Application of flow cytometry for rapid, high-throughput, multiparametric analysis of environmental microbiomes.

Quantification of the abundance and understanding of the dynamics of the microbial communities is essential to establish a basis for microbiome characterization. The conventional techniques used for the quantification of microbes are complicated and time-consuming. With scientific advancement, many techniques evolved and came into account. Among them, flow cytometry is a robust, high-throughput technique through which microbial dynamics, morphology, microbial distribution, physiological characteristics, and many more attributes can be studied in a high-throughput manner with comparatively less time and resources. Flow cytometry, when combined with other omics-based methods, offers a rapid and efficient platform to analyze and understand the composition of microbiome at the cellular level. The microbial diversity observed through flow cytometry will not be equivalent to that obtained by sequencing methods, but this integrated approach holds great potential for high throughput characterization of microbiomes. Flow cytometry is regarded as an established characterization tool in haematology, oncology, immunology, and medical microbiology research; however, its application in environmental microbiology is yet to be explored. This comprehensive review aims to delve into the diverse environmental applications of flow cytometry across various domains, including but not limited to bioremediation, landfills, anaerobic digestion, industrial bioprocesses, water quality regulation, and soil quality regulation. By conducting an in-depth analysis, this article seeks to shed light on the potential benefits and challenges associated with the utilization of flow cytometry in addressing environmental concerns.

The shifting research landscape for PAH bioremediation in water environment: a bibliometric analysis on three decades of development.

Polycyclic aromatic hydrocarbons (PAHs) with their carcinogenic, teratogenic, and mutagenic effects can cause great damage to the ecosystem and public health when present in water. With bioremediation, PAH contamination in water environment can be greatly reduced in an eco-friendly manner. It has thus become the research focus for many environmental scientists. In this study, a bibliometric analysis on three-decade (1990-2022) development of PAH bioremediation in water environment was conducted from temporal and spatial dimensions using CiteSpace. A total of 2480 publications, obtained from Web of Science core collection database, were used to explore the basic characteristics, hotspots, and prospects of the research area. The results showed that (1) bioremediation/biodegradation of PAHs in water environment has been getting researchers' attention since 1990, and is gaining even more traction as time goes on. (2) In terms of countries, China and the USA were the major contributors in this research area, while at the institutional level, the Chinese Academy of Sciences has produced the most research results. However, international cooperation across regions was lacking in the field. (3) Environment Science and Technology, Chemosphere, Applied and Environment Microbiology, Journal of Hazardous Materials, and Environment Pollution were the 5 most cited journals in this field. (4) There were three major stages the field has gone through, each with distinct research hotspots, including initial stage (1990-1994), mechanism investigation (1995-2000), and application exploration (2001-2010; 2011-2022). Finally, research perspectives were proposed, covering three directions, namely, bioavailability, immobilization, and viable but nonculturable (VBNC) bacteria.

The importance of environments and surfaces hygienization in pandemic times (Covid-19): a microbiological analysis in places for physical activity practice

The objective of this study was to analyse microbiological organisms in different locations and regions for physical activity in the city of João Pessoa, Brazil. Samples were collected on various objects used, such as: mattresses, drinking fountains, gloves, cell phones and others. The samples were collected in João Pessoa-PB, following the Standard Operating Procedure-SOP/ Microbiology of a specialized laboratory. The collection took place in the five macro-regions: North, South, East, West and Center. Foreach region samples were collected in one public place (square), a private one (gym) and one school (public or private), totaling fifteen collected sites and 450 samples. The following microorganisms were studied in all analyzed surfaces: Bacillus sp, Escherichia Coli, Klebsiella sppor Enterobacter sppand Coag. Neg. Staphylococcus.All regions had a high contamination level by some microorganism. The highest rates were found in the western, central and northern regions -96, 94 and 93% respectively. The Coag. Neg.Staphylococcus presented the highest and lowest incidence rates in the South and East regions, with 43.33 and 6.67%, respectively, as well as Klebsiella sppor Enterobacter spp, which presented high levels. It is concluded that there is a microorganisms' contamination in the most varied places and regions where physical activity practices are developed, with a predominance of Coag. Neg.Staphylococcusand Klebsiella sppor Enterobacter spp. These results lead to a warning about the hygiene importance in places for physical activity practice, especially in pandemic times (COVID-19), since almost all the evaluated surfaces were contaminated.

Infection risks related to aesthetic procedures: microbial profile and professional perception about infection prevention measures / Riscos de infecção relacionados a procedimentos estéticos: perfil microbiano e percepção profissional sobre medidas de prevenção de infecção / Riesgos de infección relacionados con los procedimientos estéticos: perfil microbiano y percepción profesional sobre las medidas de prevención de infecciones

Background and Objectives: This study aimed to identify the presence of microorganisms in the aesthetic environment and assess professionals' knowledge about relevant infection prevention measures, considering the importance of the issue and the lack of study in the area. Methods: A total of 100 clinics that perform minimally invasive aesthetic procedures in Porto Alegre (RS), Brazil, were visited. Procedures such as botulin-toxin, dermal fillers, collagen biostimulators, thread lift, chemical peels and laser hair removal were considered. A questionnaire about infection prevention measures were answered by 50 professionals. Also, 100 samples were collected from the environment for bacterial identification and antimicrobial susceptibility testing. Results: There was an infection prevention protocol in 40% of clinics, in which 95% of respondents had complete college education. Periodic professional training regarding infection control measures were performed in 72% of clinics. An autoclave was used for sterilization of materials and instruments in 66% of clinics. From the samples collected, 85% showed bacterial growth by microbiological methods. Coagulase-negative Staphylococci was the most prevalent genera found, and 16% of them were resistant to both cefoxitin, erythromycin, and clindamycin. Four isolates were positive for mecA by PCR. Conclusion: The presence of well-trained professionals is critical in aesthetic clinics so that biosafety and infection prevention measures are taken.(AU)

Justificativa e Objetivos: Este estudo teve como objetivo identificar a presença de microrganismos no ambiente estético e avaliar o conhecimento dos profissionais sobre medidas relevantes de prevenção de infecções, considerando a importância do tema e a falta de estudos nesta área. Métodos: Foram visitadas 100 clínicas que realizam procedimentos estéticos minimamente invasivos em Porto Alegre (RS), Brasil. Foram considerados procedimentos injetáveis como aplicação de toxina botulínica, preenchedores faciais, microagulhamento, bioestimuladores de colágeno, fios de sustentação, peelings químicos e depilação a laser. Um questionário sobre medidas de prevenção de infecção foi respondido por 50 profissionais. Além disso, 100 amostras foram coletadas do ambiente para identificação bacteriana e teste de sensibilidade aos antimicrobianos. Resultados: Existia protocolo de prevenção de infecção em 40% dos ambulatórios, no qual 95% dos profissionais entrevistados possuíam ensino superior completo. Treinamento profissional periódico sobre medidas de controle de infecção foi realizado em 72% dos ambulatórios. Autoclave foi utilizada para esterilização de materiais e instrumentais em 66% das clínicas. Das amostras coletadas, 85% apresentaram crescimento bacteriano nas culturas microbiológicas. Staphylococci coagulase-negativo foi o gênero mais prevalente encontrado; e 16% deles eram resistentes à cefoxitina, eritromicina e clindamicina. Quatro isolados foram positivos para mecA por PCR. Conclusão: A presença de profissionais devidamente treinados é fundamental nas clínicas de estética, para que medidas de biossegurança e prevenção de infecções sejam tomadas.(AU)

Justificación y Objetivos: Este estudio tuvo como objetivo identificar la presencia de microorganismos en el entorno estético y evaluar el conocimiento de los profesionales sobre las medidas de prevención de infecciones relevantes, considerando la importancia del tema y la falta de estudios en esta área. Métodos: Se visitaron 100 clínicas que realizan procedimientos estéticos mínimamente invasivos en Porto Alegre (RS), Brasil. Se consideraron procedimientos invasivos, como la aplicación de toxina botulínica, rellenos faciales, microagujas, bioestimuladores de colágeno, hilos de soporte, peelings químicos y depilación láser. Un cuestionario sobre medidas de prevención de infecciones fue respondido por 50 profesionales. Además, se recolectaron 100 muestras del medio ambiente para la identificación bacteriana y las pruebas de susceptibilidad a los antimicrobianos. Resultados: Existía un protocolo de prevención de infecciones en el 40% de las clínicas, en el que el 95% de los profesionales encuestados tenía educación universitaria completa. En el 72% de las clínicas se realizó capacitación profesional periódica sobre medidas de control de infecciones. Se utilizó un autoclave para la esterilización de materiales e instrumentos en el 66% de las clínicas. De las muestras recolectadas, el 85% mostró crecimiento bacteriano por métodos de cultivo microbiologicos. El Staphylococci coagulasa negativo fue el género más prevalente encontrado, y el 16% de ellos eran resistentes tanto a cefoxitina, eritromicina y clindamicina. Cuatro aislamientos fueron positivos para mecA por PCR. Conclusión: La presencia de profesionales debidamente capacitados es fundamental en las clínicas de estética, para la toma medidas de bioseguridad y prevención de infecciones.(AU)

Assessment of cleaning methods on bacterial burden of hospital privacy curtains: a pilot randomized controlled trial.

Healthcare-associated infections (HAIs) are an important global issue, leading to poor patient outcomes. A potential route of transmission of HAIs is through contact with hospital privacy curtains. The aim of this study is to evaluate cleaning on reduction of curtain bacterial burden. In this pilot cluster randomized controlled trial we compared the bacterial burden between three groups of 24 curtains on a regional burn/plastic surgery ward. A control group was not cleaned. Two groups were cleaned at 3-4 day intervals with either disinfectant spray or wipe. The primary outcome was the difference in mean CFU/cm2 between day 0 to day 21. The secondary outcome was the proportion of curtains contaminated with Methicillin-resistant Staphylococcus aureus (MRSA). By day 21, the control group was statistically higher (2.2 CFU/cm2) than spray (1.3 CFU/cm2) or wipe (1.5 CFU/cm2) (p < 0.05). After each cleaning at 3-4 day intervals, the bacterial burden on the curtains reduced to near day 0 levels; however, the level increased again over the intervening 3-4 days. By day 21, 64% of control curtains were contaminated with MRSA compared to 10% (spray) and 5% (wipe) (p < 0.05). This study show that curtains start clean and progressively become contaminated with bacteria. Regularly cleaning curtains with disinfectant spray or wipes reduces bacterial burden and MRSA contamination.

Biodegradation of binary mixtures of octane with benzene, toluene, ethylbenzene or xylene (BTEX): insights on the potential of Burkholderia, Pseudomonas and Cupriavidus isolates.

The contamination of the environment by crude oil and its by-products, mainly composed of aliphatic and aromatic hydrocarbons, is a widespread problem. Biodegradation by bacteria is one of the processes responsible for the removal of these pollutants. This study was conducted to determine the abilities of Burkholderia sp. B5, Cupriavidus sp. B1, Pseudomonas sp. T1, and another Cupriavidus sp. X5 to degrade binary mixtures of octane (representing aliphatic hydrocarbons) with benzene, toluene, ethylbenzene, or xylene (BTEX as aromatic hydrocarbons) at a final concentration of 100 ppm under aerobic conditions. These strains were isolated from an enriched bacterial consortium (Yabase or Y consortium) that prefer to degrade aromatic hydrocarbon over aliphatic hydrocarbons. We found that B5 degraded all BTEX compounds more rapidly than octane. In contrast, B1, T1 and X5 utilized more of octane over BTX compounds. B5 also preferred to use benzene over octane with varying concentrations of up to 200 mg/l. B5 possesses alkane hydroxylase (alkB) and catechol 2,3-dioxygenase (C23D) genes, which are responsible for the degradation of alkanes and aromatic hydrocarbons, respectively. This study strongly supports our notion that Burkholderia played a key role in the preferential degradation of aromatic hydrocarbons over aliphatic hydrocarbons in the previously characterized Y consortium. The preferential degradation of more toxic aromatic hydrocarbons over aliphatics is crucial in risk-based bioremediation.

Amazonocrinis nigriterrae gen. nov., sp. nov., Atlanticothrix silvestris gen. nov., sp. nov. and Dendronalium phyllosphericum gen. nov., sp. nov., nostocacean cyanobacteria from Brazilian environments.

The cyanobacterial genus Nostoc is an important contributor to carbon and nitrogen bioavailability in terrestrial ecosystems and a frequent partner in symbiotic relationships with non-diazotrophic organisms. However, since this currently is a polyphyletic genus, the diversity of Nostoc-like cyanobacteria is considerably underestimated at this moment. While reviewing the phylogenetic placement of previously isolated Nostoc-like cyanobacteria originating from Brazilian Amazon, Caatinga and Atlantic forest samples, we detected 17 strains isolated from soil, freshwater, rock and tree surfaces presenting patterns that diverged significantly from related strains when ecological, morphological, molecular and genomic traits were also considered. These observations led to the identification of the evaluated strains as representative of three novel nostocacean genera and species: Amazonocrinis nigriterrae gen. nov., sp. nov.; Atlanticothrix silvestris gen. nov., sp. nov.; and Dendronalium phyllosphericum gen. nov., sp. nov., which are herein described according to the rules of the International Code of Nomenclature for algae, fungi and plants. This finding highlights the great importance of tropical and equatorial South American ecosystems for harbouring an unknown microbial diversity in the face of the anthropogenic threats with which they increasingly struggle.

Disrupting quorum sensing alters social interactions in Chromobacterium violaceum.

Quorum sensing (QS) is a communication system used by bacteria to coordinate a wide panel of biological functions in a cell density-dependent manner. The Gram-negative Chromobacterium violaceum has previously been shown to use an acyl-homoserine lactone (AHL)-based QS to regulate various behaviors, including the production of proteases, hydrogen cyanide, or antimicrobial compounds such as violacein. By using combined metabolomic and proteomic approaches, we demonstrated that QS modulates the production of antimicrobial and toxic compounds in C. violaceum ATCC 12472. We provided the first evidence of anisomycin antibiotic production by this strain as well as evidence of its regulation by QS and identified new AHLs produced by C. violaceum ATCC 12472. Furthermore, we demonstrated that targeting AHLs with lactonase leads to major QS disruption yielding significant molecular and phenotypic changes. These modifications resulted in drastic changes in social interactions between C. violaceum and a Gram-positive bacterium (Bacillus cereus), a yeast (Saccharomyces cerevisiae), immune cells (murine macrophages), and an animal model (planarian Schmidtea mediterranea). These results underscored that AHL-based QS plays a key role in the capacity of C. violaceum to interact with micro- and macroorganisms and that quorum quenching can affect microbial population dynamics beyond AHL-producing bacteria and Gram-negative bacteria.

Rapid macrolide and amikacin resistance testing for Mycobacterium abscessus in people with cystic fibrosis.

Introduction. Mycobacterium abscessus complex (MABSC) is an environmental organism and opportunistic pathogen. MABSC pulmonary infections in people with cystic fibrosis are of growing clinical concern. Resistance data guide the use of macrolides and amikacin in MABSC pulmonary disease treatment. MABSC can acquire resistance against macrolides or amikacin via 23S or 16S rRNA gene mutations, respectively.Gap Statement. Current culture-based methods for MABSC detection and antibiotic resistance characterization are typically prolonged, limiting their utility to directly inform treatment or clinical trials. Culture-independent molecular methods may help address this limitation.Aim. To develop real-time PCR assays for characterization of key 23S or 16S rRNA gene mutations associated with constitutive resistance in MABSC.Methodology. We designed two real-time PCR assays to detect the key 23S and 16S rRNA gene mutations. The highly conserved nature of rRNA genes was a major design challenge. To reduce potential cross-reactivity, primers included non-template bases and targeted single-nucleotide polymorphisms unique to MABSC. We applied these assays, as well as a previously developed real-time PCR assay for MABSC detection, to 968 respiratory samples from people with cystic fibrosis. The results from the molecular methods were compared to those for gold standard culture methods and 23S and 16S rRNA gene sequencing.Results.The real-time PCR MABSC detection assay provided a sensitivity of 83.8 % and a specificity of 97.8 % compared to culture. The results from the real-time PCR resistance detection assays were mostly concordant (>77.4 %) with cultured isolate sequencing. The real-time PCR resistance detection assays identified several samples harbouring both resistant and susceptible MABSC, while culture-dependent methods only identified susceptible MABSC in these samples.Conclusion. Using the molecular methods described here, results for health care providers or researchers could be available days or weeks earlier than is currently possible via culture-based antibiotic susceptibility testing.

Combined Antimicrobial Effect of Bio-Waste Olive Leaf Extract and Remote Cold Atmospheric Plasma Effluent.

A novel strategy involving Olive Leaf Extract (OLE) and Cold Atmospheric Plasma (CAP) was developed as a green antimicrobial treatment. Specifically, we reported a preliminary investigation on the combined use of OLE + CAP against three pathogens, chosen to represent medical and food industries (i.e., E. coli, S. aureus and L. innocua). The results indicated that a concentration of 100 mg/mL (total polyphenols) in OLE can exert an antimicrobial activity, but still insufficient for a total bacterial inactivation. By using plain OLE, we significantly reduced the growth of Gram positive S. aureus and L. innocua, but not Gram-negative E. coli. Instead, we demonstrated a remarkable decontamination effect of OLE + CAP in E. coli, S. aureus and L. innocua samples after 6 h. This effect was optimally maintained up to 24 h in S. aureus strain. E. coli and L. innocua grew again in 24 h. In the latter strain, OLE alone was most effective to significantly reduce bacterial growth. By further adjusting the parameters of OLE + CAP technology, e.g., OLE amount and CAP exposure, it could be possible to prolong the initial powerful decontamination over a longer time. Since OLE derives from a bio-waste and CAP is a non-thermal technology based on ionized air, we propose OLE + CAP as a potential green platform for bacterial decontamination. As a combination, OLE and CAP can lead to better antimicrobial activity than individually and may replace or complement conventional thermal procedures in food and biomedical industries.

Hierarchical Bayesian modeling for predictive environmental microbiology toward a safe use of human excreta: Systematic review and meta-analysis.

The pathogen concentration in human excreta needs to be managed appropriately, but a predictive approach has yet to be implemented due to a lack of kinetics models for pathogen inactivation that are available under varied environmental conditions. Our goals were to develop inactivation kinetics models of microorganisms applicable under varied environmental conditions of excreta matrices and to identify the appropriate indicators that can be monitored during disinfection processes. We conducted a systematic review targeting previous studies that presented time-course decay of a microorganism and environmental conditions of matrices. Defined as a function of measurable factors including treatment time, pH, temperature, ammonia concentration and moisture content, the kinetic model parameters were statistically estimated using hierarchical Bayesian modeling. The inactivation kinetics models were constructed for Escherichia coli, Salmonella, Enterococcus, Ascaris eggs, bacteriophage MS2, enterobacteria phage phiX174 and adenovirus. The inactivation rates of a microorganism were predicted using the established model. Ascaris eggs were identified as the most tolerant microorganisms, followed by bacteriophage MS2 and Enterococcus. Ammonia concentration, temperature and moisture content were the critical factors for the Ascaris inactivation. Our model predictions coincided with the current WHO guidelines. The developed inactivation kinetics models enable us to predict microbial concentration in excreta matrices under varied environmental conditions, which is essential for microbiological risk management in emerging resource recovery practices from human excreta.

Azole resistance in Aspergillus isolates by different types of patients and correlation with environment - An Italian prospective multicentre study (ARiA study).

BACKGROUND: A wide range of frequency of azole-resistance in A fumigatus in different patient populations worldwide was observed threatening to reduce therapeutic options. OBJECTIVES: Estimate the prevalence of azole-resistance, investigate the molecular mechanisms of resistance, compare the genotypes of resistant clinical isolates with those from the surrounding environment. METHODS: Aspergillus isolates were collected by seven Italian hospital microbiology laboratories. Strains were isolated from different clinical samples from unselected patients. The azole-resistance was evaluated using screening test and microdilution EUCAST method. The molecular mechanism of resistance was performed sequencing the cyp51A gene. Resistant isolates were genotyped by microsatellite analysis and their profiles compared with those of azole-resistant isolates from previous Italian studies. RESULTS: 425 Aspergillus isolates from 367 patients were analysed. The azole-resistance rates were 4.9% and 6.6% considering all Aspergillus spp. isolates and the A fumigatus sensu stricto, respectively. All resistant isolates except one were from a single hospital. Two rare azole-resistant species were identified: A thermomutatus and A lentulus. The predominant resistance mechanism was TR34 /L98H. No correlation between the clinical resistant strains and environmental isolates from patients' home/work/ward was observed. The analysis of the molecular correlation between the resistant clinical strains collected in the present study and those of environmental and clinical origin collected in previous Italian studies reveals a progressive diversification of azole-resistant genotypes starting from a founder azole-resistant genotype. CONCLUSIONS: This study confirms the trend of azole-resistance rate in Italy, showing a geographical difference. Data reinforce the importance of surveillance programmes to monitor the local epidemiological situation.

Viruses in Extreme Environments, Current Overview, and Biotechnological Potential.

Virus research has advanced significantly since the discovery of the tobacco mosaic virus (TMV), the characterization of its infection mechanisms and the factors that determine their pathogenicity. However, most viral research has focused on pathogenic viruses to humans, animals and plants, which represent only a small fraction in the virosphere. As a result, the role of most viral genes, and the mechanisms of coevolution between mutualistic viruses, their host and their environment, beyond pathogenicity, remain poorly understood. This review focuses on general aspects of viruses that interact with extremophile organisms, characteristics and examples of mechanisms of adaptation. Finally, this review provides an overview on how knowledge of extremophile viruses sheds light on the application of new tools of relevant use in modern molecular biology, discussing their value in a biotechnological context.

Molecular detection of myxoma virus in the environment of vaccinated rabbitries.

Myxoma virus (MYXV) is the aetiological agent of myxomatosis, a systemic, mostly lethal disease that affects European rabbits. Vaccination against it, although widespread, has not been completely effective and disease outbreaks still take place on farms which carry out vaccination programmes. Since some of these cases have been attributed to airborne transmission or the spread of the virus via inanimate vectors, the aims of this study were to determine MYXV contamination levels and distribution in the environment of vaccinated farms and to ascertain whether the detected virus corresponded to field strains. For that, environmental samples from several areas, tools and employees from four (three infected and one uninfected) rabbitries were taken and analysed by qPCR. MYXV was detected in the environment of all the infected farms, whereas all the samples from the non-infected farm were negative. Furthermore, all the positive samples contained viral DNA compatible with field strains of the virus. These results lead us to believe that the administration of currently available commercial vaccines does not prevent infected animals from shedding the field virus. Moreover, viral DNA was also found in items that are not in direct contact with the animals, which could play a role in the transmission of the infection throughout the farm and to other farms. Therefore, this study proves that current vaccination schemes on their own are not sufficient to prevent this disease and should be accompanied by adequate biosecurity measures.

Unraveling bacterial diversity in oil refinery effluents.

Oil refinery effluents are among stressful environments, and they are characterized by alkaline pH, high concentrations of dissolved solids, electrical conductivity, and metals (mainly Fe, Al, B, Sr, Mn, Cu, Ni). In this study, bacterial diversity in these habitats was inferred from full-length 16S rRNA gene sequences obtained from the PacBio® sequencing platform. The results have shown low bacterial diversity in both raw and treated effluents, with sequences representing only two phyla: Firmicutes and Proteobacteria. Sequences from the raw effluents represent four major genera: Bacillus, Wenzhouxiangella, Rhodabaculum, and Halomonas. Whilst bacterial communities from the treated effluents are relatively more diverse as sequences represent five dominant genera: Pseudoxanthomonas, Brevundimonas, Pseudomonas, Rhodobaculum and Rhizobium. Most of the genera represented in the dataset are halophilic or halotolerant microbes known to have the competency to catabolize a broad spectrum of organic and inorganic pollutants. Hypothetically, these bacteria may be relevant for biotechnological and industrial applications, particularly for the remediation of saline industrial wastes.

Isolation of Aluminum-Tolerant and -Absorbing Yeast.

Aluminum ions are toxic to bacteria and are thus frequently used for preservation in the food industry. However, at higher concentrations, aluminum is toxic to animals. The extraction of aluminum from aluminum-contaminated foods would therefore be beneficial. Based on the discovery of yeast strains that can tolerate and absorb toxic metals, we aimed to identify strains that could tolerate and absorb aluminum. In this study, yeast were isolated from soil samples and cultured in medium containing the toxic concentration of aluminum chloride (5 mM) for Saccharomyces cerevisiae BY4741. Among aluminum-tolerant strains, two strains, Alt-OF2 and Alt-OF5, were identified as aluminum-absorbing. D1/D2 sequencing revealed that both strains belonged to the genus Schizoblastosporion (syn. Nadsonia).

Genetic Carriers and Genomic Distribution of cadA6-A Novel Variant of a Cadmium Resistance Determinant Identified in Listeria spp.

Listeria monocytogenes is a pathogen responsible for severe cases of food poisoning. Listeria spp. strains occurring in soil and water environments may serve as a reservoir of resistance determinants for pathogenic L. monocytogenes strains. A large collection of Listeria spp. strains (155) isolated from natural, agricultural, and urban areas was screened for resistance to heavy metals and metalloids, and the presence of resistance determinants and extrachromosomal replicons. Of the tested strains, 35% were resistant to cadmium and 17% to arsenic. Sequence analysis of resistance plasmids isolated from strains of Listeria seeligeri and Listeria ivanovii, and the chromosome of L. seeligeri strain Sr73, identified a novel variant of the cadAC cadmium resistance efflux system, cadA6, that was functional in L. monocytogenes cells. The cadA6 cassette was detected in four Listeria species, including strains of L. monocytogenes, isolated from various countries and sources-environmental, food-associated, and clinical samples. This resistance cassette is harbored by four novel composite or non-composite transposons, which increases its potential for horizontal transmission. Since some cadAC cassettes may influence virulence and biofilm formation, it is important to monitor their presence in Listeria spp. strains inhabiting different environments.

Comparison of three neutralizing broths for environmental sampling of low levels of Listeria monocytogenes desiccated on stainless steel surfaces and exposed to quaternary ammonium compounds.

BACKGROUND: An effective environmental sampling method involves the use of a transport/neutralizing broth with the ability to neutralize sanitizer residues that are collected during sampling and to maintain viability of stressed Listeria monocytogenes (Lm) cells. RESULTS: We applied Lm onto stainless steel surfaces and then subjected Lm to desiccation stress for 16-18 h at room temperature (RT, 21-24 °C). This was followed by the subsequent application of Whisper™ V, a quaternary ammonium compound (QAC)-based sanitizer, diluted to 400 ppm and 8000 ppm of active quat, for 6 h. We then sampled Lm with sponges pre-moistened in three transport broths, Dey/Engley (D/E) broth, Letheen broth and HiCap™ broth, to generate environmental samples that contained sanitizer residues and low levels of stressed Lm, which were subsequently analyzed by an enrichment-based method. This scheme conformed with validation guidelines of AOAC International by using 20 environmental test portions per broth that contained low levels of Lm such that not all test portions were positive (i.e., fractional positive). We showed that D/E broth, Letheen broth and HiCap™ broth performed similarly when no quat or 400 ppm of quat was applied to the Lm contaminating stainless steel surfaces. However, when 8000 ppm of quat was applied, Letheen broth did not effectively neutralize the QAC in the samples. These comparisons were performed on samples stored under three conditions after collection to replicate scenarios of sample transport, RT for 2 h, 4 °C for 24 h and 4 °C for 72 h. Comparisons under the three different scenarios generally reached the same conclusions. In addition, we further demonstrated that storing Letheen and HiCap™ broths at RT for two months before sampling did not reduce their capacity to neutralize sanitizers. CONCLUSIONS: We developed a scheme to evaluate the ability of transport broths to neutralize QAC sanitizers. The three transport broths performed similarly with a commonly used concentration of quat, but Letheen broth could not effectively neutralize a very high concentration of QAC. The performance of transport broths was not significantly affected under the assessed pre-sampling and post-sampling storage conditions.

Porphyromonas spp. have an extensive host range in ill and healthy individuals and an unexpected environmental distribution: A systematic review and meta-analysis.

Studies on the anaerobic bacteria Porphyromonas, mainly focused on P. gingivalis, have revealed new bacterial structures, metabolic pathways, and physiologic functionalities. Porphyromonas are mainly described as being associated with mammals and involved in chronic oral infections and secondary pathologies such as cancers or neurodegenerative diseases. In this review, we collected and analyzed information regarding Porphyromonas isolation sites and associated conditions and showed that Porphyromonas are detected in numerous pristine and anthropic environments and that their host range appears wider than previously believed, including aquatic animals, arthropods, and birds, even if their predominant hosts remain humans, pets, and farm animals. Our analyses also revealed their presence in multiple organs and in a substantial proportion of healthy contexts. Overall, the growing numbers of microbiota studies have allowed unprecedented advances in the understanding of Porphyromonas ecology but raise questions regarding their phylogenic assignment. In conclusion, this systematic and meta-analysis provides an overview of current knowledge regarding Porphyromonas ecological distribution and encourages additional research to fill the knowledge gaps to better understand their environmental distribution and inter- and intra-species transmission.

Detection of Coronavirus Disease 2019 Viral Material on Environmental Surfaces of an Ophthalmology Examination Room.

IMPORTANCE: The new coronavirus disease 2019 (COVID-19) pandemic poses a particular threat to health care professionals; however, there appear to be no objective data that demonstrate the risks of encountering individuals carrying the virus asymptomatically in the case of maintained elective examinations. OBJECTIVE: To investigate the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on the environmental surfaces of an ophthalmology examination room after visits by patients who were asymptomatic and had passed COVID-19 triage. DESIGN, SETTING, AND PARTICIPANTS: This is a quality improvement study conducted 1 week after the first officially confirmed COVID-19 case in Izmir Tepecik Training and Research Hospital, Izmir, Turkey, on March 20, 2020. A triage system was used to determine the risk of COVID-19 from patients who were asymptomatic and presented for examination in an ophthalmology clinic. Real-time polymerase chain reaction testing was used to detect the presence of viral RNA material in samples from the biomicroscope stage, slitlamp breath shield, phoropter, tonometer, and door handles. The first group of samples was taken before the beginning of the examinations, and the second group of the samples was taken after the last patient had left the room. MAIN OUTCOMES AND MEASURES: The main outcome was the presence of viral material on surfaces in 5 circular zones with a diameter of 1 m each around where the patients sat. RESULTS: Thirty-one persons visited the room, of whom 22 underwent ophthalmic examination and 9 were companions. The mean (SD) examination time was 9 (4) minutes (range, 5-13 minutes). Seven samples were taken before examinations and 7 after examinations. Two samples that were taken after examinations were found to be positive for COVID-19, 1 from the slitlamp breath shield and 1 from the phoropter. CONCLUSIONS AND RELEVANCE: This study showed the presence of COVID-19 viral material in a circle 1 m in diameter around where the patients sat. However, real-time polymerase chain reaction could only detect viral material, not the infectivity of these virus samples.