Phylogenetic Analysis and Antimicrobial Profiles of Cultured Emerging Opportunistic Pathogens (Phyla Actinobacteria and Proteobacteria) Identified in Hot Springs

Correlation between bacterial microbiome and Legionella species in water from public bath facilities by 16S rRNA gene amplicon sequencing

Public bath facilities are a major source of Legionella infections in Japan. In this study, we performed 16S rRNA gene amplicon sequencing to characterize the bacterial community in bath and shower water from public bath facilities, along with chemical parameters, and investigated the effect of the bacterial microbiome on the presence of Legionella species. Although no significant difference in bacterial community richness was observed between bath and shower water samples, there was a remarkable difference in the bacterial community structure between them. Distance-based redundancy analysis revealed that several factors (free residual chlorine, pH, and conductivity) were correlated with the bacterial community in bath water. The most abundant bacterial genera in the samples were Pseudomonas (13.7%) in bath water and Phreatobacter (13.6%) in shower water, as indicated by the taxonomic composition, and the dominant bacteria differed between these environmental samples. Legionella pneumophila was the most frequently detected Legionella species, with additional 15 other Legionella species detected in water samples. In Legionella-positive water samples, several unassigned and uncultured bacteria were enriched together. In addition, the co-occurrence network showed that Legionella was strongly interconnected with two uncultured bacteria. Corynebacterium and Sphingomonas negatively correlated with Legionella species. The present study reveals the ecology of Legionella species, especially their interactions with other bacteria that are poorly understood to date.

IMPORTANCE

Public bath facilities are major sources of sporadic cases and outbreaks of Legionella infections. Recently, 16S rRNA gene amplicon sequencing has been used to analyze bacterial characteristics in various water samples from both artificial and natural environments, with a particular focus on Legionella bacterial species. However, the relationship between the bacterial community and Legionella species in the water from public bath facilities remains unclear. In terms of hygiene management, it is important to reduce the growth of Legionella species by disinfecting the water in public bath facilities. Our findings contribute to the establishment of appropriate hygiene management practices and provide a basis for understanding the potential health effects of using bath and shower water available in public bath facilities.

Shotgun Metagenomics-Guided Prediction Reveals the Metal Tolerance and Antibiotic Resistance of Microbes in Poly-Extreme Environments in the Danakil Depression, Afar Region

The occurrence and spread of antibiotic resistance genes (ARGs) in environmental microorganisms, particularly in poly-extremophilic bacteria, remain underexplored and have received limited attention. This study aims to investigate the prevalence of ARGs and metal resistance genes (MRGs) in shotgun metagenome sequences obtained from water and salt crust samples collected from Lake Afdera and the Assale salt plain in the Danakil Depression, northern Ethiopia. Potential ARGs were characterized by the comprehensive antibiotic research database (CARD), while MRGs were identified by using BacMetScan V.1.0. A total of 81 ARGs and 39 MRGs were identified at the sampling sites. We found a copA resistance gene for copper and the β-lactam encoding resistance genes were the most abundant the MRG and ARG in the study area. The abundance of MRGs is positively correlated with mercury (Hg) concentration, highlighting the importance of Hg in the selection of MRGs. Significant correlations also exist between heavy metals, Zn and Cd, and ARGs, which suggests that MRGs and ARGs can be co-selected in the environment contaminated by heavy metals. A network analysis revealed that MRGs formed a complex network with ARGs, primarily associated with β-lactams, aminoglycosides, and tetracyclines. This suggests potential co-selection mechanisms, posing concerns for both public health and ecological balance.

Hyperthermophile diversity microbes in the Calientes geothermal field, Tacna, Peru

Hyperthermophile microorganisms have been discovered worldwide, and several studies regarding biodiversity and the potential biotechnological applications have been reported. In this work, we describe for the first time the diversity of hyperthermophile communities in the Calientes Geothermal Field (CGF) located 4400 m above sea level in Tacna Region, Perú. Three hot springs were monitored and showed a temperature around 84 to 88 °C, for the microbiome analyzed was taken by sampling of sediment and water (pH 7.3-7.6). The hyperthermophile diversity was determined by PCR, DGGE, and DNA sequencing. The sediments analyzed showed a greater diversity than water samples. Sediments showed a more abundant population of bacteria than archaea, with the presence of at least 9 and 5 phylotypes, respectively. Most interestingly, in some taxa of bacteria (Bacillus) and archaea (Haloarcula and Halalkalicoccus), any of operational taxonomic units (OTUs) have not been observed before in hyperthermophile environments. Our results provide insight in the hyperthermophile diversity and reveal the possibility to develop new biotechnological applications based on the kind of environments.

Recommendations for hand hygiene in community settings: a scoping review of current international guidelines

BACKGROUND

Hand hygiene is an important measure to prevent disease transmission.

OBJECTIVE

To summarise current international guideline recommendations for hand hygiene in community settings and to assess to what extent they are consistent and evidence based.

ELIGIBILITY CRITERIA

We included international guidelines with one or more recommendations on hand hygiene in community settings-categorised as domestic, public or institutional-published by international organisations, in English or French, between 1 January 1990 and 15 November 2021.

DATA SOURCES

To identify relevant guidelines, we searched the WHO Institutional Repository for Information Sharing Database, Google, websites of international organisations, and contacted expert organisations and individuals.

CHARTING METHODS

Recommendations were mapped to four areas related to hand hygiene: (1) effective hand hygiene; (2) minimum requirements; (3) behaviour change and (4) government measures. Recommendations were assessed for consistency, concordance and whether supported by evidence.

RESULTS

We identified 51 guidelines containing 923 recommendations published between 1999 and 2021 by multilateral agencies and international non-governmental organisations. Handwashing with soap is consistently recommended as the preferred method for hand hygiene across all community settings. Most guidelines specifically recommend handwashing with plain soap and running water for at least 20 s; single-use paper towels for hand drying; and alcohol-based hand rub (ABHR) as a complement or alternative to handwashing. There are inconsistent and discordant recommendations for water quality for handwashing, affordable and effective alternatives to soap and ABHR, and the design of handwashing stations. There are gaps in recommendations on soap and water quantity, behaviour change approaches and government measures required for effective hand hygiene. Less than 10% of recommendations are supported by any cited evidence.

CONCLUSION

While current international guidelines consistently recommend handwashing with soap across community settings, there remain gaps in recommendations where clear evidence-based guidance might support more effective policy and investment.

Coexistence of Heavy Metal Tolerance and Antibiotic Resistance in Thermophilic Bacteria Belonging to Genus Geobacillus

Hot springs are thought to be potential repositories for opportunistic infections, such as antibiotic-resistant strains. However, there is a scarcity of information on the mechanisms of antibiotic resistance gene (ARG) uptake, occurrence, and expression in thermophilic bacteria. Furthermore, because the genesis and proliferation of ARGs in environmental microorganisms are unknown, the research on antibiotic resistance profiles and probable mechanisms in thermophilic bacteria will become increasingly important. The goals of this study are to explore bacterial diversity, antibiotic and heavy metal resistance, and the prevalence and presence of ARG and metal resistance gene (MRG) in Geobacillus species. The 16S rRNA sequencing was used to determine the culturable bacterium diversity of 124 isolates. Standard Kirby Bauer Disc Diffusion and tube dilution procedures were used to determine antibiotic sensitivity and minimum inhibitory concentration (MIC). The tube dilution method was also used to check metal tolerance. To detect ARG and heavy MRG (HMRG), whole genome sequencing studies of the type species of the genus Geobacillus and five randomly selected Geobacillus species were performed. Graph Pad Prism and XLSTAT were used to perform statistical analyses such as ANOVA, EC50 analysis, and principal component analysis (PCA). The phylum Firmicutes and the genus Geobacillus dominated the culture-dependent bacterial diversity. Surprisingly, all thermophilic isolates, i.e., Geobacillus species, were sensitive to at least 10 different antibiotics, as evidenced by the lack of ARGs in whole genome sequencing analysis of numerous Geobacillus species. However, some of these isolates were resistant to at least five different heavy metals, and whole genome sequencing revealed the presence of MRGs in these thermophilic bacteria. The thermophilic genus Geobacillus is generally antibiotic sensitive, according to this study. In contrast, heavy metal is tolerated by them. As a result, it is possible that ARGs and MRGs do not coexist in these bacteria living in hot springs.

The Gram-Negative Bacilli Isolated from Caves-Sphingomonas paucimobilis and Hafnia alvei and a Review of Their Involvement in Human Infections

The opportunistic infections with Gram-negative bacilli are frequently reported. The clinical studies are focused on the course of human infectious and very often the source of infection remain unclear. We aim to see if the Gram-negative bacilli isolated from a non-contaminated environment—the caves—are reported in human infections. Eleven samples were collected from six Romanian caves. We used the standard procedure used in our clinical laboratory for bacterial identification and for antibiotic susceptibility testing of the cave isolates. Out of the 14 bacterial strains, three isolates are Gram-negative bacilli—one isolate belong to Hafnia alvei and two strains belong to Sphingomonas paucimobilis. We screened for the published studies—full-text original articles or review articles—that reported human infections with S. paucimobilis and H. alvei. Data sources—PubMed and Cochrane library. We retrieved 447 cases from 49 references—262 cases (58.61%) are S. paucimobilis infections and 185 cases (41.39%) are H. alvei infections. The types of infections are diverse but there are some infections more frequent; there are 116 cases (44.27%) and many infections of the bloodstream with S. paucimobilius (116 cases) and 121 cases (65.41%) are urinary tract infections with H. alvei. The acquired source of the bloodstream infections is reported for 93 of S. paucimobilis bloodstream infections—50 cases (43%) are hospital-acquired, and 40 cases (37%) are community-acquired. Most of the infections are reported in patients with different underlying conditions. There are 80 cases (17.9%) are reported of previously healthy persons. Out of the 72 cases of pediatric infections, 62 cases (86.11%) are caused by S. paucimobilis. There are ten death casualties—three are H. alvei infections, and seven are S. paucimobilis infections.

Mucilaginibacter sp. Strain Metal(loid) and Antibiotic Resistance Isolated from Estuarine Soil Contaminated Mine Tailing from the Fundão Dam

In 2015 a mine dam with Mn-Fe-rich tailings collapsed releasing million tons of sediments over an estuary, in the Southwest of Brazil. The tailings have a high concentration of metals that contaminated soil until the present day. The high contaminant concentrations possibly caused a selection for microorganisms able to strive in such harsh conditions. Here, we isolated metal(loid) and anti-biotic resistance bacteria from the contaminated estuarine soil. After 16S rDNA sequencing to identify the strains, we selected the Mucilaginibacter sp. strain for a whole-genome sequence due to the bioprospective potential of the genus and the high resistance profile. We obtained a complete genome and a genome-guided characterization. Our finding suggests that the 21p strain is possibly a new species of the genus. The species presented genes for resistance for metals (i.e., As, Zn, Co, Cd, and Mn) beyond resistance and cross-resistance for antibiotics (i.e., quinolone, aminoglycoside, β-lactamase, sulphonamide, tetracycline). The Mucilaginibacter sp. 21p description as new species should be further explored, as their extracellular polymeric substances and the potential of this strain as bioremediation and as a growth promoter in high met-al(loid) contaminated soil.

Microbial Abundance and Diversity in Subsurface Lower Oceanic Crust at Atlantis Bank, Southwest Indian Ridge

International Ocean Discovery Program Expedition 360 drilled Hole U1473A at Atlantis Bank, an oceanic core complex on the Southwest Indian Ridge, with the aim of recovering representative samples of the lower oceanic crust. Recovered cores were primarily gabbro and olivine gabbro. These mineralogies may host serpentinization reactions that have the potential to support microbial life within the recovered rocks or at greater depths beneath Atlantis Bank. We quantified prokaryotic cells and analyzed microbial community composition for rock samples obtained from Hole U1473A and conducted nutrient addition experiments to assess if nutrient supply influences the composition of microbial communities. Microbial abundance was low (≤10⁴ cells cm^-3) but positively correlated with the presence of veins in rocks within some depth ranges. Due to the heterogeneous nature of the rocks downhole (alternating stretches of relatively unaltered gabbros and more significantly altered and fractured rocks), the strength of the positive correlations between rock characteristics and microbial abundances was weaker when all depths were considered. Microbial community diversity varied at each depth analyzed. Surprisingly, addition of simple organic acids, ammonium, phosphate, or ammonium plus phosphate in nutrient addition experiments did not affect microbial diversity or methane production in nutrient addition incubation cultures over 60 weeks. The work presented here from Site U1473A, which is representative of basement rock samples at ultraslow spreading ridges and the usually inaccessible lower oceanic crust, increases our understanding of microbial life present in this rarely studied environment and provides an analog for basement below ocean world systems such as Enceladus. IMPORTANCE The lower oceanic crust below the seafloor is one of the most poorly explored habitats on Earth. The rocks from the Southwest Indian Ridge (SWIR) are similar to rock environments on other ocean-bearing planets and moons. Studying this environment helps us increase our understanding of life in other subsurface rocky environments in our solar system that we do not yet have the capability to access. During an expedition to the SWIR, we drilled 780 m into lower oceanic crust and collected over 50 rock samples to count the number of resident microbes and determine who they are. We also selected some of these rocks for an experiment where we provided them with different nutrients to explore energy and carbon sources preferred for growth. We found that the number of resident microbes and community structure varied with depth. Additionally, added nutrients did not shape the microbial diversity in a predictable manner.

Medication adherence, self-efficacy and health literacy among patients with glaucoma: a mixed-methods study protocol

INTRODUCTION

As the world population ages, glaucoma is becoming an increasingly significant cause of blindness. A key component in the management of glaucoma is the use of prescribed medications and the adherence to treatment. However, there is evidence of low adherence to prescribed medication in chronic diseases, such as glaucoma. This study aims to explore the level of medication adherence, self-efficacy, social support and health literacy among the patients with glaucoma and to determine if there are any correlations between them. The ultimate aim is to use the information to develop an educational programme for patients with glaucoma at a later stage.

METHODS AND ANALYSIS

This is a mixed-methods study which includes two stages: a descriptive study (stage 1) and focus group discussions (stage 2).

SAMPLE

Patients with glaucoma or ocular hypertension, using at least one kind of drops, from two ophthalmology clinics. Selected measures include: The Glaucoma Treatment Compliance Assessment Tool, The European Health Literacy Survey Questionnaire, The Glaucoma Medication Self-Efficacy Questionnaire and The Multidimensional Scale of Perceived Social Support. Two focus groups will be used for the collection of qualitative data, aiming to enrich the study with the patients' experiences. The data will be analysed with SPSS, using descriptive and inferential statistics for stage 1 whereas content analysis will be used for the data from the focus group discussions (stage 2).

ETHICS AND DISSEMINATION

Permission to conduct the study was received from the National Bioethics Committee and the board of management of the two ophthalmology clinics. All participants will be informed fully on the purpose and methods of the study. Consent forms will be signed and at any time participants will have the right to withdraw. Confidentiality and the protection of data will be respected at all times.

Visual impairment and social isolation, depression and life satisfaction among older adults in Ghana: analysis of the WHO's Study on global AGEing and adult health (SAGE) Wave 2

AIM

To estimate the prevalence of visual impairment (VI) and associated factors and further quantify its association with social isolation, depression and life satisfaction among older adults in Ghana.

METHODS

WHO Study on Global AGEing and Adult Health Ghana dataset for older adults 50 years and above was used for this study. Social isolation, depression and life satisfaction were our primary outcomes with VI being our secondary outcome. We employed negative binomial, Poisson and generalised negative binomial regression models individually modified with Coarsened Exact Matching method of analysis. All analysis was performed by adopting robust SE estimation using Stata V.15.

RESULTS

The prevalence of VI was 17.1% (95% CI14.3 to 20.2) and the factors associated include age groups, educational level, religion, region, where the participant was born, and difficulty in work/households activity (p<0.05). The inferential analysis shows that the significant log-likelihood score of social isolation and life satisfaction for older adults with VI was 0.25 more (95% CI 0.03 to 0.47) and 0.04 less (95% CI -0.08 to -0.01), respectively, compared with those without VI. The prevalence of depression among older adults with VI was significantly 90% higher compared with non-VI (adjusted prevalence ratio (95% CI) = 1.90 (1.17 to 3.09), p<0.001).

CONCLUSION

The prevalence of VI is associated with increasing age, educational level and self-rated health. VI was identified to be associated with social isolation, depression and diminishing life satisfaction. In order to achieve sustainable development goal #3, a national focus on geriatric care as part of the implementation of the National Ageing Policy will garner improvement in the quality of life of older adults with visual VI in Ghana. Eye health practitioners at all levels of the health systems should consider the psychosocial consequences of VI for the optimum care of the older adult client.

Subchronic oral mercury caused intestinal injury and changed gut microbiota in mice

Mercury is a key global pollutant, yet the mechanism by which mercury-exposure causes intestinal injury is not clear, we aimed to investigate the mechanism of intestinal injury and gut microbiota changes caused by mercury-exposure. Twelve Kunming mice were divided into two groups (n = 6), and the two groups were treated with 0 mg/L and 80 mg/L HgCl₂ in drinking water for 90 days respectively. Our results showed that mercury-exposure prominently effected body weight gain and glucose levels. The mercury-exposed mice showed intestinal injury, which was diagnosed by Histopathological Examination and Transmission Electron Microscopy. Meanwhile, RT-PCR indicated that mercury-exposure significantly increased the expression of pro-apoptotic genes including Bax, JNK, ASK1, caspase3 and TNF-α, and significantly decreased the expression of the anti-apoptotic gene Bcl-2. Furthermore, high-throughput sequencing analysis showed that at the genus level some microbial populations including Coprococcus, Oscillospira and Helicobacter were significantly increased whereas some microbial populations including Lgnatzschineria, Salinicoccus and Bacillus were significantly decreased. Moreover, PICRUSt analysis revealed potential metabolic changes. Correlation analysis indicated that microorganisms were significantly correlated with apoptotic gene expression. In summary, our results indicated that mercury-exposure affected the growth and development of mice, induced intestinal microbiota dysbiosis and metabolic disorder, and aggravated apoptosis in mice.

Diversity analysis and metagenomic insights into antibiotic and metal resistance among Himalayan hot spring bacteriobiome insinuating inherent environmental baseline levels of antibiotic and metal tolerance

OBJECTIVES

Mechanisms of occurrence and expression of antibiotic resistance genes (ARGs) in thermophilic bacteria are still unknown owing to limited research and data. In this research, comparative profiling of ARGs and metal tolerance genes among thermophilic bacteria has been done by functional metagenomic methods.

METHODS

Shotgun metagenomic sequence data were generated using Illumina HiSeq 4000. Putative ARGs from the PROKKA predicted genes were identified with the ardbAnno V.1.0 script available from the ARDB (Antibiotic Resistance Genes Database) consortium using the non-redundant resistance genes as a reference. Putative metal resistance genes (MRGs) were identified by using BacMetScan V.1.0. The whole-genome sequencing for bacterial isolates was performed using Illumina HiSeq 4000 sequencing technology with a paired-end sequencing module.

RESULTS

Metagenomic analysis showed the dominance of Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes in two hot springs of Sikkim. ARG analysis through shotgun gene sequencing was found to be negative in the case of thermophilic bacteria. However, few genes were detected but they showed maximum similarity with mesophilic bacteria. Concurrently, MRGs were also detected in the metagenome sequence of isolates from hot springs. Detection of MRGs and absence of ARGs investigated by whole-genome sequencing in the reference genome sequence of thermophilic Geobacillus also conveyed the same message.

CONCLUSION

The study of ARGs and MRGs (Heavy metal resistance gene) among culturable and non-culturable bacteria from the hot springs of Sikkim via metagenomics showed a preferential selection of MRGs over ARGs. The absence of ARGs also does not support the co-selection of ARGs and MRGs in these environments. This evolutionary selection of metal resistance over antibiotic genes may have been necessary to survive in the geological craters which have an abundance of different metals from earth sediments rather than antibiotics. Furthermore, the selection could be environment driven depending on the susceptibility of ARGs in a thermophilic environments as it reduces the chances of horizontal gene transfer.

Bacteria From the Multi-Contaminated Tinto River Estuary (SW, Spain) Show High Multi-Resistance to Antibiotics and Point to Paenibacillus spp. as Antibiotic-Resistance-Dissemination Players

Bacterial resistance to antibiotics is an ever-increasing phenomenon that, besides clinical settings, is generally assumed to be prevalent in environmental soils and waters. The analysis of bacteria resistant to each one of 11 antibiotics in waters and sediments of the Huelva’s estuary, a multi-contaminated environment, showed high levels of bacteria resistant mainly to Tm, among others. To further gain knowledge on the fate of multi-drug resistance (MDR) in environmental bacteria, 579 ampicillin-resistant bacteria were isolated tested for resistance to 10 antibiotics. 92.7% of the isolates were resistant to four or more antibiotic classes, indicating a high level of multi-resistance. 143 resistance profiles were found. The isolates with different MDR profiles and/or colony morphologies were phylogenetically ascribed based on 16S rDNA to phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, including 48 genera. Putative intrinsic resistance was detected in different phylogenetic groups including genera Altererythrobacter, Bacillus, Brevundimonas, Erythrobacter, Mesonia, Ochrobactrum, and Ponticaulis. Correlation of the presence of pairs of the non-intrinsic-resistances in phylogenetic groups based on the kappa index (κ) highlighted the co-habitation of some of the tested pairs at different phylogenetic levels. Maximum correlation (κ = 1.000) was found for pairs Cz^R/Tc^R in Betaproteobacteria, and Cc^R/Tc^R and Em^R/Sm^R in Sphingobacteriia at the class level, while at the genus level, was found for Cc^R/Tc^R and Nx^R/Tm^R in Mesonia, Cz^R/Tm^R and Em^R/Km^R in Paenibacillus, and Cc^R/Em^R and Rp^R/Tc^R in Pseudomonas. These results could suggest the existence of intra-class and intra-genus-transmissible genetic elements containing determinants for both members of each pair. Network analysis based on κ values higher than 0.4 indicated the sharing of paired resistances among several genera, many of them centered on the Paenibacillus node and raising the hypothesis of inter-genera transmission of resistances interconnected through members of this genus. This is the first time that a possible hotspot of resistance interchange in a particular environment may have been detected, opening up the possibility that one, or a few, bacterial members of the community could be important promoters of antibiotic resistance (AR) dissemination in this environment’s bacterial population. Further studies using the available isolates will likely give insights of the possible mechanisms and genetic elements involved.

Relationships Between Copper-Related Proteomes and Lifestyles in β Proteobacteria

Copper is an essential transition metal whose redox properties are used for a variety of enzymatic oxido-reductions and in electron transfer chains. It is also toxic to living beings, and therefore its cellular concentration must be strictly controlled. We have performed in silico analyses of the predicted proteomes of more than one hundred species of β proteobacteria to characterize their copper-related proteomes, including cuproproteins, i.e., proteins with active-site copper ions, copper chaperones, and copper-homeostasis systems. Copper-related proteomes represent between 0 and 1.48% of the total proteomes of β proteobacteria. The numbers of cuproproteins are globally proportional to the proteome sizes in all phylogenetic groups and strongly linked to aerobic respiration. In contrast, environmental bacteria have considerably larger proportions of copper-homeostasis systems than the other groups of bacteria, irrespective of their proteome sizes. Evolution toward commensalism, obligate, host-restricted pathogenesis or symbiosis is globally reflected in the loss of copper-homeostasis systems. In endosymbionts, defense systems and copper chaperones have disappeared, whereas residual cuproenzymes are electron transfer proteins for aerobic respiration. Lifestyle is thus a major determinant of the size and composition of the copper-related proteome, and it is particularly reflected in systems involved in copper homeostasis. Analyses of the copper-related proteomes of a number of species belonging to the Burkholderia, Bordetella, and Neisseria genera indicates that commensals are in the process of shedding their copper-homeostasis systems and chaperones to greater extents yet than pathogens.

Antibiotic resistance and heavy metal tolerance in cultured bacteria from hot springs as indicators of environmental intrinsic resistance and tolerance levels

Antibiotic resistance (AR) in the environment is a growing and global concern for public health, and intrinsic AR from pristine sites untouched by pharmaceutical antibiotics is not commonly studied. Forty aerobic bacteria were isolated from water and sediment samples of hot springs in South Africa. Resistance against ten antibiotics (carbenicillin, gentamicin, kanamycin, streptomycin, tetracycline, chloramphenicol, ceftriaxone, co-trimoxazole, nalidixic acid and norfloxacin) was tested using a standard disk diffusion assay. Resistance to one or two antibiotics were equally found in 37.5%, while the remaining 22% showed complete sensitivity. Intermediate resistance was found for ceftriaxone (52.5%), nalidixic acid (37.5%) and carbenicillin (22.5%), while low levels of resistance were observed for streptomycin (5%) and kanamycin (2.5%), and total sensitivity towards the other antibiotics. Twenty-nine isolates were also tested against eight different heavy-metal salts (Al, Cr, Cu, Fe, Hg, Mn, Ni and Pb) at 10 and 40 mM. All isolates were tolerant and able to grow on ≥2 heavy-metal salts at both concentrations. No association was observed between AR and heavy metal tolerance (HMT). Based on the relatively low AR levels, hot spring sites are pristine environments reflecting baseline levels for comparison to other potentially contaminated groundwater sites.

Microbial life beyond the grave: 16S rRNA gene-based metagenomic analysis of bacteria diversity and their functional profiles in cemetery environments

Recent studies have identified cemeteries as potential environmental reservoirs of multi-drug resistant pathogenic bacteria that could contaminate groundwater sources posing public health threats. However, these findings were based on the identification of culturable bacteria and at times not below burial grounds. Investigation on the bacterial diversity and functional profiles of bacterial communities above and below burial grounds in human cemeteries are few. The current study used high-throughput sequencing techniques to determine the bacterial composition and their associated functional profiles in cemetery soil samples collected at the surface and below burial ground in two South African cemeteries (Maitland Cemetery in Cape Town and Fontein Street Cemetery in Middelburg) to evaluate the potential health threat to surrounding populations through contamination of groundwater. Significant differences were observed between sample depths with the clustering of the surface (0 m) and the 2 m samples into separate groups. Pseudomonas and Corynebacterium were the most abundant genera across all samples. Pseudomonas and Rhodococcus were the dominant genera in the 2 m samples while Prauserella and Staphylococcus were dominant in the surface samples. The 2 m samples showed a lower alpha diversity but recorded higher proportions of human diseases functional classes compared to the surface samples. Human disease functional profiles revealed involvement, in infectious (cholera), neurodegenerative (Alzheimer's disease) cardiovascular (hypertrophic cardiomyopathy) immune system (Systemic lupus erythematosus) metabolic (Type I & II diabetes) diseases and cancer. Antibiotic resistance and antibiotics synthesis signatures were also identified. Thus, cemeteries could be potential sources of microbial and antibiotic pollution in groundwater, especially in areas with shallow water tables such as Maitland. Selection of sites for use as cemeteries should, therefore, require a proper understanding of the hydrogeological characteristics of the selected site. However, further studies are required to trace the actual movement of these pollutants into groundwater resources.

Environmental strains potentially contribute to the proliferation and maintenance of antibiotic resistance in drinking water: A case study of Cupriavidus metallidurans

Fitness costs of antibiotic resistance detrimentally affect the fate of resistance carriers. Intriguingly, numerous antibiotic resistant bacteria (ARB) have been detected despite the low concentration of antibiotics in drinking water. To reveal the causes of this discrepancy, we investigated the fitness cost of antimicrobial resistance in strain Cupriavidus metallidurans CR2 which was isolated from a drinking water filter. Pure culture and 1:1 competitive experiments were established at different nutrient levels. The growth rates of strain C. metallidurans CR2 significantly decreased when pure cultured under poor nutrient conditions, however, the multi-resistance and the resistance megaplasmids were well maintained. Competitiveness costs were observed in C. metallidurans when separately co-cultured with environmentally-isolated Flectobacillus BS1 and Pseudomonas sp. S3, while C. metallidurans was outnumbered by the rivals with a decrease of 1-2 logs. But the majority of C. metallidurans retained the plasmids under oligotrophic conditions even after 144 h (1.99 and 0.199 mg C/L). Additionally, C. metallidurans CR2 has a higher tolerance to chlorine and chloramine, which potentially could become prevalent in the subsequent distribution systems other than drinking water treatment plant. As a potential pathogen, the prevalence of Cupriavidus metallidurans in drinking water would also pose certain threats to human health.

Screening of potential bioremediation enzymes from hot spring bacteria using conventional plate assays and liquid chromatography - Tandem mass spectrometry (Lc-Ms/Ms)

The search for an eco-friendly, non-toxic, economical and efficient means of cleaning water through bioremediation is not only more favourable but critical to maintaining water quality globally especially in water-scarce countries. Thermophilic bacteria including Bacillus species are an important source of novel enzymes for biotechnology applications. In this study, 56 bacterial isolates which were cultured from five hot springs in South Africa were identified predominantly as Bacillus sp. or Bacillus-related spp by 16S rDNA gene sequencing. These isolates were screened for potentially useful enzymes for water bioremediation. Using conventional agar plate assays, 56% (n = 43), 68% (n = 38) and 16% (n = 31) were positive for amylase, protease and bromothymol blue decolorisation respectively. In liquid starch culture, three amylase-positive isolates differentially degraded starch by 34% (isolate 20S) to 98% (isolate 9T). Phenol degradation revealed that five out of thirty reduced phenol up to 42% by colorimetric assay. A thermophilic strain of Anoxybacillus rupiensis 19S (optimal growth temperature of 50 °C), which degraded starch, protein and phenol, was selected for further analysis by tandem LC-MS/MS. This newer technique identified potential enzymes for water bioremediation relating to pollutants from the food industry (amylase, proteases), polyaromatic hydrocarbons and dye pollutants (catalase peroxidase, superoxide dismutase, azoreductase, quinone oxidoreductase), antibiotic residues (ribonucleases), solubilisation of phosphates (inorganic pyrophosphatase) and reduction of chromate and lead. In addition, potential enzymes for biomonitoring of environmental pollutants were also identified. Specifically, dehydrogenases were found to decrease as the level of inorganic heavy metals and petroleum increased in soil samples. This study concludes that bacteria found in South African hot springs are a potential source of novel enzymes with tandem LC-MS/MS revealing substantially more information compared with conventional assays, which can be used for various applications of water bioremediation.

Reconstituting the History of Cronobacter Evolution Driven by Differentiated CRISPR Activity

Cronobacter strains harboring the CRISPR-Cas system are important foodborne pathogens causing serious neonatal infections. However, the specific role of the CRISPR-Cas system in bacterial evolution remains relatively unexplored. In this study, we investigated the impact of the CRISPR-Cas system on Cronobacter evolution and obtained 137 new whole-genome Cronobacter sequences by next-generation sequencing technology. Among the strains examined (n = 240), 90.6% (193/213) of prevalent species Cronobacter sakazakii, Cronobactermalonaticus, and Cronobacterdublinensis strains had intact CRISPR-Cas systems. Two rare species, Cronobactercondimenti (n = 2) and Cronobacteruniversalis (n = 6), lacked and preserved the CRISPR-Cas system at a low frequency (1/6), respectively. These results suggest that the presence of one CRISPR-Cas system is important for a Cronobacter species to maintain genome homeostasis for survival. The Cronobacter ancestral strain is likely to have harbored both subtype I-E and I-F CRISPR-Cas systems; during the long evolutionary process, subtype I-E was retained while subtype I-F selectively degenerated in Cronobacter species and was even lost by the major Cronobacter pathovars. Moreover, significantly higher CRISPR activity was observed in the plant-associated species Cdublinensis than in the virulence-related species C. sakazakii and Cmalonaticus Similar spacers of CRISPR arrays were rarely found among species, suggesting intensive change through adaptive acquisition and loss. Differentiated CRISPR activity appears to be the product of environmental selective pressure and might contribute to the bidirectional divergence and speciation of CronobacterIMPORTANCE This study reports the evolutionary history of Cronobacter under the selective pressure of the CRISPR-Cas system. One CRISPR-Cas system in Cronobacter is important for maintaining genome homeostasis, whereas two types of systems may be redundant and not conducive to acquiring beneficial DNA for environmental adaptation and pathogenicity. Differentiated CRISPR activity has contributed to the bidirectional divergence and genetic diversity of Cronobacter This perspective makes a significant contribution to the literature by providing new insights into CRISPR-Cas systems in general, while further expanding the roles of CRISPR beyond conferring adaptive immunity and demonstrating a link to adaptation and species divergence in a genus. Moreover, our study provides new insights into the balance between genome homeostasis and the uptake of beneficial DNA related to CRISPR-based activity in the evolution of Cronobacter.