Genotypic diversity and antibiotic resistance in Sphingomonadaceae isolated from hospital tap water

Trace Element Exposure during Pregnancy Has a Persistent Influence on Perinatal Gut Microbiota in Mother-Infant Dyads

Trace elements have been recognized as the modifiers of the gut microbiota. However, population-based evidence about their effects on maternal gut microbiota dynamics, as well as the intergenerational impacts on neonatal gut microbiota, has been lacking. We examined the longitudinal microbiota data from mother-infant dyads and demonstrated that maternal trace element exposure played a pivotal role in shaping the composition and similarity of the mother-infant gut microbiota. Specifically, serum levels of cobalt (Co), molybdenum (Mo), and rubidium (Rb) were identified to cause further fluctuation in the shift of the maternal gut microbiota. Antibiotic usage shortly before or on the delivery day, as well as maternal zinc (Zn) exposure, affected the gut microbiota similarity within mother-infant dyads. Rb demonstrated an intergenerational effect on meconium Bifidobacterium abundance by altering its abundance in the maternal gut. Notably, this effect was strengthened in the vaginal delivery group without antibiotic usage, while it was attenuated in the c-section delivery group. Our results suggest that maternal trace element exposure has a persistent influence on perinatal gut microbiota, which offers novel insights into promoting mother and infant health.

Effects of tea polyphenols disinfectant on microbial communities and potential pathogenic bacteria in water

The structural and abundance changes in water disinfected by tea polyphenols were investigated in high-abundance microbial communities (HAMC), medium-abundance microbial communities (MAMC), and low-abundance microbial communities (LAMC), also included the interactions within and between these communities. The antibacterial effect of tea polyphenols was observed at concentrations of 20-300 mg/L. If the tea polyphenols concentration is greater than or equal to 200 mg/L, it can continue to inhibit the growth of bacteria, and keep the total number of bacteria in 48 hours no more than100 CFU/ml, and this reflected the continuity of tea polyphenols disinfectant in the pipe network. The relative abundance of some chlorine-resistant bacteria such as Blastomonas, Sphingomonas and Pseudomonas decreased significantly after disinfection with tea polyphenols, which indicates that tea polyphenols have the advantage of removing some chlorine-resistant bacteria. Samples of HAMC, MAMC and LAMC showed similar structure. Co-occurrence network analysis within microbial communities revealed the most complex interrelationships in HAMC. Co-occurrence network analysis between microbial communities showed that HAMC and MAMC were most closely related. In the co-occurrence network, 8 key bacteria genera were identified, in which 5 key genera belonged to medium-abundance and low-abundance. Potential pathogens were identified in the study and potential pathogens were Aerococcus and Staphylococcus were pointed out after tea polyphenols disinfection as the key potential pathogen genera by co-occurrence network analysis. The co-occurrence relationship between these key potential pathogens and other potential pathogens indicates that water quality safety can be controlled by the number of key potential pathogens.

Insight into the microbial community of denitrification process using different solid carbon sources: Not only bacteria

There is a lack of understanding about the bacterial, fungal and archaeal communities' composition of solid-phase denitrification (SPD) systems. We investigated four SPD systems with different carbon sources by analyzing microbial gene sequences based on operational taxonomic unit (OTU) and amplicon sequence variant (ASV). The results showed that the corncob-polyvinyl alcohol sodium alginate-polycaprolactone (CPSP, 0.86±0.04 mg NO3--N/(g·day)) and corncob (0.85±0.06 mg NO3--N/(g·day)) had better denitrification efficiency than polycaprolactone (PCL, 0.29±0.11 mg NO3--N/(g·day)) and polyvinyl alcohol-sodium alginate (PVA-SA, 0.24±0.07 mg NO3--N/(g·day)). The bacterial, fungal and archaeal microbial composition was significantly different among carbon source types such as Proteobacteria in PCL (OTU: 83.72%, ASV: 82.49%) and Rozellomycota in PVA-SA (OTU: 71.99%, ASV: 81.30%). ASV methods can read more microbial units than that of OTU and exhibit higher alpha diversity and classify some species that had not been identified by OTU such as Nanoarchaeota phylum, unclassified_ f_ Xanthobacteraceae genus, etc., indicating ASV may be more conducive to understand SPD microbial communities. The co-occurring network showed some correlation between the bacteria fungi and archaea species, indicating different species may collaborate in SPD systems. Similar KEGG function prediction results were obtained in two bioinformatic methods generally and some fungi and archaea functions should not be ignored in SPD systems. These results may be beneficial for understanding microbial communities in SPD systems.

Bacterial community assessment of drinking water and downstream distribution systems in highland localities of Ecuador

Bacterial communities in drinking water provide a gauge to measure quality and confer insights into public health. In contrast to urban systems, water treatment in rural areas is not adequately monitored and could become a health risk. We performed 16S rRNA amplicon sequencing to analyze the microbiome present in the water treatment plants at two rural communities, one city, and the downstream water for human consumption in schools and reservoirs in the Andean highlands of Ecuador. We tested the effect of water treatment on the diversity and composition of bacterial communities. A set of physicochemical variables in the sampled water was evaluated and correlated with the structure of the observed bacterial communities. Predominant bacteria in the analyzed communities belonged to Proteobacteria and Actinobacteria. The Sphingobium genus, a chlorine resistance group, was particularly abundant. Of health concern in drinking water reservoirs were Fusobacteriaceae, Lachnospiraceae, and Ruminococcaceae; these families are associated with human and poultry fecal contamination. We propose the latter families as relevant biomarkers for establishing local standards for the monitoring of potable water systems in highlands of Ecuador. Our assessment of bacterial community composition in water systems in the Ecuadorian highlands provides a technical background to inform management decisions.

Incidence of co-resistance to antibiotics and chlorine in bacterial biofilm of hospital water systems: Insights into the risk of nosocomial infections

The presence of biofilms in drinking water distribution systems (DWDS) in healthcare settings poses a considerable risk to the biological security of water, particularly when the biofilm bacteria demonstrate antimicrobial resistance characteristics. This study aimed to investigate the occurrence of antibiotic-resistant bacteria (ARB) in biofilms within DWDS of hospitals. The chlorine resistance of the isolated ARB was analyzed, and then chlorine-resistant bacteria (CRB) were identified using molecular methods. Additionally, the presence of several antibiotic resistance genes (ARGs) was monitored in the isolated ARB. Out of the 41 biofilm samples collected from hospitals, ARB were detected in 32 (78%) of the samples. A total of 109 colonies of ARB were isolated from DWDS of hospitals, with β-lactam resistant bacteria, including ceftazidime-resistant and ampicillin-resistant bacteria, being the most frequently isolated ARB. Analyzing of ARGs revealed the highest detection of aac6, followed by sul1 gene. However, the β-lactamase genes blaCTX-M and blaTEM were not identified in the ARB, suggesting the presence of other β-lactamase genes not included in the tested panel. Exposure of ARB to free chlorine at a concentration of 0.5 mg/l showed that 64% of the isolates were CRB. However, increasing the chlorine concentration to 4 mg/l decreased the high fraction of ARB (91%). The domi‌‌nant CRB identified were Sphingomonas, Brevundimonas, Stenotrophomonas, Bacillus and Staphylococcus with Bacillus exhibiting the highest frequency. The results highlight the potential risk of biofilm formation in the DWDS of hospitals, leading to the dissemination of ARB in hospital environments, which is a great concern for the health of hospitalized patients, especially vulnerable individuals. Surveillance of antimicrobial resistance in DWDS of hospitals can provide valuable insights for shaping antimicrobial use policies and practices that ensure their efficacy.

The composition of planktonic prokaryotic communities in a hospital building water system depends on both incoming water and flow dynamics

In recent years, the frequency of nosocomial infections has increased. Hospital water systems support the growth of microbes, especially opportunistic premise plumbing pathogens. In this study, planktonic prokaryotic communities present in water samples taken from hospital showers and hand basins, collected over three different sampling phases, were characterized by 16S rRNA gene amplicon sequencing. Significant differences in the abundance of various prokaryotic taxa were found through univariate and multivariate analysis. Overall, the prokaryotic communities of hospital water were taxonomically diverse and dominated by biofilm forming, corrosion causing, and potentially pathogenic bacteria. The phyla Proteobacteria, Actinobacteriota, Bacteroidota, Planctomycetota, Firmicutes, and Cyanobacteria made up 96% of the relative abundance. The α-diversity measurements of prokaryotic communities showed no difference in taxa evenness and richness based on sampling sites (shower or hand basins), sampling phases (months), and presence or absence of Vermamoeba vermiformis. However, β-diversity measurements showed significant clustering of prokaryotic communities based on sampling phases, with the greatest difference observed between the samples collected in phase 1 vs phase 2/3. Importantly, significant difference was observed in prokaryotic communities based on flow dynamics of the incoming water. The Pielou's evenness diversity index revealed a significant difference (Kruskal Wallis, p < 0.05) and showed higher species richness in low flow regime (< 13 minutes water flushing per week and ≤ 765 flushing events per six months). Similarly, Bray-Curtis dissimilarity index found significant differences (PERMANOVA, p < 0.05) in the prokaryotic communities of low vs medium/high flow regimes. Furthermore, linear discriminant analysis effect size showed that several biofilm forming (e.g., Pseudomonadales), corrosion causing (e.g., Desulfobacterales), extremely environmental stress resistant (e.g., Deinococcales), and potentially pathogenic (e.g., Pseudomonas) bacterial taxa were in higher amounts under low flow regime conditions. This study demonstrated that a hospital building water system consists of a complex microbiome that is shaped by incoming water quality and the building flow dynamics arising through usage.

Profile and actual transmissibility of Carbapenem resistance genes: Intracellular and extracellular DNA in hospital wastewater

The current worldwide spread of carbapenem resistance genes (CRGs) has posed a major public health threat, which continues to grow in severity. Hospital wastewaters (HWWs) are major reservoirs for antibiotic resistance genes, while resistomes in HWWs are still poorly characterized when it comes to CRGs. We comprehensively characterized the profile and actual transmissibility of extracellular CRGs (eCRGs) and intracellular CRGs (iCRGs) in HWWs for the first time. In this study, CRGs showed similar relative abundance in treated and untreated HWWs. Meanwhile, HWWs treatments led to the enrichment of bla_IMP-8, probably attributed to the promotion of Novosphingobium and Prosthecobacter after treatment. To evaluate the transmission potential of CRGs, extracellular and intracellular carbapenem-resistant plasmids were captured from HWWs by transformation and conjugation, respectively. We found an interesting phenomenon regarding the transmission characteristics of CRGs: bla_KPC-carrying plasmids could only be captured by transformation, while bla_NDM-carrying plasmids were captured by conjugation. Further experiments showed that HWW treatments increased the conjugation ability of bla_NDM. In conclusion, our study demonstrated that HWWs are significant reservoirs of CRGs and various CRGs exhibit different modes of transmission in HWWs. CRGs cannot be removed by membrane bioreactor and chlorine disinfection. An urgent need is to develop more efficient wastewater treatments to limit CRG dissemination.

Distinct Microbial Community of Accumulated Biofilm in Dental Unit Waterlines of Different Specialties

The contamination of dental unit waterlines (DUWLs) is a serious problem and directly affects the dental care. This study aims to explore the microbial community of biofilm in DUWL from different specialties and investigate the associated factors. A total of 36 biofilm samples from 18 DUWL of six specialties (i.e., prosthodontics, orthodontics, pediatrics, endodontics, oral surgery, and periodontics) at two time points (i.e., before and after daily dental practice) were collected with a novel method. Genomic DNA of samples was extracted, and then 16S ribosomal DNA (rDNA) (V3–V4 regions) and ITS2 gene were amplified and sequenced. Kruskal–Wallis and Wilcoxon rank test were adopted for statistical analysis. Microbial community with high diversity of bacteria (631 genera), fungi (193 genera), and viridiplantae was detected in the biofilm samples. Proteobacteria was the dominant bacteria (representing over 65.74–95.98% of the total sequences), and the dominant fungi was Ascomycota (93.9–99.3%). Microorganisms belonging to multiple genera involved in human diseases were detected including 25 genera of bacteria and eight genera of fungi, with relative abundance of six genera over 1% (i.e., Acinetobacter, Pseudomonas, Enterobacter, Aspergillus, Candida, and Penicillium). The biofilm microbiome may be influenced by the characteristics of dental specialty and routine work to some extent. The age of dental chair unit and overall number of patients had the strongest impact on the overall bacteria composition, and the effect of daily dental practices (associated with number of patients and dental specialty) on the fungi composition was the greatest. For the first time, biofilm in DUWL related to dental specialty was comprehensively evaluated, with more abundance of bacterial and fungal communities than in water samples. Biofilm accumulation with daily work and multiple kinds of opportunistic pathogen emphasized the infectious risk with dental care and the importance of biofilm control.

Antibiotic and Disinfectant Resistance in Tap Water Strains - Insight into the Resistance of Environmental Bacteria

Although antibiotic-resistant bacteria (ARB) have been isolated from tap water worldwide, the knowledge of their resistance patterns is still scarce. Both horizontal and vertical gene transfer has been suggested to contribute to the resistance spread among tap water bacteria. In this study, ARB were isolated from finished water collected at two independent water treatment plants (WTPs) and tap water collected at several point-of-use taps during summer and winter sampling campaigns. A total of 24 strains were identified to genus or species level and subjected to antibiotic and disinfectant susceptibility testing. The investigated tap water ARB belonged to phyla Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes. The majority of the isolates proved multidrug resistant and resistant to chemical disinfectant. Neither seasonal nor WTP-dependent variabilities in antibiotic or disinfectant resistance were found. Antibiotics most effective against the investigated isolates included imipenem, tetracyclines, erythromycin, and least effective - aztreonam, cefotaxime, amoxicillin, and ceftazidime. The most resistant strains originate from Afipia sp. and Methylobacterium sp. Comparing resistance patterns of isolated tap water ARB with literature reports concerning the same genera or species confirms intra-genus or even intra-specific variabilities of environmental bacteria. Neither species-specific nor acquired resistance can be excluded.

Spatiotemporal Changes of Antibiotic Resistance and Bacterial Communities in Drinking Water Distribution System in Wrocław, Poland

Antibiotic resistance of bacteria is an emerging problem in drinking water treatment. This paper presents the comparison of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) prevalence during the summer and winter season in a full-scale drinking water distribution system (DWDS) supplied by two water treatment plants (WTPs). The effect of distance from WTP and physical–chemical water parameters on its microbial properties was also tested. Bacterial consortia dwelling in bulk tap water were additionally compared by means of denaturating gradient gel electrophoresis (DGGE). The results showed that among ARB, bacteria resistant to ceftazidime (CAZ) were the most abundant, followed by bacteria resistant to amoxicillin (AML), ciprofloxacin (CIP), and tetracycline (TE). Numerous ARGs were detected in tested tap water samples. Only CAZ resistant bacteria were more prevalent in the season of increased antibiotic consumption, and only AML resistant bacteria relative abundances increase was statistically significant with the distance from a WTP. The investigated tap water meets all legal requirements. It is therefore safe to drink according to the law. Nevertheless, because antibiotic resistance could pose a threat to consumer health, it should be further monitored in DWDSs.

Water as a Source of Antimicrobial Resistance and Healthcare-Associated Infections

Healthcare-associated infections (HAIs) are one of the most common patient complications, affecting 7% of patients in developed countries each year. The rise of antimicrobial resistant (AMR) bacteria has been identified as one of the biggest global health challenges, resulting in an estimated 23,000 deaths in the US annually. Environmental reservoirs for AMR bacteria such as bed rails, light switches and doorknobs have been identified in the past and addressed with infection prevention guidelines. However, water and water-related devices are often overlooked as potential sources of HAI outbreaks. This systematic review examines the role of water and water-related devices in the transmission of AMR bacteria responsible for HAIs, discussing common waterborne devices, pathogens, and surveillance strategies. AMR strains of previously described waterborne pathogens including Pseudomonas aeruginosa, Mycobacterium spp., and Legionella spp. were commonly isolated. However, methicillin-resistant Staphylococcus aureus and carbapenem-resistant Enterobacteriaceae that are not typically associated with water were also isolated. Biofilms were identified as a hot spot for the dissemination of genes responsible for survival functions. A limitation identified was a lack of consistency between environmental screening scope, isolation methodology, and antimicrobial resistance characterization. Broad universal environmental surveillance guidelines must be developed and adopted to monitor AMR pathogens, allowing prediction of future threats before waterborne infection outbreaks occur.

Effects of industrial effluents containing moderate levels of antibiotic mixtures on the abundance of antibiotic resistance genes and bacterial community composition in exposed creek sediments

Environmental discharges of very high (mg/L) antibiotic levels from pharmaceutical production contributed to the selection, spread and persistence of antibiotic resistance. However, the effects of less antibiotic-polluted effluents (μg/L) from drug-formulation on exposed aquatic microbial communities are still scarce. Here we analyzed formulation effluents and sediments from the receiving creek collected at the discharge site (DW0), upstream (UP) and 3000 m downstream of discharge (DW3000) during winter and summer season. Chemical analyses indicated the largest amounts of trimethoprim (up to 5.08 mg/kg) and azithromycin (up to 0.39 mg/kg) at DW0, but sulfonamides accumulated at DW3000 (total up to 1.17 mg/kg). Quantitative PCR revealed significantly increased relative abundance of various antibiotic resistance genes (ARGs) against β-lactams, macrolides, sulfonamides, trimethoprim and tetracyclines in sediments from DW0, despite relatively high background levels of some ARGs already at UP site. However, only sulfonamide (sul2) and macrolide ARG subtypes (mphG and msrE) were still elevated at DW3000 compared to UP. Sequencing of 16S rRNA genes revealed pronounced changes in the sediment bacterial community composition from both DW sites compared to UP site, regardless of the season. Numerous taxa with increased relative abundance at DW0 decreased to background levels at DW3000, suggesting die-off or lack of transport of effluent-originating bacteria. In contrast, various taxa that were more abundant in sediments than in effluents increased in relative abundance at DW3000 but not at DW0, possibly due to selection imposed by high sulfonamide levels. Network analysis revealed strong correlation between some clinically relevant ARGs (e.g. bla_GES, bla_OXA, ermB, tet39, sul2) and taxa with elevated abundance at DW sites, and known to harbour opportunistic pathogens, such as Acinetobacter, Arcobacter, Aeromonas and Shewanella. Our results demonstrate the necessity for improved management of pharmaceutical and rural waste disposal for mitigating the increasing problems with antibiotic resistance.

Insights on sulfamethoxazole bio-transformation by environmental Proteobacteria isolates

Although sulfonamide residues are frequently reported as freshwaters contaminants, information on the ability of native bacteria to modify these synthetic antibiotics is scarce. Our purpose was to investigate the potential of bacteria from different aquatic environments to cleave or transform sulfamethoxazole (SMX) and infer on their ability to reduce the toxicity of this antibiotic. From a collection of about 100 Proteobacteria, 47 strains previously isolated from drinking water, surface water, and wastewater grew in the presence of 200 μM_SMX, and were further studied. Out of these, 14 strains, mostly from mineral drinking water, transformed SMX into equimolar amounts of the lesser toxic derivative N⁴-acetyl-sulfamethoxazole. The highest percentage of SMX transformation was recorded for two strains affiliated to Pseudomonas mandelii. For P. mandelii McBPA4 higher SMX transformation rate and extent were observed in fed-batch (∼8 μM_SMX/h, 81%) than in batch conditions (∼5 μM_SMX/h, 25%), but similar specific transformation rates were found in both cultivation modes (∼20 μmol_SMX/g_{cell dry weight}/h), indicating the dependence of the process on the microbial load. These results evidence that the capacity to transform synthetic antibiotics may be common among bacteria and highlight the potential of environmental bacteria in attenuating the potential adverse effects of pollution with sulfonamides.

Latent environment allocation of microbial community data

As data for microbial community structures found in various environments has increased, studies have examined the relationship between environmental labels given to retrieved microbial samples and their community structures. However, because environments continuously change over time and space, mixed states of some environments and its effects on community formation should be considered, instead of evaluating effects of discrete environmental categories. Here we applied a hierarchical Bayesian model to paired datasets containing more than 30,000 samples of microbial community structures and sample description documents. From the training results, we extracted latent environmental topics that associate co-occurring microbes with co-occurring word sets among samples. Topics are the core elements of environmental mixtures and the visualization of topic-based samples clarifies the connections of various environments. Based on the model training results, we developed a web application, LEA (Latent Environment Allocation), which provides the way to evaluate typicality and heterogeneity of microbial communities in newly obtained samples without confining environmental categories to be compared. Because topics link words and microbes, LEA also enables to search samples semantically related to the query out of 30,000 microbiome samples.

In the past decade, microbiomes from various natural and human symbiotic environments have been thoroughly studied. However, our knowledge is limited as to what types of environments affect the structure of a microbial community. In the first place, how can we define “environments”, in particular, the environmental entities that are often continuously varying and difficult to discretely categorize? We assumed that environments could be represented from microbiome data because the structure of microbial communities reflect the state of the environment. We applied a probabilistic topic model to a dataset containing taxonomic composition data and natural language sample descriptions of >30,000 microbiome samples and extracted “latent environments” of the microbial communities, which are core elements of environmental mixtures. Integrating the training results of the model, we developed a web application to explore the microbiome universe and to place new metagenomic data on this universe like a global positioning system. Our tool shows what kinds of the environment naturally exist and are similar to each other on the perspective of the structural patterns of microbiome, and provides the way to evaluate the commonality and the heterogeneity of users’ microbiome samples.

Arctic antibiotic resistance gene contamination, a result of anthropogenic activities and natural origin

The increasing global prevalence of antibiotic resistance genes (ARGs) in the environment is attributed to anthropogenic activities, particularly the misuse of antimicrobial drugs in human care and animal production. In the present study, we first examined Arctic/sub-Arctic (polar) sediments for the abundance and diversity of 30 ARGs against sulfonamide, tetracycline, aminoglycoside, quinolone, macrolide, and β-lactam antibiotics. Polar sediment ARGs were detected by qPCR at relatively low levels (10^-9 to 10^-5 copies/16S rRNA gene copies) compared to the reference sites, which were heavily impacted regions of China (the Haihe River, the Tianjin Water Park water and the Qilihai Wetland water, at 10^-8 to 10^-2 copies/16S rRNA gene copies). A human mitochondrial gene target, Hmt, was first used to aid in the identification of ARGs associated with anthropogenic activities, being relatively persistent, in high copy number and a human-specific molecular marker. Hmt was consistently present in easily quantifiable amounts in the polar sediment samples, indicating their relationship with human-impact, and it was also positively correlated with the relative abundance of ARGs and to the concentrations of modern-day antibiotics. Phylogenetic analyses of resistance sequences from both the Arctic marine sediments and a major database of human pathogens indicated that the ARGs in polar region were the result of a mix of human influence and natural origins. To our knowledge, this is the first study to show that ARGs in Arctic marine sediments appear to be a mixture of both natural origins and recent human influence. This study provides a significant reference regarding the global reach of antibiotic resistance, which is associated with anthropogenic activities.

Enrichment and characterization of a bacterial mixture capable of utilizing C-mannosyl tryptophan as a carbon source

C-Mannosylation, a protein-modification found in various eukaryotes, involves the attachment of a single mannose molecule to selected tryptophan residues of proteins. Since C-mannosyl tryptophan (CMW) was detected in human urine, it is generally thought that CMW is not catabolized inside our body and instead is excreted via the urine. This paper reports enrichment of a bacterial consortium from soil that degrades CMW. The bacteria grew in minimal medium supplemented with CMW as the carbon source. Interestingly, even after successive clonal picks of individual colonies, several species were still present in each colony as revealed by 16S rRNA gene sequence analysis, indicating that a single species may not be responsible for this activity. A next generation sequencing (NGS) analysis was therefore carried out in order to determine which bacteria were responsible for the catabolism of CMW. It was found that a species of Sphingomonadaceae family, but not others, increased with simultaneous decrease of CMW in the media, suggesting that this species is most likely the one that is actively involved in the degradation of CMW.

Complex migration of antibiotic resistance in natural aquatic environments

Antibiotic resistance is a worsening global concern, and the environmental behaviors and migration patterns of antibiotic resistance genes (ARGs) have attracted considerable interest. Understanding the long-range transport of ARG pollution is crucial. In this study, we characterized the dynamics of ARG changes after their release into aquatic environments and demonstrated the importance of traditional chemical contaminants in the transmission mechanisms of ARGs. We hypothesized that the main route of ARG proliferation switches from active transmission to passive transmission. This antibiotic-dominated switch is motivated and affected by non-corresponding contaminants. The effect of anthropogenic activities gradually weakens from inland aquatic environments to ocean environments; however, the effect of changes in environmental conditions is enhanced along this gradient. The insights discussed in this study will help to improve the understanding of the distribution and migration of ARG pollution in various aquatic environments, and provide a modern perspective to reveal the effect of corresponding contaminants and non-corresponding contaminants in the process of antibiotic resistance proliferation.

Ubiquitous and persistent Proteobacteria and other Gram-negative bacteria in drinking water

Drinking water comprises a complex microbiota, in part shaped by the disinfection and distribution systems. Gram-negative bacteria, mainly members of the phylum Proteobacteria, represent the most frequent bacteria in drinking water, and their ubiquity and physiological versatility raises questions about possible implications in human health. The first step to address this concern is the identification and characterization of such bacteria that is the first objective of this study, aiming at identifying ubiquitous or persistent Gram-negative bacteria, Proteobacteria or members of other phyla, isolated from tap water or from its source. >1000 bacterial isolates were characterized and identified, and a selected group (n=68) was further analyzed for the minimum inhibitory concentrations (MIC) to antibiotics (amoxicillin and gentamicin) and metals (copper and arsenite). Total DNA extracts of tap water were examined for the presence of putatively acquired antibiotic resistance or related genes (intI1, bla_TEM, qnrS and sul1). The ubiquitous tap water genera comprised Proteobacteria of the class Alpha- (Blastomonas, Brevundimonas, Methylobacterium, Sphingobium, Sphingomonas), Beta- (Acidovorax, Ralstonia) and Gamma- (Acinetobacter and Pseudomonas). Persistent species were members of genera such as Aeromonas, Enterobacter or Dechloromonas. Ralstonia spp. showed the highest MIC values to gentamicin and Acinetobacter spp. to arsenite. The genes intI1, bla_TEM or sul1 were detected, at densities lower than 2.3×10⁵copies/L, 2.4×10⁴copies/L and 4.6×10²copies/L, respectively, in most tap water samples. The presence of some bacterial groups, in particular of Beta- or Gammaproteobacteria (e.g. Ralstonia, Acinetobacter, Pseudomonas) in drinking water may deserve attention given their potential as reservoirs or carriers of resistance or as opportunistic pathogens.

Antibiotic treatment at delivery shapes the initial oral microbiome in neonates

Oral microorganisms are important determinants of health and disease. The source of the initial neonatal microbiome and the factors dictating initial human oral microbiota development are unknown. This study aimed to investigate this in placental, oral and gut microbiome profiles from 36 overweight or obese mother-baby dyads as determined by 16S rRNA sequencing. Expression of five antibiotic resistance genes of the β-lactamase class was analysed in the infant oral microbiota samples by QPCR. The neonatal oral microbiota was 65.35% of maternal oral, 3.09% of placental, 31.56% of unknown and 0% of maternal gut origin. Two distinct neonatal oral microbiota profiles were observed: one strongly resembling the maternal oral microbiota and one with less similarity. Maternal exposure to intrapartum antibiotics explained the segregation of the profiles. Families belonging to Proteobacteria were abundant after antibiotics exposure while the families Streptococcaceae, Gemellaceae and Lactobacillales dominated in unexposed neonates. 26% of exposed neonates expressed the Vim-1 antibiotic resistance gene. These findings indicate that maternal intrapartum antibiotic treatment is a key regulator of the initial neonatal oral microbiome.

Rapid assemblage of diverse environmental fungal communities on public restroom floors

An increasing proportion of humanity lives in urban environments where they spend most of their lives indoors. Recent molecular studies have shown that bacterial assemblages in built environments (BEs) are extremely diverse, but BE fungal diversity remains poorly understood. We applied culture-independent methods based on next-generation sequencing (NGS) of the fungal internal transcribed spacer to investigate the diversity and temporal dynamics of fungi in restrooms. Swab samples were collected weekly from three different surfaces in two public restrooms (male and female) in San Diego, CA, USA, over an 8-week period. DNA amplification and culturing methods both found that the floor samples had significantly higher fungal loads than other surfaces. NGS sequencing of floor fungal assemblages identified a total of 2550 unique phylotypes (~800 per sample), less than half of which were identifiable. Of the known fungi, the majority came from environmental sources and we found little evidence of known human skin fungi. Fungal assemblages reformed rapidly in a highly consistent manner, and the variance in the species diversity among samples was low. Overall, our study contributes to a better understanding of public restroom floor fungal communities.

Domestic shower hose biofilms contain fungal species capable of causing opportunistic infection

The domestic environment can be a source of pathogenic bacteria. We show here that domestic shower hoses may harbour potentially pathogenic bacteria and fungi. Well-developed biofilms were physically removed from the internal surface of shower hoses collected in four locations in England and Scotland. Amplicon pyrosequencing of 16S and 18S rRNA targets revealed the presence of common aquatic and environmental bacteria, including members of the Actinobacteria, Alphaproteobacteria, Bacteroidetes and non-tuberculous Mycobacteria. These bacteria are associated with infections in immunocompromised hosts and are widely reported in shower systems and as causes of water-acquired infection. More importantly, this study represents the first detailed analysis of fungal populations in shower systems and revealed the presence of sequences related to Exophiala mesophila, Fusarium fujikuroi and Malassezia restricta. These organisms can be associated with the environment and healthy skin, but also with infection in compromised and immuno-competent hosts and occurrence of dandruff. Domestic showering may result in exposure to aerosols of bacteria and fungi that are potentially pathogenic and toxigenic. It may be prudent to limit development of these biofilms by the use of disinfectants, or regular replacement of hoses, where immuno-compromised persons are present.

Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections

Although the source of drinking water (DW) used in hospitals is commonly disinfected, biofilms forming on water pipelines are a refuge for bacteria, including possible pathogens that survive different disinfection strategies. These biofilm communities are only beginning to be explored by culture-independent techniques that circumvent the limitations of conventional monitoring efforts. Hence, theories regarding the frequency of opportunistic pathogens in DW biofilms and how biofilm members withstand high doses of disinfectants and/or chlorine residuals in the water supply remain speculative. The aim of this study was to characterize the composition of microbial communities growing on five hospital shower hoses using both 16S rRNA gene sequencing of bacterial isolates and whole-genome shotgun metagenome sequencing. The resulting data revealed a Mycobacterium-like population, closely related to Mycobacterium rhodesiae and Mycobacterium tusciae, to be the predominant taxon in all five samples, and its nearly complete draft genome sequence was recovered. In contrast, the fraction recovered by culture was mostly affiliated with Proteobacteria, including members of the genera Sphingomonas, Blastomonas, and Porphyrobacter.The biofilm community harbored genes related to disinfectant tolerance (2.34% of the total annotated proteins) and a lower abundance of virulence determinants related to colonization and evasion of the host immune system. Additionally, genes potentially conferring resistance to β-lactam, aminoglycoside, amphenicol, and quinolone antibiotics were detected. Collectively, our results underscore the need to understand the microbiome of DW biofilms using metagenomic approaches. This information might lead to more robust management practices that minimize the risks associated with exposure to opportunistic pathogens in hospitals.

16S-23S rRNA Gene Intergenic Spacer Region Variability Helps Resolve Closely Related Sphingomonads

Sphingomonads comprise a physiologically versatile group many of which appear to be adapted to oligotrophic environments, but several also had features in their genomes indicative of host associations. In this study, the extent variability of the 16S–23S rDNA intergenic spacer (ITS) sequences of 14 ATCC reference sphingomonad strains and 23 isolates recovered from drinking water was investigated through PCR amplification and sequencing. Sequencing analysis of the 16S–23S rRNA gene ITS region revealed that the ITS sizes for all studied isolates varied between 415 and 849 bp, while their G+C content was 42.2–57.9 mol%. Five distinct ITS types were identified: ITS^none (without tRNA genes), ITS^Ala(TGC), ITS^{Ala(TGC)+Ile(GAT)}, ITS^{Ile(GAT)+Ala(TGC)}, and ITS ^{Ile(GAT)+Pseudo}. All of the identified tRNA^Ala(TGC) molecules consisted of 73 bases, and all of the tRNA^Ile(GAT) molecules consisted of 74 bases. We also detected striking variability in the size of the ITS region among the various examined isolates. Highest variability was detected within the ITS-2. The importance of this study is that this is the first comparison of the 16S–23S rDNA ITS sequence similarities and tRNA genes from sphingomonads. Collectively the data obtained in this study revealed the heterogeneity and extent of variability within the ITS region compared to the 16S rRNA gene within closely related isolates. Sequence and length polymorphisms within the ITS region along with the ITS types (tRNA-containing or lacking and the type of tRNA) and ITS-2 size and sequence similarities allowed us to overcome the limitation we previously encountered in resolving closely related isolates based on the 16S rRNA gene sequence.

Bacterial diversity associated with wild caught Anopheles mosquitoes from Dak Nong Province, Vietnam using culture and DNA fingerprint

Background

Microbiota of Anopheles midgut can modulate vector immunity and block Plasmodium development. Investigation on the bacterial biodiversity in Anopheles, and specifically on the identification of bacteria that might be used in malaria transmission blocking approaches, has been mainly conducted on malaria vectors of Africa. Vietnam is an endemic country for both malaria and Bancroftian filariasis whose parasitic agents can be transmitted by the same Anopheles species. No information on the microbiota of Anopheles mosquitoes in Vietnam was available previous to this study.

Method

The culture dependent approach, using different mediums, and culture independent (16S rRNA PCR – TTGE) method were used to investigate the bacterial biodiversity in the abdomen of 5 Anopheles species collected from Dak Nong Province, central-south Vietnam. Molecular methods, sequencing and phylogenetic analysis were used to characterize the microbiota.

Results and Discussion

The microbiota in wild-caught Anopheles was diverse with the presence of 47 bacterial OTUs belonging to 30 genera, including bacterial genera impacting Plasmodium development. The bacteria were affiliated with 4 phyla, Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria, the latter being the dominant phylum. Four bacterial genera are newly described in Anopheles mosquitoes including Coxiella, Yersinia, Xanthomonas, and Knoellia. The bacterial diversity per specimen was low ranging from 1 to 4. The results show the importance of pairing culture and fingerprint methods to better screen the bacterial community in Anopheles mosquitoes.

Conclusion

Sampled Anopheles species from central-south Vietnam contained a diverse bacterial microbiota that needs to be investigated further in order to develop new malaria control approaches. The combination of both culture and DNA fingerprint methods allowed a thorough and complementary screening of the bacterial community in Anopheles mosquitoes.