Antibiotic resistant bacteria and antibiotic resistance genes as contaminants of emerging concern: Occurrences, impacts, mitigations and future guidelines.

Antibiotic resistance, driven by the proliferation of antibiotic resistance genes (ARGs) and antibiotic resistance bacteria (ARBs), has emerged as a pressing global health concern. Antimicrobial resistance is exacerbated by the widespread use of antibiotics in agriculture, aquaculture, and human medicine, leading to their accumulation in various environmental compartments such as soil, water, and sediments. The presence of ARGs in the environment, particularly in municipal water, animal husbandry, and hospital environments, poses significant risks to human health, as they can be transferred to potential human pathogens. Current remediation strategies, including the use of pyroligneous acid, coagulants, advanced oxidation, and bioelectrochemical systems, have shown promising results in reducing ARGs and ARBs from soil and water. However, these methods come with their own set of challenges, such as the need for elevated base levels in UV-activated persulfate and the long residence period required for photocatalysts. The future of combating antibiotic resistance lies in the development of standardized monitoring techniques, global collaboration, and the exploration of innovative remediation methods. Emphasis on combination therapies, advanced oxidation processes, and monitoring horizontal gene transfer can pave the way for a comprehensive approach to mitigate the spread of antibiotic resistance in the environment.

A metagenomic study of antibiotic resistance genes in a hypereutrophic subtropical lake contaminated by anthropogenic sources.

Antibiotic resistance genes (ARGs) are a major threat to human and environmental health. This study investigated the occurrence and distribution of ARGs in Lake Cajititlán, a hypereutrophic subtropical lake in Mexico contaminated by anthropogenic sources (urban wastewater and runoff from crop and livestock production). ARGs (a total of 475 genes) were detected in 22 bacterial genera, with Pseudomonas (144 genes), Stenotrophomonas (88 genes), Mycobacterium (54 genes), and Rhodococcus (27 genes) displaying the highest frequencies of ARGs. Among these, Pseudomonas aeruginosa and Stenotrophomonas maltophilia showed the highest number of ARGs. The results revealed a diverse array of ARGs, including resistance to macrolides (11.55 %), aminoglycosides (8.22 %), glycopeptides (6.22 %), tetracyclines (4 %), sulfonamides (4 %), carbapenems (1.11 %), phenicols (0.88 %), fluoroquinolones (0.44 %), and lincosamides (0.22 %). The most frequently observed ARGs were associated with multidrug resistance (63.33 %), with MexF (42 genes), MexW (36 genes), smeD (31 genes), mtrA (25 genes), and KHM-1 (22 genes) being the most common. Lake Cajititlán is a recreational area for swimming, fishing, and boating, while also supporting irrigation for agriculture and potentially acting as a drinking water source for some communities. This raises concerns about the potential for exposure to antibiotic-resistant bacteria through these activities. The presence of ARGs in Lake Cajititlán poses a significant threat to both human and environmental health. Developing strategies to mitigate the risks of antibiotic resistance, including improving wastewater treatment, and promoting strategic antibiotic use and disposal, is crucial. This study represents a significant advancement in the understanding of antibiotic resistance dynamics in a hypereutrophic subtropical lake in a developing country, providing valuable insights for the scientific community and policymakers.

Chemical attributes, bacterial community, and antibiotic resistance genes are affected by intensive use of soil in agro-ecosystems of the Atlantic Forest, Southeastern Brazil.

Soil is one of the largest reservoirs of microbial diversity in nature. Although soil management is vital for agricultural purposes, intensive practices can have a significant impact on fertility, microbial community, and resistome. Thus, the aim of this study was to evaluate the effects of an intensive soil management system on the chemical attributes, composition and structure of prevalent bacterial communities, and presence and abundance of antimicrobial resistance genes (ARGs). The chemical characterization, bacterial diversity and relative abundance of ARGs were evaluated in soils from areas of intensive vegetable cultivation and forests. Results indicate that levels of nutrients and heavy metals were higher in soil samples from cultivated areas. Similarly, greater enrichment and diversity of bacterial genera was detected in agricultural areas. Of the 18 target ARGs evaluated, seven were detected in studied soils. The oprD gene exhibited the highest abundance among the studied genes and was the only one that showed a significantly different prevalence between areas. The oprD gene was identified only from soil of the cultivated areas. The blaSFO, erm(36), oprD and van genes, in addition to the pH, showed greater correlation with in soil of cultivated areas, which in turn exhibited higher contents of nutrients. Thus, in addition to changes in chemical attributes and in the microbial community of the soil, intensive agricultural cultivation systems cause a modification of its resistome, reinforcing the importance of the study of antimicrobial resistance in a One Health approach.

Systematic analysis of the scientific-technological production on the use of the UV, H2O2, and/or Cl2 systems in the elimination of bacteria and associated antibiotic resistance genes.

This study presents a systematic review of the scientific and technological production related to the use of systems based on UV, H2O2, and Cl2 for the elimination of antibiotic-resistant bacteria (ARB) and genes associated with antibiotic resistance (ARGs). Using the Pro Know-C (Knowledge Development Process-Constructivist) methodology, a portfolio was created and analyzed that includes 19 articles and 18 patents published between 2011 and 2022. The results show a greater scientific-technological production in UV irradiation systems (8 articles and 5 patents) and the binary combination UV/H2O2 (9 articles and 4 patents). It was emphasized that UV irradiation alone focuses mainly on the removal of ARB, while the addition of H2O2 or Cl2, either individually or in binary combinations with UV, enhances the removal of ARB and ARG. The need for further research on the UV/H2O2/Cl2 system is emphasized, as gaps in the scientific-technological production of this system (0 articles and 2 patents), especially in its electrochemically assisted implementation, have been identified. Despite the gaps identified, there are promising prospects for the use of combined electrochemically assisted UV/H2O2/Cl2 disinfection systems. This is demonstrated by the effective removal of a wide range of contaminants, including ARB, fungi, and viruses, as well as microorganisms resistant to conventional disinfectants, while reducing the formation of toxic by-products.

Beach sand plastispheres are hotspots for antibiotic resistance genes and potentially pathogenic bacteria even in beaches with good water quality.

Massive amounts of microplastics are transported daily from the oceans and rivers onto beaches. The ocean plastisphere is a hotspot and a vector for antibiotic resistance genes (ARGs) and potentially pathogenic bacteria. However, very little is known about the plastisphere in beach sand. Thus, to describe whether the microplastics from beach sand represent a risk to human health, we evaluated the bacteriome and abundance of ARGs on microplastic and sand sampled at the drift line and supralittoral zones of four beaches of poor and good water quality. The bacteriome was evaluated by sequencing of 16S rRNA gene, and the ARGs and bacterial abundances were evaluated by high-throughput real-time PCR. The results revealed that the microplastic harbored a bacterial community that is more abundant and distinct from that of beach sand, as well as a greater abundance of potential human and marine pathogens, especially the microplastics deposited closer to seawater. Microplastics also harbored a greater number and abundance of ARGs. All antibiotic classes evaluated were found in the microplastic samples, but not in the beach sand ones. Additionally, 16 ARGs were found on the microplastic alone, including genes related to multidrug resistance (blaKPC, blaCTX-M, tetM, mdtE and acrB_1), genes that have the potential to rapidly and horizontally spread (blaKPC, blaCTX-M, and tetM), and the gene that confers resistance to antibiotics that are typically regarded as the ultimate line of defense against severe multi-resistant bacterial infections (blaKPC). Lastly, microplastic harbored a similar bacterial community and ARGs regardless of beach water quality. Our findings suggest that the accumulation of microplastics in beach sand worldwide may constitute a potential threat to human health, even in beaches where the water quality is deemed satisfactory. This phenomenon may facilitate the emergence and dissemination of bacteria that are resistant to multiple drugs.

Deciphering the Role of WWTPs in Cold Environments as Hotspots for the Dissemination of Antibiotic Resistance Genes.

Cold environments are the most widespread extreme habitats in the world. However, the role of wastewater treatment plants (WWTPs) in the cryosphere as hotspots in antibiotic resistance dissemination has not been well established. Hence, a snapshot of the resistomes of WWTPs in cold environments, below 5 °C, was provided to elucidate their role in disseminating antibiotic resistance genes (ARGs) to the receiving waterbodies. The resistomes of two natural environments from the cold biosphere were also determined. Quantitative PCR analysis of the aadA, aadB, ampC, blaSHV, blaTEM, dfrA1, ermB, fosA, mecA, qnrS, and tetA(A) genes indicated strong prevalences of these genetic determinants in the selected environments, except for the mecA gene, which was not found in any of the samples. Notably, high abundances of the aadA, ermB, and tetA(A) genes were found in the influents and activated sludge, highlighting that WWTPs of the cryosphere are critical hotspots for disseminating ARGs, potentially worsening the resistance of bacteria to some of the most commonly prescribed antibiotics. Besides, the samples from non-disturbed cold environments had large quantities of ARGs, although their ARG profiles were highly dissimilar. Hence, the high prevalences of ARGs lend support to the fact that antibiotic resistance is a common issue worldwide, including environmentally fragile cold ecosystems.

Antibiotic resistance in tick-borne bacteria: A One Health approach perspective.

The emergence and re-emergence of tick-borne bacteria (TBB) as a public health problem raises the uncertainty of antibiotic resistance in these pathogens, which could be dispersed to other pathogens. The impact of global warming has led to the emergence of pathogenic TBB in areas where they were not previously present and is another risk that must be taken into account under the One Health guides. This review aimed to analyze the existing information regarding antibiotic-resistant TBB and antibiotic-resistance genes (ARG) present in the tick microbiome, considering the potential to be transmitted to pathogenic microorganisms. Several Ehrlichia species have been reported to exhibit natural resistance to fluoroquinolones and typhus group Rickettsiae are naturally susceptible to erythromycin. TBB have a lower risk of acquiring ARG due to their natural habitat, but there is still a probability of acquiring them; furthermore, studies of these pathogens are limited. Pathogenic and commensal bacteria coexist within the tick microbiome along with ARGs for antibiotic deactivation, cellular protection, and efflux pumps; these ARGs confer resistance to antibiotics such as aminoglycosides, beta-lactamase, diaminopyrimidines, fluoroquinolones, glycopeptides, sulfonamides, and tetracyclines. Although with low probability, TBB can be a reservoir of ARGs.

Role of a typical swine liquid manure treatment plant in reducing elements of antibiotic resistance.

Biological treatment of swine liquid manure may be a favorable environment for the enrichment of bacteria carrying antibiotic resistance genes (ARGs), raising the alert about this public health problem. The present work sought to investigate the performance of a swine wastewater treatment plant (SWWTP), composed of a covered lagoon biodigester (CLB) followed by three facultative ponds, in the removal of usual pollutants, antibiotics, ARGs (blaTEM, ermB, qnrB, sul1, and tetA), and intI1. The SWWTP promoted a 70% of organic matter removal, mainly by the digester unit. The facultative ponds stood out in the solids' retention carried from the anaerobic stage and contributed to ammonia volatilization. The detected antibiotic in the raw wastewater was norfloxacin (< 0.79 to 60.55 µg L-1), and the SWWTP seems to equalize peaks of norfloxacin variation probably due to sludge adsorption. CLB reduced the absolute abundance of ARGs by up to 2.5 log, while the facultative stage does not seem to improve the quality of the final effluent in terms of resistance elements. Considering the relative abundances, the reduction rates of total and ARG-carrying bacteria appear to be similar. Finally, correlation tests also revealed that organic matter and solids control in liquid manure treatment systems could help reduce the spread of ARGs after the waste final disposal.

Hydrothermal pre-treatment followed by anaerobic digestion for the removal of tylosin and antibiotic resistance agents from poultry litter.

Hydrothermal pretreatment (HPT) followed by anaerobic digestion (AD) is an alternative for harvesting energy and removing organic contaminants from sewage sludge and animal manure. This study investigated the use, in an energetically sustainable way, of HPT and AD, alone or combined, to produce methane and remove tylosin and antimicrobial resistance genes (ARG) from poultry litter (PL). The results showed that HPT at 80 °C (HPT80), followed by single-stage AD (AD-1S), led to the production of 517.9 ± 4.7 NL CH4 kg VS-1, resulting in 0.11 kWh kg PL-1 of electrical energy and 0.75 MJ kg PL-1 of thermal energy, thus supplying 33.6% of the energy spent on burning firewood at a typical farm. In this best-case scenario, the use of HPT alone reduced tylosin concentration from PL by 23.6%, while the process involving HPT followed by AD-1S led to the removal of 91.6% of such antibiotic. The combined process (HPT80 + AD-1S), in addition to contributing to reduce the absolute and relative abundances of ARG ermB (2.13 logs), intI1 (0.39 logs), sul1 (0.63 logs), and tetA (0.74 logs), led to a significant removal in the relative abundance of tylosin-resistant bacteria present in the poultry litter.

Watershed urbanization enhances the enrichment of pathogenic bacteria and antibiotic resistance genes on microplastics in the water environment.

Microplastics (MPs) serve as vectors for microorganisms and antibiotic resistance genes (ARGs) and contribute to the spread of pathogenic bacteria and ARGs across various environments. Patterns of microbial communities and ARGs in the biofilm on the surface of MPs, also termed as plastisphere, have become an issue of global concern. Although antibiotic resistome in the plastisphere has been detected, how watershed urbanization affects patterns of potential pathogens and ARGs in the microplastic biofilms is still unclear. Here, we compared the bacterial communities, the interaction between bacterial taxa, pathogenic bacteria, and ARGs between the plastisphere and their surrounding water, and revealed the extensive influence of urbanization on them. Our results showed that bacterial communities and interactions in the plastisphere differed from those in their surrounding water. Microplastics selectively enriched Bacteroidetes from water. In non-urbanized area, the abundance of Oxyphotobacteria was significantly (p < 0.05) higher in plastisphere than that in water, while α-Proteobacteria was significantly (p < 0.05) higher in plastisphere than those in water of urbanized area. Pathogenic bacteria, ARGs, and mobile genetic elements (MGEs) were significantly (p < 0.05) higher in the urbanized area than those in non-urbanized area. MPs selectively enriched ARG-carrying potential pathogens, i.e., Klebsiella pneumoniae and Enterobacter cloacae, and exhibited a distinct effect on the relative abundance of ARG and pathogens in water with different urbanization levels. We further found ARGs were significantly correlated to MGEs and pathogenic bacteria. These results suggested that MPs would promote the dissemination of ARGs among microbes including pathogenic bacteria, and urbanization would affect the impact of MPs on microbes, pathogens, and ARGs in water. A high level of urbanization could enhance the enrichment of pathogens and ARGs by MPs in aquatic systems and increase microbial risk in aquatic environments. Our findings highlighted the necessity of controlling the spread of ARGs among pathogens and the usage of plastic products in ecosystems of urban areas.

Genomic analysis of plasmid content in food isolates of E. coli strongly supports its role as a reservoir for the horizontal transfer of virulence and antibiotic resistance genes.

The link between E. coli strains contaminating foods and human disease is unclear, with some reports supporting a direct transmission of pathogenic strains via food and others highlighting their role as reservoirs for resistance and virulence genes. Here we take a genomics approach, analyzing a large set of fully-assembled genomic sequences from E. coli available in GenBank. Most of the strains isolated in food are more closely related to each other than to clinical strains, arguing against a frequent direct transmission of pathogenic strains from food to the clinic. We also provide strong evidence of genetic exchanges between food and clinical strains that are facilitated by plasmids. This is based on an overlapped representation of virulence and resistance genes in plasmids isolated from these two sources. We identify clusters of phylogenetically-related plasmids that are largely responsible for the observed overlap and see evidence of specialization, with some food plasmid clusters preferentially transferring virulence factors over resistance genes. Consistent with these observations, food plasmids have a high mobilization potential based on their plasmid taxonomic unit classification and on an analysis of mobilization gene content. We report antibiotic resistance genes of high clinical relevance and their specific incompatibility group associations. Finally, we also report a striking enrichment for adhesins in food plasmids and their association with specific IncF replicon subtypes. The identification of food plasmids with specific markers (Inc and PTU combinations) as mediators of horizontal transfer between food and clinical strains opens new research avenues and should assist with the design of surveillance strategies.

Exploring the microbiome, antibiotic resistance genes, mobile genetic element, and potential resistant pathogens in municipal wastewater treatment plants in Brazil.

Wastewater treatment plants (WWTPs) have been widely investigated in Europe, Asia and North America regarding the occurrence and fate of antibiotic resistance (AR) elements, such as antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and antibiotic resistant bacteria and pathogens. However, monitoring data about AR elements in municipal WWTPs in Brazil are scarce. This study investigated the abundance of intI1, five ARGs (sul1, tetA, blaTEM, ermB and qnrB) and 16S rRNA in raw and treated wastewater of three WWTPs, using different sewage treatments named CAS (Conventional activated sludge), UASB/BTF (UASB followed by biological trickling filter) and MAS/UV (modified activated sludge with UV disinfection stage). Bacterial diversity and the presence of potentially pathogenic groups were also evaluated, and associations between genetic markers and the bacterial populations were presented. All WWTPs decreased the loads of genetic markers finally discharged to receiving water bodies and showed no evidence of being hotspots for antimicrobial resistance amplification in wastewater, since the abundances of intI1 and ARGs within the bacterial population were not increased in the treated effluents. UASB/BTF showed a similar performance to that of the CAS and MAS/UV, reinforcing the sanitary and environmental advantages of this biological treatment, widely applied for wastewater treatment in warm climate regions. Bacterial diversity and richness increased after treatments, and bacterial communities in wastewater samples differed due to catchment areas and treatment typologies. Potential pathogenic population underwent considerable decrease after the treatments; however, strong significant correlations with intI1 and ARGs revealed potential multidrug-resistant pathogenic bacteria (Aeromonas, Arcobacter, Enterobacter, Escherichia-Shigella, Stenotrophomonas and Streptococcus) in the treated effluents, although in reduced relative abundances. These are contributive results for understanding the fate of ARGs, MGEs and potential pathogenic bacteria after wastewater treatments, which might support actions to mitigate their release into Brazilian aquatic environments in the near future.

Portación nasal de Staphylococcus aureus en el personal de salud de áreas críticas de un Hospital Pediátrico durante julio-setiembre 2018 / Nasal carriage of Staphylococcus aureus in health personnel in critical areas of a Pediatric Hospital during July-September 2018 / Transporte nasal de Staphylococcus aureus em profissionais de saúde em áreas críticas de um Hospital Pediátrico durante julho-setembro de 2018

Las infecciones intrahospitalarias (IIH) son causa de elevada morbimortalidad y representan un problema sanitario importante. El personal de salud es reservorio y potencial transmisor de los agentes etiológicos de las mismas. S. aureus es uno de los microorganismos implicados, por lo tanto es importante conocer la frecuencia de portación en el personal de salud y establecer el perfil de susceptibilidad antimicrobiana para contribuir con la elaboración de medidas de prevención incluyendo actividades educativas. Objetivo: Conocer la frecuencia de portación de S. aureus, distribución y antibiotipos de las cepas presentes en el personal sanitario del Hospital Pediátrico de Referencia (HPR). Materiales y métodos: Se realizó un estudio descriptivo durante el periodo julio-setiembre del año 2018. Se incluyeron muestras de hisopados nasales de trabajadores de la salud de distintas áreas de internación que consintieron participar en el estudio. Se excluyeron aquellos que recibieron antibióticos dentro de los 3 meses previos al estudio. Las muestras fueron sembradas en agar sangre ovina al 5% (ASO) y se incubaron a 35-37ºC en aerobiosis por 24-48 horas. La identificación de las colonias sospechosas de Staphylococcus aureus por métodos convencionales y MALDI-TOF. El patrón de resistencia antimicrobiana de S. aureus se detectó por disco-difusión. En los cultivos resistentes a meticilina (SAMR) se determinó la presencia del gen mecA y se realizó la tipificación del SCCmec por pruebas de reacción en cadena de polimerasa. Resultados: Se obtuvieron 225 hisopados a partir de 225 trabajadores, presentaron desarrollo 212. En 49 se recuperaron cultivos de S. aureus. Correspondieron a SAMR 11 de las 49 cepas, todas portaban el gen mecA. Hubo predominio en el personal de enfermería (7/11), en los servicios de hemato-oncología (3/11) y cuidados intensivos neonatales (4/11). Asociaron resistencia a macrólidos y clindamicina 8 de 11 aislamientos SAMR, a gentamicina 2 y a mupirocina uno. El SCCmec más frecuentemente identificado fue el tipo IV (7/11). Conclusiones: Los resultados muestran la presencia de cepas SAMR entre el personal de salud del CHPR y aportan información complementaria para efectuar prevención y control de las IIH, actuando sobre todo en el personal de salud encargado de la atención de pacientes susceptibles.

Hospital-acquired infections (IIH) are a cause of high morbidity and mortality and represent a major health problem. Health personnel are reservoirs and potential transmitters of their etiological agents. S. aureus is one of the microorganisms involved, therefore it is important to know the frequency of carriage in health personnel and establish the antimicrobial susceptibility profile to contribute to the development of prevention measures, including educational activities. Objective: To know the frequency of carriage of S. aureus, distribution and antibiotypes of the strains present in the health personnel of the Reference Pediatric Hospital (HPR). Materials and methods: A descriptive study was carried out during the period July-September 2018. Nasal swab samples from health workers from different hospitalization areas who agreed to participate in the study were included. Those who received antibiotics within 3 months prior to the study were excluded. The samples were seeded in 5% sheep blood agar (ASO) and incubated at 35-37ºC in aerobiosis for 24-48 hours. Identification of suspicious Staphylococcus aureus colonies by conventional methods and MALDI-TOF. The antimicrobial resistance pattern of S. aureus was detected by disc diffusion. In methicillin-resistant cultures (MRSA), the presence of the mecA gene was determined and SCCmec was typified by polymerase chain reaction tests. Results: 225 swabs were obtained from 225 workers, 212 showed development. S. aureus cultures were recovered from 49. 11 of the 49 strains corresponded to MRSA, all of them carried the mecA gene. There was a predominance in the nursing staff (7/11), in the hematology-oncology services (3/11) and neonatal intensive care (4/11). They associated resistance to macrolides and clindamycin in 8 of 11 MRSA isolates, 2 to gentamicin, and 1 to mupirocin. The most frequently identified SCCmec was type IV (7/11). Conclusions: The results show the presence of MRSA strains among the health personnel of the CHPR and provide complementary information to carry out prevention and control of IIH, acting especially on the health personnel in charge of the care of susceptible patients.

As infecções hospitalares (HII) são causa de alta morbidade e mortalidade e representam um importante problema de saúde. Os profissionais de saúde são reservatórios e potenciais transmissores de seus agentes etiológicos. O S. aureus é um dos micro-organismos envolvidos, por isso é importante conhecer a frequência de portadores em profissionais de saúde e estabelecer o perfil de suscetibilidade antimicrobiana para contribuir no desenvolvimento de medidas de prevenção incluindo atividades educativas. Objetivo: Conhecer a frequência de portadores de S. aureus, distribuição e antibiótipos das cepas presentes no pessoal de saúde do Hospital Pediátrico de Referência (HPR). Materiais e métodos: Foi realizado um estudo descritivo durante o período de julho a setembro de 2018. Foram incluídas amostras de swab nasal de profissionais de saúde de diferentes áreas de internação que concordaram em participar do estudo. Aqueles que receberam antibióticos nos 3 meses anteriores ao estudo foram excluídos. As amostras foram semeadas em 5% de ágar sangue de carneiro (ASO) e incubadas a 35-37ºC em aerobiose por 24-48 horas. Identificação de colônias suspeitas de Staphylococcus aureus por métodos convencionais e MALDI-TOF. O padrão de resistência antimicrobiana de S. aureus foi detectado por difusão em disco. Em culturas resistentes à meticilina (MRSA), a presença do gene mecA foi determinada e SCCmec foi tipificado por testes de reação em cadeia da polimerase. Resultados: 225 swabs foram obtidos de 225 trabalhadores, 212 apresentaram desenvolvimento. Culturas de S. aureus foram recuperadas de 49. 11 das 49 cepas correspondiam a MRSA, todas carregavam o gene mecA. Houve predominância na equipe de enfermagem (7/11), nos serviços de hematologia-oncologia (3/11) e de terapia intensiva neonatal (4/11). Eles associaram resistência a macrolídeos e clindamicina em 8 de 11 isolados de MRSA, 2 à gentamicina e 1 à mupirocina. O SCCmec mais frequentemente identificado foi o tipo IV (7/11). Conclusões: Os resultados mostram a presença de cepas de MRSA entre os profissionais de saúde do CHPR e fornecem informações complementares para realizar a prevenção e controle da HII, atuando principalmente sobre os profissionais de saúde responsáveis ​​pelo atendimento de pacientes suscetíveis.

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, ß-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 resistance: The role of efflux pump superfamilies and their respective substrates.

The microorganism resistance to antibiotics has become one of the most worrying issues for science due to the difficulties related to clinical treatment and the rapid spread of diseases. Efflux pumps are classified into six groups of carrier proteins that are part of the different types of mechanisms that contribute to resistance in microorganisms, allowing their survival. The present study aimed to carry out a bibliographic review on the superfamilies of carriers in order to understand their compositions, expressions, substrates, and role in intrinsic resistance. At first, a search for manuscripts was carried out in the databases Medline, Pubmed, ScienceDirect, and Scielo, using as descriptors: efflux pump, expression, pump inhibitors and efflux superfamily. For article selection, two criteria were taken into account: for inclusion, those published between 2000 and 2020, including textbooks, and for exclusion, duplicates and academic collections. In this research, 139,615 published articles were obtained, with 312 selected articles and 7 book chapters that best met the aim. From the comprehensive analysis, it was possible to consider that the chromosomes and genetic elements can contain genes encoding efflux pumps and are responsible for multidrug resistance. Even though this is a well-explored topic in the scientific community, understanding the behavior of antibiotics as substrates that increase the expression of pump-encoding genes has challenged medicine. This review study succinctly summarizes the most relevant features of these systems, as well as their contribution to multidrug resistance.

Effects of activated sludge and UV disinfection processes on the bacterial community and antibiotic resistance profile in a municipal wastewater treatment plant.

Wastewater tertiary treatment has been pointed out as an effective alternative for reducing the concentration of antibiotic resistant bacteria and genes (ARB and ARGs) in wastewaters. The present work aimed to build on the current knowledge about the effects of activated sludge and UV irradiation on antibiotic resistance determinants in biologically treated wastewaters. For that, the microbial community and ARGs' composition of samples collected after preliminary (APT), secondary (AST), and tertiary (ATT) treatments in a full-scale wastewater treatment plant using a modified activated sludge (MAS) system followed by an UV stage (16 mJ/cm2) were investigated through culture-dependent and independent approaches (including metagenomics). A total of 24 phyla and 460 genera were identified, with predominance of Gammaproteobacteria in all samples. Pathogenic genera corresponded to 8.6% of all sequences on average, mainly Acinetobacter and Streptococcus. Significant differences (p < 0.05) in the proportion of pathogens were observed between APT and the other samples, suggesting that the secondary treatment reduced its abundance. The MAS achieved 64.0-99.7% average removal efficiency for total (THB) and resistant heterotrophic bacteria, although the proportions of ARB/THB have increased for sulfamethoxazole, cephalexin, ciprofloxacin, and tetracycline. A total of 107 copies/mL of intI1 gene remained in the final effluent, suggesting that the treatment did not significantly remove this gene and possibly other ARGs. In accordance, metagenomic results suggested that number of reads recruited to plasmid-associated ARGs became more abundant in the pool throughout the treatment, suggesting that it affected more the bacteria without these ARGs than those with it. In conclusion, disinfected effluents are still a potential source for ARB and ARGs, which highlights the importance to investigate ways to mitigate their release into the environment.

Antimicrobial resistance and mecA gene in Staphylococcus spp. isolates from horses used in family farming / Resistência antimicrobiana e gene mecA em Staphylococcus spp. isolados de cavalos usados na agricultura familiar

Horses can contribute to the spread of bacterial diseases, which can be caused mainly by, Staphylococcus spp., which are part of the animals' commensal microbiota, but it is also considered a pathogenic microorganism capable of causing serious infections. vancomycin, when it is resistant to methicillin. Antimicrobial resistance is considered a major health problem by the World Health Organization and the emergence of the mecA gene, responsible for resistance to the class of beta-lactam antibiotics. Thus, the aim of this work was to investigate the antimicrobial resistance profile and the presence of the mecA gene in Staphylococcus spp. isolated from the nasal, oral and auricular microbiota of horses used as animal traction on small family farms. Nasal, oral and auricular swabs were collected from 38 horses, with 29 (76.3%) isolated in nasal swab, 15 (39.4%) in auricular swab and 9 (23.6%) in oral swab, totaling 53 Staphylococcus spp. and 50 (94.33%) samples were resistant to the 11 antimicrobials tested, none of which were positive for molecular tests to identify the mecA gene. The results demonstrate the presence of Staphylococcus spp. associated with high (94.33%) bacterial resistance, indicating that horses can be considered reservoirs of multi-resistant microorganisms.

Os equinos podem contribuir para a disseminação de doenças bacterianas, podendo ser causadas principalmente pelo, Staphylococcus spp., que fazem parte da microbiota comensal dos animais, mas também é considerado microrganismo patogênico capaz de causar infecções graves, em seu tratamento o medicamento mais utilizado é a vancomicina, quando há resistência a meticilina. A resistência antimicrobiana é considerada um dos principais problemas de saúde pela Organização Mundial de Saúde e o surgimento do gene mecA, responsável pela resistência à classe dos antibióticos beta-lactâmicos. Deste modo, o objetivo deste trabalho foi investigar o perfil de resistência antimicrobiana e a presença do gene mecA em Staphylococcus spp. isoladas da microbiota nasal, oral e auricular de cavalos usados como tração animal em pequenas propriedades familiares. Foram coletados swabs nasal, oral e auricular de 38 cavalos, sendo identificados 29 (76,3%) isolados em swab nasal, 15 (39,4%) em swab auricular e 9 (23,6%) em swab oral, totalizando 53 Staphylococcus spp. e 50 (94,33%) amostras foram resistentes aos 11 antimicrobianos testados, nenhuma amostra foi positiva aos testes moleculares para identificação do gene mecA. Os resultados demonstram a presença de Staphylococcus spp. associada à alta (94,33%) resistência bacteriana, indicando que os cavalos podem ser considerados reservatórios de microrganismos multirresistentes.

Metagenomic strategies identify diverse integron-integrase and antibiotic resistance genes in the Antarctic environment.

The objective of this study is to identify and analyze integrons and antibiotic resistance genes (ARGs) in samples collected from diverse sites in terrestrial Antarctica. Integrons were studied using two independent methods. One involved the construction and analysis of intI gene amplicon libraries. In addition, we sequenced 17 metagenomes of microbial mats and soil by high-throughput sequencing and analyzed these data using the IntegronFinder program. As expected, the metagenomic analysis allowed for the identification of novel predicted intI integrases and gene cassettes (GCs), which mostly encode unknown functions. However, some intI genes are similar to sequences previously identified by amplicon library analysis in soil samples collected from non-Antarctic sites. ARGs were analyzed in the metagenomes using ABRIcate with CARD database and verified if these genes could be classified as GCs by IntegronFinder. We identified 53 ARGs in 15 metagenomes, but only four were classified as GCs, one in MTG12 metagenome (Continental Antarctica), encoding an aminoglycoside-modifying enzyme (AAC(6´)acetyltransferase) and the other three in CS1 metagenome (Maritime Antarctica). One of these genes encodes a class D ß-lactamase (blaOXA-205) and the other two are located in the same contig. One is part of a gene encoding the first 76 amino acids of aminoglycoside adenyltransferase (aadA6), and the other is a qacG2 gene.

Metagenomic analysis of MWWTP effluent treated via solar photo-Fenton at neutral pH: Effects upon microbial community, priority pathogens, and antibiotic resistance genes.

The effectiveness of advanced technologies on eliminating antibiotic resistant bacteria (ARB) and resistance genes (ARGs) from wastewaters have been recently investigated. Solar photo-Fenton has been proven effective in combating ARB and ARGs from Municipal Wastewater Treatment Plant effluent (MWWTPE). However, most of these studies have relied solely on cultivable methods to assess ARB removal. This is the first study to investigate the effect of solar photo-Fenton upon ARB and ARGs in MWWTPE by high throughput metagenomic analysis (16S rDNA sequencing and Whole Genome Sequencing). Treatment efficiency upon priority pathogens and resistome profile were also investigated. Solar photo-Fenton (30 mg L-1 of Fe2+ intermittent additions and 50 mg L-1 of H2O2) reached 76-86% removal of main phyla present in MWWTPE. An increase in Proteobacteria abundance was observed after solar photo-Fenton and controls in which H2O2 was present as an oxidant (Fenton, H2O2 only, solar/H2O2). Hence, tolerance mechanisms presented by this group should be further assessed. Solar photo-Fenton achieved complete removal of high priority Staphylococcus and Enterococcus, as well as Klebsiella pneumoniae and Pseudomonas aeruginosa. Substantial reduction of intrinsically multi-drug resistant bacteria was detected. Solar photo-Fenton removed nearly 60% of ARGs associated with sulfonamides, macrolides, and tetracyclines, and complete removal of ARGs related to ß-lactams and fluoroquinolones. These results indicate the potential of using solar-enhanced photo-Fenton to limit the spread of antimicrobial resistance, especially in developing tropical countries.

Microbial biofilm: formation, architecture, antibiotic resistance, and control strategies.

The assembly of microorganisms over a surface and their ability to develop resistance against available antibiotics are major concerns of interest. To survive against harsh environmental conditions including known antibiotics, the microorganisms form a unique structure, referred to as biofilm. The mechanism of biofilm formation is triggered and regulated by quorum sensing, hostile environmental conditions, nutrient availability, hydrodynamic conditions, cell-to-cell communication, signaling cascades, and secondary messengers. Antibiotic resistance, escape of microbes from the body's immune system, recalcitrant infections, biofilm-associated deaths, and food spoilage are some of the problems associated with microbial biofilms which pose a threat to humans, veterinary, and food processing sectors. In this review, we focus in detail on biofilm formation, its architecture, composition, genes and signaling cascades involved, and multifold antibiotic resistance exhibited by microorganisms dwelling within biofilms. We also highlight different physical, chemical, and biological biofilm control strategies including those based on plant products. So, this review aims at providing researchers the knowledge regarding recent advances on the mechanisms involved in biofilm formation at the molecular level as well as the emergent method used to get rid of antibiotic-resistant and life-threatening biofilms.