Profiling the plasmid conjugation potential of urinary Escherichia coli

Escherichia coli is often associated with urinary tract infection (UTI). Antibiotic resistance in E. coli is an ongoing challenge in managing UTI. Extrachromosomal elements – plasmids – are vectors for clinically relevant traits, such as antibiotic resistance, with conjugation being one of the main methods for horizontal propagation of plasmids in bacterial populations. Targeting of conjugation components has been proposed as a strategy to curb the spread of plasmid-borne antibiotic resistance. Understanding the types of conjugative systems present in urinary E. coli isolates is fundamental to assessing the viability of this strategy. In this study, we profile two well-studied conjugation systems (F-type and P-type) in the draft genomes of 65 urinary isolates of E. coli obtained from the bladder urine of adult women with and without UTI-like symptoms. Most of these isolates contained plasmids and we found that conjugation genes were abundant/ubiquitous, diverse and often associated with IncF plasmids. To validate conjugation of these urinary plasmids, the plasmids from two urinary isolates, UMB1223 (predicted to have F-type genes) and UMB1284 (predicted to have P-type genes), were transferred by conjugation into the K-12 E. coli strain MG1655. Overall, the findings of this study support the notion that care should be taken in targeting any individual component of a urinary E. coli isolate’s conjugation system, given the inherent mechanistic redundancy, gene diversity and different types of conjugation systems in this population

Characterizing Plasmids in Bacteria Species Relevant to Urinary Health

The urinary tract has a microbial community (the urinary microbiota or urobiota) that has been associated with human health. Whole genome sequencing of bacteria is a powerful tool, allowing investigation of the genomic content of the urobiota, also called the urinary microbiome (urobiome). Bacterial plasmids are a significant component of the urobiome yet are understudied. Because plasmids can be vectors and reservoirs for clinically relevant traits, they are important for urobiota dynamics and thus may have relevance to urinary health. In this project, we sought plasmids in 11 clinically relevant urinary species: Aerococcus urinae, Corynebacterium amycolatum, Enterococcus faecalis, Escherichia coli, Gardnerella vaginalis, Klebsiella pneumoniae, Lactobacillus gasseri, Lactobacillus jensenii, Staphylococcus epidermidis, Streptococcus anginosus, and Streptococcus mitis. We found evidence of plasmids in E. faecalis, E. coli, K. pneumoniae, S. epidermidis, and S. anginosus but insufficient evidence in other species sequenced thus far. Some identified plasmidic assemblies were predicted to have putative virulence and/or antibiotic resistance genes, although the majority of their annotated coding regions were of unknown predicted function. In this study, we report on plasmids from urinary species as a first step to understanding the role of plasmids in the bacterial urobiota. IMPORTANCE The microbial community of the urinary tract (urobiota) has been associated with human health. Whole genome sequencing of bacteria permits examination of urobiota genomes, including plasmids. Because plasmids are vectors and reservoirs for clinically relevant traits, they are important for urobiota dynamics and thus may have relevance to urinary health. Currently, urobiota plasmids are understudied. Here, we sought plasmids in 11 clinically relevant urinary species. We found evidence of plasmids in E. faecalis, E. coli, K. pneumoniae, S. epidermidis, and S. anginosus but insufficient evidence in the other 6 species. We identified putative virulence and/or antibiotic resistance genes in some of the plasmidic assemblies, but most of their annotated coding regions were of unknown function. This is a first step to understanding the role of plasmids in the bacterial urobiota

Whole-Genome Sequencing of Staphylococcus aureus and Staphylococcus haemolyticus Clinical Isolates from Egypt

Infections caused by antibiotic-resistant Staphylococcus are a global concern. This is true in the Middle East, where increasingly resistant Staphylococcus aureus and Staphylococcus haemolyticus strains have been detected. While extensive surveys have revealed the prevalence of infections caused by antibiotic-resistant staphylococci in Europe, Asia, and North America, the population structure of antibiotic-resistant staphylococci recovered from patients and clinical settings in Egypt remains uncharacterized. We performed whole-genome sequencing of 56 S. aureus and 10 S. haemolyticus isolates from Alexandria Main University Hospital; 46 of the S. aureus genomes and all 10 of the S. haemolyticus genomes carry mecA, which confers methicillin resistance. Supplemented with additional publicly available genomes from the other parts of the Middle East (34 S. aureus and 6 S. haemolyticus), we present the largest genomic study to date of staphylococcal isolates from the Middle East. These genomes include 20 S. aureus multilocus sequence types (MLST), including 3 new ones. They also include 9 S. haemolyticus MLSTs, including 1 new one. Phylogenomic analyses of each species’ core genome largely mirrored those of the MLSTs, irrespective of geographical origin. The hospital-acquired spa t037/ST239-SCCmec III/MLST CC8 clone represented the largest clade, comprising 22% of the S. aureus isolates. Like S. aureus genome surveys of other regions, these isolates from the Middle East have an open pangenome, a strong indicator of gene exchange of virulence factors and antibiotic resistance genes with other reservoirs. Our genome analyses will inform antibiotic stewardship and infection control plans in the Middle East

Investigation of Plasmids Among Clinical Staphylococcus aureus and Staphylococcus haemolyticus Isolates From Egypt

Staphylococci can cause a wide array of infections that can be life threatening. These infections become more deadly when the isolates are antibiotic resistant and thus harder to treat. Many resistance determinants are plasmid-mediated; however, staphylococcal plasmids have not yet been fully characterized. In particular, plasmids and their contributions to antibiotic resistance have not been investigated within the Arab states, where antibiotic use is not universally regulated. Here, we characterized the putative plasmid content among 56 Staphylococcus aureus and 10 Staphylococcus haemolyticus clinical isolates from Alexandria, Egypt. Putative plasmid sequences were detected in over half of our collection. In total, we identified 72 putative plasmid sequences in 27 S. aureus and 1 S. haemolyticus isolates. While these isolates typically carried one or two plasmids, we identified one isolate—S. aureus AA53—with 11 putative plasmids. The plasmid sequences most frequently encoded a Rep_1, RepL, or PriCT_1 type replication protein. As expected, antibiotic resistance genes were widespread among the identified plasmid sequences. Related plasmids were identified amongst our clinical isolates; homologous plasmids present in multiple isolates clustered into 11 groups based upon sequence similarity. Plasmids from the same cluster often shared antibiotic resistance genes, including blaZ, which is associated with β-lactam resistance. Our analyses suggest that plasmids are a key factor in the pathology and epidemiology of S. aureus in Egypt. A better characterization of plasmids and the role they contribute to the success of Staphylococci as pathogens will guide the design of effective control strategies to limit their spread

Genomic Survey of E. coli From the Bladders of Women With and Without Lower Urinary Tract Symptoms

Urinary tract infections (UTIs) are one of the most common human bacterial infections. While UTIs are commonly associated with colonization by Escherichia coli, members of this species also have been found within the bladder of individuals with no lower urinary tract symptoms (no LUTS), also known as asymptomatic bacteriuria. Prior studies have found that both uropathogenic E. coli (UPEC) strains and E. coli isolates that are not associated with UTIs encode for virulence factors. Thus, the reason(s) why E. coli sometimes causes UTI-like symptoms remain(s) elusive. In this study, the genomes of 66 E. coli isolates from adult female bladders were sequenced. These isolates were collected from four cohorts, including women: (1) without lower urinary tract symptoms, (2) overactive bladder symptoms, (3) urgency urinary incontinence, and (4) a clinical diagnosis of UTI. Comparative genomic analyses were conducted, including core and accessory genome analyses, virulence and motility gene analyses, and antibiotic resistance prediction and testing. We found that the genomic content of these 66 E. coli isolates does not correspond with the participant’s symptom status. We thus looked beyond the E. coli genomes to the composition of the entire urobiome and found that the presence of E. coli alone was not sufficient to distinguish between the urobiomes of individuals with UTI and those with no LUTS. Because E. coli presence, abundance, and genomic content appear to be weak predictors of UTI status, we hypothesize that UTI symptoms associated with detection of E. coli are more likely the result of urobiome composition

Early mobilisation in critically ill COVID-19 patients: a subanalysis of the ESICM-initiated UNITE-COVID observational study

Background Early mobilisation (EM) is an intervention that may improve the outcome of critically ill patients. There is limited data on EM in COVID-19 patients and its use during the first pandemic wave. Methods This is a pre-planned subanalysis of the ESICM UNITE-COVID, an international multicenter observational study involving critically ill COVID-19 patients in the ICU between February 15th and May 15th, 2020. We analysed variables associated with the initiation of EM (within 72 h of ICU admission) and explored the impact of EM on mortality, ICU and hospital length of stay, as well as discharge location. Statistical analyses were done using (generalised) linear mixed-effect models and ANOVAs. Results Mobilisation data from 4190 patients from 280 ICUs in 45 countries were analysed. 1114 (26.6%) of these patients received mobilisation within 72 h after ICU admission; 3076 (73.4%) did not. In our analysis of factors associated with EM, mechanical ventilation at admission (OR 0.29; 95% CI 0.25, 0.35; p = 0.001), higher age (OR 0.99; 95% CI 0.98, 1.00; p ≤ 0.001), pre-existing asthma (OR 0.84; 95% CI 0.73, 0.98; p = 0.028), and pre-existing kidney disease (OR 0.84; 95% CI 0.71, 0.99; p = 0.036) were negatively associated with the initiation of EM. EM was associated with a higher chance of being discharged home (OR 1.31; 95% CI 1.08, 1.58; p = 0.007) but was not associated with length of stay in ICU (adj. difference 0.91 days; 95% CI − 0.47, 1.37, p = 0.34) and hospital (adj. difference 1.4 days; 95% CI − 0.62, 2.35, p = 0.24) or mortality (OR 0.88; 95% CI 0.7, 1.09, p = 0.24) when adjusted for covariates. Conclusions Our findings demonstrate that a quarter of COVID-19 patients received EM. There was no association found between EM in COVID-19 patients' ICU and hospital length of stay or mortality. However, EM in COVID-19 patients was associated with increased odds of being discharged home rather than to a care facility. Trial registration ClinicalTrials.gov: NCT04836065 (retrospectively registered April 8th 2021)

F Plasmids in Escherichia coli Decrease Permissivity to Coliphage

The urinary tract contains a community of bacteria called the urinary microbiota (urobiota) thatmay be relevant to health; the genomic component of the urobiota is the urinary microbiome (urobiome). Urinary bacteria have been associated with both asymptomatic states and disease conditions, such as urinary tract infection (UTI), overactive bladder (OAB), and urge urinary incontinence (UUI). Some bacteria, such as E. coli, are considered urinary pathogens (uropathogens) but also can be commensals. Bacteriophage (phage) are ubiquitous in nature and likely shape bacterial populations in every niche; thus, phage may be one factor that modulates the urobiota. Phages have a specific host range dictated not just by host receptor compatibility, but also by traits of the bacterial host. To understand the genetic determinants of phage infection in urinary bacteria, we have used a model system consisting of urinary E. coli and the lytic E. coli phages (coliphages). Urinary E. coli that are less permissive to coliphage infection often carry plasmid-related genes. To determine whether these genes relate to permissivity, plasmids present in urinary microbiota (UMB) were conjugated into a naïve E. coli K-12 background; E. coli K-12 acquisition of F plasmids from urinary isolates UMB0928 and UMB1284 decreased permissivity to infection by the lytic coliphages P1vir, Greed, and Lust. Analysis of the plasmidome of urinary E. coli indicated that more than half of these isolates are predicted to contain a plasmid; most of these urinary plasmids are of the F plasmid group. Antibiotic resistance and virulence genes were common in F plasmids. The F plasmids pU0928 and pU1284 reduced permissiveness to phage in E. coli K-12. These two plasmids were stable and conferred multiple antibiotic resistances Given the selective pressure imposed by the rapid propagation and evolution of phages,plasmids could be a vehicle to deliver and maintain anti-phage genes in a bacteria population. Phage selective pressure also could result in the acquisition and maintenance of plasmid-linked content, such as genes for antibiotic resistance and virulence factors. Urinary bacteria, phage, and plasmid dynamics could be important for clinically relevant traits of urinary bacteria and overall urobiota dynamics

Urinary Plasmids Reduce Permissivity to Coliphage Infection

The microbial community of the urinary tract (urinary microbiota or urobiota) has been associated with human health. Bacteriophages (phages) and plasmids present in the urinary tract, like in other niches, may shape urinary bacterial dynamics. While urinary Escherichia coli strains associated with urinary tract infection (UTI) and their phages have been catalogued for the urobiome, bacterium-plasmid-phage interactions have yet to be explored. In this study, we characterized urinary E. coli plasmids and their ability to decrease permissivity to E. coli phage (coliphage) infection. Putative F plasmids were predicted in 47 of 67 urinary E. coli isolates, and most of these plasmids carried genes that encode toxin-antitoxin (TA) modules, antibiotic resistance, and/or virulence. Urinary E. coli plasmids, from urinary microbiota strains UMB0928 and UMB1284, were conjugated into E. coli K-12 strains. These transconjugants included genes for antibiotic resistance and virulence, and they decreased permissivity to coliphage infection by the laboratory phage P1vir and the urinary phages Greed and Lust. Plasmids in one transconjugant were maintained in E. coli K-12 for up to 10 days in the absence of antibiotic resistance selection; this included the maintenance of the antibiotic resistance phenotype and decreased permissivity to phage. Finally, we discuss how F plasmids present in urinary E. coli strains could play a role in coliphage dynamics and the maintenance of antibiotic resistance in urinary E. coli. IMPORTANCE The urinary tract contains a resident microbial community called the urinary microbiota or urobiota. Evidence exists that it is associated with human health. Bacteriophages (phages) and plasmids present in the urinary tract, like in other niches, may shape urinary bacterial dynamics. Bacterium-plasmid-phage interactions have been studied primarily in laboratory settings and are yet to be thoroughly tested in complex communities. This is especially true of the urinary tract, where the bacterial genetic determinants of phage infection are not well understood. In this study, we characterized urinary E. coli plasmids and their ability to decrease permissivity to E. coli phage (coliphage) infection. Urinary E. coli plasmids, encoding antibiotic resistance and transferred by conjugation into naive laboratory E. coli K-12 strains, decreased permissivity to coliphage infection. We propose a model by which urinary plasmids present in urinary E. coli strains could help to decrease phage infection susceptibility and maintain the antibiotic resistance of urinary E. coli. This has consequences for phage therapy, which could inadvertently select for plasmids that encode antibiotic resistance

Fabricación de ladrillos con polvo-residuo de mármol en México. Propiedades físicas y mecánicas del polvo residuo de mármol de la provincia de la Comarca Lagunera, en México

The marble industry generates a large amount of dust waste. These wastes do not have a proper management plan, as well as being highly contaminating the population surrounding the site of the deposits for these materials. To offer a solution, this article shows the results of the development of a brick-based marble powder to achieve sufficient compressive strength for the construction of masonry walls in low-rise housing. The experimental program includes 16 different dosages that varies the amount of cement, lime, and sand, and keep constant the marble powder. The program includes the compressive tests for 160 bricks, compressive tests for 3 small walls, validated adherence under compression tests for 3 small walls, and absorption tests for 48 bricks. The results of the test showed that the compression strength of the individual bricks and wall is 4.0 MPa y 1.9 MPa, respectively, and the absorption of the bricks is 21 %. These results of absorption, compression and adhesion are a first indicator of the feasibility of used these bricks for the construction of load-bearing walls in housing projects developed in areas of low seismic demandsLa industria del mármol genera gran cantidad de desperdicio en polvo. Estos desechos carecen de un adecuado plan de manejo, además de resultar altamente contaminantes para la población que rodea el lugar de los depósitos de dichos materiales. Para ofrecer una solución, en este artículo se presentan los resultados del desarrollo de un ladrillo a base del polvo de mármol, que tenga una resistencia a compresión suficiente para construir muros de mampostería en viviendas de baja altura. El programa experimental incluye 16 dosificaciones diferentes, en las que se varía la cantidad de cemento, cal comercial para albañilería y arena, y se deja constante la de polvo-residuo de mármol. El programa incluye el ensaye a compresión de 160 ladrillos, 3 ensayos a compresión en muretes, 3 pruebas de adherencia validada a compresión en muretes y 48 pruebas de absorción. Los resultados de los ensayos demostraron que la resistencia a compresión de las piezas individuales y de muretes es de 4,0 MPa y de 1,9 MPa, respectivamente, y la absorción de las piezas es del 21 %. Estos resultados de absorción, compresión y adherencia son el primer indicativo de la viabilidad del uso de estos ladrillos para la construcción de muros de carga en vivienda desarrolladas en zonas de amenaza sísmica baja