and activity across different basal ice types. We investigated these parameters in four different types of basal ice from a cold-based and temperate glacier and used a meta-analysis to compare our findings with microbiome studies from other frozen environments. We found basal ice environments harbor a diverse range of microbiomes whose composition and activity can vary significantly between basal ice types, even within adjacent facies from the same glacier. In some debris-rich basal ices, elevated ATP concentrations, isotopic gas signatures, and high ratios of amplified sequences for 16S rRNA relative to that for 16S rRNA genes implicated certain bacterial taxa (e.g., Paenisporosarcina, Desulfocapsa, Syntrophus, Desulfosporosinus) as being potentially active, with ice temperature appearing to be an important predictor for the diversity of taxa inferred to be active. Compared to those of other sympagic environments, these microbiomes often resembled those found in permafrost or perennial cave ice rather than other glacial ice environments. In contrast, debris-poor basal ices harbored microbiomes more like those found in oligotrophic englacial ice. Collectively, these results suggest that different basal ice types contain distinct microbiomes that are actively structured by the diagenesis of their habitat. IMPORTANCEThe discharge of material from the basal ice zones of glaciers and ice sheets is an important source of dissolved organic matter, nutrients, and trace metals to downstream environments. Microorganisms with the ability to remain metabolically active while frozen have the potential to alter these substrates before they are released and may thus be a vital biogeochemical component of proglacial environments. However, basal ice environments are among the least explored areas of the cryosphere and information on their microbiology is limited. Here, we examine several basal ice types that were collected from different glaciers to investigate how their microbiomes varied. Our results indicate that sediment-rich basal ice from cold-based and temperate glaciers harbor microbiomes that conduct biogeochemical transformations at subzero temperatures and raises the intriguing possibility that subsurface regions of the cryosphere may be more biogeochemically active than previously thought.

microbiology↗

bioRxiv2021

Robotic Antimicrobial Susceptibility Platform (RASP): A Next Generation Approach to One-Health Surveillance of Antimicrobial Resistance.

BackgroundSurveillance of antimicrobial resistance (AMR) is critical to reducing its wide-reaching impact. Its reliance on sample size invites solutions to longstanding constraints regarding scalability. A robotic platform (RASP) was developed for high-throughput AMR surveillance in accordance with internationally recognised standards (CLSI and ISO 20776-1:2019) and validated through a series of experiments. MethodsExperiment A compared RASPs ability to achieve consistent MICs to that of a human technician across eight replicates for four E. coli isolates. Experiment B assessed RASPs agreement with human performed MICs across 91 E. coli isolates with a diverse range of AMR profiles. Additionally, to demonstrate its real-world applicability, the RASP workflow was then applied to five faecal samples where a minimum of 47 E. coli per animal (239 total) were evaluated using an AMR indexing framework. ResultsFor each drug-rater-isolate combination in experiment A, there was a clear consensus of the MIC and deviation from the consensus remained within one doubling-dilution (the exception being gentamicin at two dilutions). Experiment B revealed a concordance correlation coefficient of 0.9670 (95%CI: 0.9670 - 0.9670) between the robot and human performed MICs. RASPs application to the five faecal samples highlighted the intra-animal diversity of gut commensal E. coli, identifying between five and nine unique isolate AMR phenotypes per sample. ConclusionsWhile adhering to internationally accepted guidelines, RASP was superior in throughput, cost and data resolution when compared to an experienced human technician. Integration of robotics platforms in the microbiology laboratory is a necessary advancement for future One-Health AMR endeavours.

microbiology↗

bioRxiv2021

Antibiotic Resistance in Bacillus-based Biopesticide Products

The crisis of antibiotic resistant bacterial infections is one of the most pressing public health issues. Common agricultural practices have been implicated in the generation of antibiotic resistant bacteria. Biopesticides, live bacteria used for pest control, are non-pathogenic and considered safe for consumption. Application of bacteria-based pesticides to crops in high concentrations raises the possibility of unintentional contributions to the movement and generation of antibiotic resistance genes in the environment. However, the presence of clinically relevant antibiotic resistance genes and their resistance phenotypes are currently unknown. Here we use a combination of multiple bioinformatic and microbiological techniques to define resistomes of widely used biopesticides and determine how the presence of suspected antibiotic resistance genes translates to observable resistance phenotypes in several biopesticide products. Our results demonstrate that biopesticide products are reservoirs of clinically relevant antibiotic resistance genes and bear resistance to multiple drug classes. ImportanceThis is the first study to specifically address antibiotic resistance in widely distributed bacterial strains used as commercial biopesticides. Safety assessments of commercial live bacterial biopesticide products do not include antibiotic resistance phenotype identification. We identify antibiotic resistance genes in all live bacterial strains examined, and resistant phenotypes in all strains tested for antibiotic susceptibility. This work demonstrates that biopesticides potentially play a critical role as reservoirs and vectors of antibiotic resistance in the broader environmental resistome that is to date, unstudied.

microbiology↗

bioRxiv2021

Amotosalen is a bacterial multidrug efflux pump substrate potentially affecting its pathogen inactivation activity

Pathogen inactivation is a strategy to improve the safety of transfusion products. The Cerus Intercept technology makes use of a psoralen compound called amotosalen in combination with UVA light to inactivate bacteria, viruses and protozoa. Psoralens have structural similarity to bacterial multidrug-efflux pump substrates. As these efflux pumps are often overexpressed in multidrug-resistant pathogens and with recent reported outbreaks of transfusion-associated sepsis with Acinetobacter, we tested whether contemporary drug-resistant pathogens might show resistance to amotosalen and other psoralens based on multidrug efflux mechanisms through microbiological, biophysical and molecular modeling analysis. The main efflux systems in Enterobacterales and Acinetobacter baumannii, tripartite RND (resistance-nodulation-cell division) systems which span the inner and outer membranes of Gram-negative pathogens and expel antibiotics from the bacterial cytoplasm into the extracellular space, were specifically examined. We found that amotosalen was an efflux substrate for the TolC-dependent RND efflux pumps in E. coli and the AdeABC efflux pump from Acinetobacter baumannii, and that minimal inhibitory concentrations for contemporary bacterial isolates in vitro approached and exceeded the concentration of amotosalen used in the approved platelet and plasma inactivation procedures. These findings suggest that otherwise safe and effective inactivation methods should be further studied to exclude possible gaps in their ability to inactivate contemporary, multidrug-resistant bacterial pathogens. ImportancePathogen inactivation is a strategy to enhance the safety of transfused blood products. We identify the compound, amotosalen, widely used for pathogen inactivation, as a bacterial multidrug efflux substrate. Specifically, experiments suggest that amotosalen is pumped out of bacteria by the major TolC-dependent RND efflux pumps in E. coli and the AdeABC efflux pump in Acinetobacter baumannii. Such efflux pumps are often overexpressed in multidrug-resistant pathogens. Importantly, the minimal inhibitory concentrations for contemporary multidrug-resistant Enterobacterales, Acinetobacter baumannii, Pseudomonas aeruginosa, Burkholderia spp., and Stenotrophomonas maltophilia isolates approached or exceeded the amotosalen concentration used in approved platelet and plasma inactivation procedures, potentially as a result of efflux pump activity. Although there are important differences in methodology between our experiments and blood product pathogen inactivation, these findings suggest that otherwise safe and effective inactivation methods should be further studied to exclude possible gaps in their ability to inactivate contemporary, multidrug-resistant bacterial pathogens.

microbiology↗

bioRxiv2021

Genomic Evidence of Environmental and Resident Salmonella Senftenberg and Montevideo Contamination in the Pistachio Supply-chain

Pistachios have been implicated in two salmonellosis outbreaks and multiple recalls in the U.S. This study performed a retrospective data analysis of Salmonella associated with pistachios and a storage study to evaluate the survivability of Salmonella on inoculated inshell pistachios to further understand the genetics and microbiological dynamics of this commodity-pathogen pair. The retrospective data analysis on isolates associated with pistachios was performed from both short-read and long-read sequencing technologies. The sequence data were analyzed using the FDAs Center for Food Safety and Applied Nutrition Single Nucleotide Polymorphism (SNP) analysis and Whole Genome Multi-locus Sequence Typing (wgMLST) pipeline. The storage study evaluated the survival of five strains of Salmonella on pistachios, both in a cocktail as well as individually. Our results demonstrate: i) evidence of persistent Salmonella Senftenberg and Salmonella Montevideo strains in pistachio environments, some of which may be due to clonal resident strains and some of which may be due to preharvest contamination; ii) presence of the Copper Homeostasis and Silver Resistance Island (CHASRI) in Salmonella Senftenberg and Montevideo strains in the pistachio supply chain; and iii) different serovars of Salmonella enterica, including Salmonella Senftenberg and Salmonella Montevideo, are able to survive in pistachios over an extended period of time. ImportancePistachios have been linked to multistate outbreaks caused by Salmonella serovar Senftenberg (2013, 2016) and serovar Montevideo (2016). This comprehensive study of whole-genome-sequence (WGS) data from Senftenberg and Montevideo isolates associated with pistachio outbreaks, recalls, and investigations over a nine-year period (2009-2018) was conducted to provide insights into evolutionary relationships and persistence. Multiple analytical approaches were applied including MLST, wgMLST and phylogenetic SNP analysis. The CHASRI was identified in all isolates associated with the sequence type 14 (ST14) and ST316, suggesting an adaptation in response to extrinsic pressures, such as in the farm environment. There is evidence of persistent Salmonella Senftenberg and Montevideo strains in pistachio pre-harvest and post-harvest environments. Utilizing metagenomic sequencing during an inoculated storage study of pistachios allowed for determination of surviving serovars over an extended period of time. Defining the mechanisms of persistence of these strains is of high importance to public health.

microbiology↗

bioRxiv2021

Kenyan Traditional Medicine: Exploring Old Solutions to the Modern Antibacterial Crises Through Natural Products Chemistry

Infectious diseases are a major cause of morbidity and mortality around the world, accounting for approximately 50% of all deaths in tropical countries. Despite remarkable progress in the field of microbiology, inability to control or mitigate, epidemics caused by drug-resistant microorganisms pose a serious health hazard to the global population. New therapeutic strategies must be developed as a global initiative for the prevention and control of infectious diseases. This study focuses on Kenyan medicinal plants and their activity against bacteria. Plant extracts obtained from seven Kenyan plants used in traditional medicine, were screened for their antibacterial activity against Escherichia coli, Pseudomonas aeruginosa, Bacillus cereus, and Mycobacterium smegmatis. Extracts from all these plants showed antibacterial activity against at least one of the tested organisms at a concentration of 2 mg/mL. Chemical screening showed the presence of different classes of phytochemicals such as alkaloids, terpenes, tannins, in some active extracts.

microbiology↗

bioRxiv2021

Long-Term Persistence of Plasmids Targeted by CRISPR Interference in Bacterial Populations

CRISPR-Cas systems provide prokaryotes with an RNA-guided defense against foreign mobile genetic elements (MGEs) such as plasmids and viruses. A common mechanism by which MGEs avoid interference by CRISPR consists of acquisition of escape mutations in regions targeted by CRISPR. Here, using microbiological, live microscopy, and microfluidics analyses we demonstrated that plasmids can persist in Escherichia coli cells at conditions of continuous targeting by the type I-E CRISPR-Cas system without acquiring any genetic alterations. We used mathematical modeling to show how plasmid persistence in a subpopulation of cells mounting CRISPR interference is achieved due to the stochastic nature of CRISPR interference and plasmid replication events. We hypothesize that the observed complex dynamics provides bacterial populations with long-term benefits due to the presence of mobile genetic elements in some cells, leading to diversification of phenotypes in the entire community and allowing rapid changes in the population structure to meet the demands of a changing environment.

microbiology↗

bioRxiv2021

OASIS evaluation of the French surveillance network for antimicrobial resistance in diseased animals (RESAPATH): success factors at the basis of a well-performing volunteer system

Antimicrobial resistance is a One Health issue requiring the development of surveillance systems in the human, environmental and animal sectors. In Europe, the surveillance of antimicrobial resistance on zoonotic pathogens and indicator bacteria in healthy food-producing animals has been implemented on a legal basis, while countries are also expected to extend their surveillance to diseased animals in the frame of national action plans. In this context, evaluating existing antimicrobial resistance surveillance systems in veterinary medicine is important to improve systems in place, but also to help other countries learn from these experiences, understand success factors and anticipate challenges. With this aim, the French surveillance network for antimicrobial resistance in bacteria from diseased animals (RESAPATH) was evaluated using the OASIS assessment tool. Key performance factors included (i) a strong and inclusive central institutional organization defining clear and well-accepted surveillance objectives, scope and procedures, (ii) strong skills in epidemiology and microbiology and (iii) a win-win approach enabling the volunteer participation of 71 field laboratories and where a free annual proficiency testing plays a pivotal role. The main area of improvement of RESAPATH was its time-consuming data management system.

microbiology↗