Vessel transport of antibiotic resistance genes across oceans and its implications for ballast water management

Diverse bacterial hosts and potential risk of antibiotic resistomes in ship ballast water revealed by metagenomic binning

Ship ballast water promoting the long-range migration of antibiotic resistance genes (ARGs) has raised a great concern. This study attempted to reveal ARGs profile in ballast water and decipher their hosts and potential risk using metagenomic approaches. In total, 710 subtypes across 26 ARG types were identified among the ballast water samples from 13 ships of 11 countries and regions, and multidrug resistance genes were the most dominant ARGs. The composition of ARGs were obviously different across samples, and only 5% of the ARG subtypes were shared by all samples. Procrustes analysis showed the bacterial community contributed more than the mobile genetic elements (MGEs) in shaping the antibiotic resistome. Further, 79 metagenome-assembled genomes (46 genera belong to four phyla) were identified as ARG hosts, with predominantly affiliated with the Proteobacteria. Notably, potential human pathogens (Alcaligenes, Mycolicibacterium, Rhodococcus and Pseudomonas) were also recognized as the ARG hosts. Above 30% of the ARGs hosts contained the MGEs simultaneously, supporting a pronounced horizontal gene transfer capability. A total of 43 subtypes (six percent of overall ARGs) of ARGs were assessed with high-risk, of which 23 subtypes belonged to risk Rank I (including rsmA, ugd, etc.) and 20 subtypes to the risk Rank II (including aac(6)-I, sul1, etc.). In addition, antibiotic resistance risk index indicated the risk of ARGs in ballast water from choke points of maritime trade routes was significantly higher than that from other regions. Overall, this study offers insights for risk evaluation and management of antibiotic resistance in ballast water.

Antimicrobial resistance and geographical distribution of Staphylococcus sp. isolated from whiting (Merlangius merlangus) and seawater in the English Channel and the North sea

Staphylococcus is a significant food safety hazard. The marine environment serves as a source of food for humans and is subject to various human-induced discharges, which may contain Staphylococcus strains associated with antimicrobial resistance (AMR). The aim of this study was to assess the occurrence and geographical distribution of AMR Staphylococcus isolates in seawater and whiting (Merlangius merlangus) samples collected from the English Channel and the North Sea. We isolated and identified 238 Staphylococcus strains, including 12 coagulase-positive (CoPs) and 226 coagulase-negative (CoNs) strains. All CoPs isolates exhibited resistance to at least one of the 16 antibiotics tested. Among the CoNs strains, 52% demonstrated resistance to at least one antibiotic, and 7 isolates were classified as multi-drug resistant (MDR). In these MDR strains, we identified AMR genes that confirmed the resistance phenotype, as well as other AMR genes, such as quaternary ammonium resistance. One CoNS strain carried 9 AMR genes, including both antibiotic and biocide resistance genes. By mapping the AMR phenotypes, we demonstrated that rivers had a local influence, particularly near the English coast, on the occurrence of AMR Staphylococcus. The analysis of marine environmental parameters revealed that turbidity and phosphate concentration were implicated in the occurrence of AMR Staphylococcus. Our findings underscore the crucial role of wild whiting and seawater in the dissemination of AMR Staphylococcus within the marine environment, thereby posing a risk to human health.

Monitoring indicator genes to assess antimicrobial resistance contamination in phytoplankton and zooplankton communities from the English Channel and the North Sea

Phytoplankton and zooplankton play a crucial role in marine ecosystems as the basis of the food webs but are also vulnerable to environmental pollutants. Among emerging pollutants, antimicrobial resistance (AMR) is a major public health problem encountered in all environmental compartments. However, the role of planktonic communities in its dissemination within the marine environment remains largely unexplored. In this study, we monitored four genes proposed as AMR indicators (tetA, blaTEM, sul1, and intI1) in phytoplankton and zooplankton samples collected in the English Channel and the North Sea. The indicator gene abundance was mapped to identify the potential sources of contamination. Correlation was assessed with environmental parameters to explore the potential factors influencing the abundance of AMR in the plankton samples. The prevalence in phytoplankton and zooplankton of sul1 and intI1, the most quantified indicator genes, ranged from 63 to 88%. A higher level of phytoplankton and zooplankton carrying these genes was observed near the French and English coasts in areas subjected to anthropogenic discharges from the lands but also far from the coasts. Correlation analysis demonstrated that water temperature, pH, dissolved oxygen and turbidity were correlated to the abundance of indicator genes associated with phytoplankton and zooplankton samples. In conclusion, the sul1 and intI1 genes would be suitable indicators for monitoring AMR contamination of the marine environment, either in phytoplankton and zooplankton communities or in seawater. This study fills a part of the gaps in knowledge about the AMR transport by marine phytoplankton and zooplankton, which may play a role in the transmission of resistance to humans through the marine food webs.

Genomic surveillance for antimicrobial resistance - a One Health perspective

Antimicrobial resistance (AMR) - the ability of microorganisms to adapt and survive under diverse chemical selection pressures - is influenced by complex interactions between humans, companion and food-producing animals, wildlife, insects and the environment. To understand and manage the threat posed to health (human, animal, plant and environmental) and security (food and water security and biosecurity), a multifaceted 'One Health' approach to AMR surveillance is required. Genomic technologies have enabled monitoring of the mobilization, persistence and abundance of AMR genes and mutations within and between microbial populations. Their adoption has also allowed source-tracing of AMR pathogens and modelling of AMR evolution and transmission. Here, we highlight recent advances in genomic AMR surveillance and the relative strengths of different technologies for AMR surveillance and research. We showcase recent insights derived from One Health genomic surveillance and consider the challenges to broader adoption both in developed and in lower- and middle-income countries.

Traditional and new proposals for environmental microbial indicators-a review

The continuous increment in world population coupled with the greatest natural resource consumption and waste generation has an enormous impact on the environment. To date, using biological indicators (bioindicators) to evaluate the biological quality of natural environments is very common. Nonetheless, selecting those suitable for each ecosystem or contaminant is one of the most important issues for environmental sciences. Bacteria and helminths are mainly related to fecal contamination, while antibiotic-resistant bacteria, fungi, viruses, and microalgae are organisms used to determine deteriorated ecosystems by diverse contaminants. Nowadays, each bioindicator is used as a specific agent of different contaminant types, but detecting and quantifying these bioindicator microorganisms can be performed from simple microscopy and culture methods up to a complex procedure based on omic sciences. Developing new techniques based on the metabolism and physiological responses of traditional bioindicators is shown in a fast environmental sensitivity analysis. Therefore, the present review focuses on analyzing different bioindicators to facilitate developing suitable monitoring environmental systems according to different pollutant agents. The traditional and new methods proposed to detect and quantify different bioindicators are also discussed. Their vital role is considered in implementing efficient ecosystem bioprospection, restoration, and conservation strategies directed to natural resource management.

Distribution and antibiotic resistance of vibrio population in an urbanized tropical lake-the Vembanad-in the southwest coast of India

Among the diverse Vibrio spp. autochthonous to coastal ecosystems, V. cholerae, V. fluvialis, V. vulnificus and V. parahaemolyticus are pathogenic to humans. Increasing sea-surface temperature, sea-level rise and water-related disasters associated with climate change have been shown to influence the proliferation of these bacteria and change their geographic distribution. We investigated the spatio-temporal distribution of Vibrio spp. in a tropical lake for 1 year at a 20-day interval. The abundance of Vibrio spp. was much higher during the south-west monsoon in 2018, when the lake experienced a once-in-a-century flood. The distribution of Vibrio spp. was influenced by salinity (r = 0.3, p < 0.001), phosphate (r = 0.18, p < 0.01) and nitrite (r = 0.16, p < 0.02) in the water. We isolated 470 colonies of Vibrio-like organisms and 341 could be revived further and identified using 16S rRNA gene sequencing. Functional annotations showed that all the 16 Vibrio spp. found in the lake could grow in association with animals. More than 60% of the isolates had multiple antibiotic resistance (MAR) index greater than 0.5. All isolates were resistant to erythromycin and cefepime. The proliferation of multiple antibiotic-resistant Vibrio spp. is a threat to human health. Our observations suggest that the presence of a diverse range of Vibrio spp. is favoured by the low-saline conditions brought about by heavy precipitation. Furthermore, infections caused by contact with Vibrio-contaminated waters may be difficult to cure due to their multiple antibiotic resistances. Therefore, continuous monitoring of bacterial pollution in the lakes is essential, as is the generation of risk maps of vibrio-infested waters to avoid public contact with contaminated waters and associated disease outbreaks.

Marine bacteria harbor the sulfonamide resistance gene sul4 without mobile genetic elements

Marine bacteria are possible reservoirs of antibiotic-resistance genes (ARGs) originating not only from clinical and terrestrial hot spots but also from the marine environment. We report here for the first time a higher rate of the sulfonamide-resistance gene sul4 in marine bacterial isolates compared with other sul genes. Among four sulfonamide-resistance genes (sul1, sul2, sul3, and sul4), sul4 was most abundant (45%) in 74 sulfonamide-resistant marine isolates by PCR screening. The order of abundance was sul4 (33 isolates) >sul2 (6 isolates) >sul3 (5 isolates) >sul1 (1 isolate). Whole-genome sequencing of 23 isolates of sul4-expressing α- and γ-proteobacteria and bacilli revealed that sul4 was not accompanied by known mobile genetic elements. This suggests that sul4 in these marine isolates is clonally transferred and not horizontally transferable. Folate metabolism genes formed a cluster with sul4, suggesting that the cluster area plays a role in folate metabolism, at which sul4 functions as a dihydropteroate synthase. Thus, sul4 might be expressed in marine species and function in folate synthesis, but it is not a transferable ARG.

Study on the effectiveness of membrane separation + N2 deoxidation process for the treatment of bacteria in ballast water

Effects of the membrane separation + N₂ deoxidation process on the abundance and activity of bacteria were examined under two salinity conditions at Yangshan Port, Shanghai, China. Sequencing of 16S rRNA gene amplicons demonstrated a decrease in the diversity and activity of bacteria in fresh water and marine water, with a total removal rate of approximately 63 % and 69 %, respectively. Indicator bacteria decreased to 10 CFU·100 mL^-1, which met the IMO D-2 standard. A total of 13 potential pathogens were detected after treatment, indicating that there is still a risk of pathogenic bacteria invasion in the discharge water, particularly marine bacteria, and that the D-2 standard may be insufficient as a preventive measure against pathogenic bacteria transfer. The results will provide reference for government supervision, and will also be important for monitoring foreign bacteria and technology development.

Bacterial communities in ballast tanks of cargo vessels - Shaped by salinity, treatment and the point of origin of the water but "hatch" its typical microbiome

Ballast water is a main vector of introduction of potentially harmful or pathogenic aquatic organisms. The development of genetic tools for ballast water monitoring has been underway and highlighted as a source for accurate and reliable data for decision making. We used 16S rRNA gene amplicon sequencing to analyze the microbial communities found in the ballast water of fifteen commercial ships routed through two Estonian ports. In parallel, samples from the port area were collected at the same time each ship visited. Fluorescence microscopy was utilized to assess the effectiveness of the treatment applied to ballast water. In addition, supplemental samples were collected from Hamburg Port (Germany) and a ballast tank decontamination system used at this port. The composition and diversity of bacterial communities varied greatly between obtained samples. The application of UV treatment did not demonstrate significant reduction in species richness estimates. The composition of microbial communities was significantly influenced by salinity, treatment (mainly untreated or UV treated) and the point of origin of the ballast water. Over a hundred potentially pathogenic bacterial taxa were found in relatively high abundance, including in ballast water that had received UV treatment. These shortcomings of stand-alone UV treatment of ballast water, especially when weak treatment is applied insufficiently, highlight the danger of possible harmful effects arising over time and the need for genetic tools for ballast water monitoring and management.

Seasonal distribution of antibiotic resistance genes under the influence of land-ocean interaction in a semi-enclosed bay

The irrational use of antibiotics has given rise to the proliferation of antibiotic resistance genes (ARGs) in coastal bays. There were few reports on the seasonal distribution of ARGs under the influence of land-ocean interaction in coastal bay. This work studied the seasonal and spatial proliferation of ARGs under the influences of land-ocean interaction in the Sishili Bay. Ten ARGs including tetB, tetG, tetX, sul1, sul2, qnrA, qnrB, qnrS, ermF, ermT and class 1 integron-integrase gene (intI1) were detected and quantified. The relative abundances of intI1 and most of ARGs were in orders of magnitude of 1 × 10^-7-2 copies/16S rRNA copies. The abundances of total ARGs in autumn and summer were much higher than those in the other seasons. Estuary, port and aquaculture farms were important reservoirs of ARGs in the bay. The nutrient levels in coastal water were positively associated with most of the ARGs and intI1, indicating that the water quality was an important driver of ARGs and their transmission. The land-based discharge and seawater stratification were proved to be the dominant driving factors for the seasonal distribution of ARGs in the coastal bay. The land-based discharge and seawater stratification were enhanced from spring to summer, which led to the sharp increase in ARGs in the surface water of the bay.

Occurrence of Indicator Genes of Antimicrobial Resistance Contamination in the English Channel and North Sea Sectors and Interactions With Environmental Variables

The marine environment is a potential natural reservoir of antimicrobial resistance genes (ARGs), subject to anthropogenic effluents (wastewater, industrial, and domestic), and known as a final receiving system. The aim of this study was to investigate the abundance and geographical distribution of the three bla_TEM , sul1, and intI1 genes, proposed as indicators of contamination to assess the state of antimicrobial resistance in environmental settings, added to the tetA gene and the microbial population (tuf gene) in the English Channel and North Sea areas. Bacterial DNA was extracted from 36 seawater samples. The abundance of these genes was determined by quantitative PCR (qPCR) and was analyzed in association with environmental variables and geographical locations to determine potential correlations. The bla_TEM and tetA genes were quantified in 0% and 2.8% of samples, respectively. The sul1 and intI1 genes were detected in 42% and 31% of samples, respectively, with an apparent co-occurrence in 19% of the samples confirmed by a correlation analysis. The absolute abundance of these genes was correlated with the microbial population, with results similar to the relative abundance. We showed that the sul1 and intI1 genes were positively correlated with dissolved oxygen and turbidity, while the microbial population was correlated with pH, temperature and salinity in addition to dissolved oxygen and turbidity. The three tetA, sul1, and intI1 genes were quantified in the same sample with high abundances, and this sample was collected in the West Netherlands coast (WN) area. For the first time, we have shown the impact of anthropogenic inputs (rivers, man-made offshore structures, and maritime activities) and environmental variables on the occurrence of three indicators of environmental contamination by antimicrobial resistance in the North Sea and English Channel seawaters.

A Correlation Study of the Microbiota Between Oral Cavity and Tonsils in Children With Tonsillar Hypertrophy

Tonsillar hypertrophy is a common disease in 3-to-6-year-old children, which may cause serve symptoms like airway obstruction. Microbiological factors play an important role in the etiology of tonsillar hypertrophy. As the starting point of digestive and respiratory tracts, the microbial composition of the oral cavity is not only unique but also closely related to the resident microbiota in other body sites. Here we reported a correlation study of the microbiota between oral cavity and tonsils in children with tonsillar hypertrophy. Saliva, supragingival plaque, and wiped samples from the tonsil surface were collected from both tonsillar hypertrophy patients and participants with healthy tonsils and were then analyzed using Illumina Miseq Sequencing of the 16S rRNA gene. In the tonsillar hypertrophic state, more genera were detected on the tonsil surface than in the tonsil parenchyma, with more intra-microbiota correlations. When tonsillar hypertrophy occurred, both the oral cavity and tonsil surface endured microbiome shift with increased genera category and more active bacterial interactions. Over half of the newly detected genera from the tonsillar hypertrophic state were associated with infection and inflammation process or exhibited antibiotic-resistant characters. Of each individual, the microbial composition and structure of saliva seemed more similar to that of the tonsil surface, compared with the supragingival plaque. In salivary microbiota, genus Johnsonella might be relative with the healthy state of tonsils, while Pseudoxanthomonas might be relative with tonsillar hypertrophy. Our study supported the link between oral microbiota with the healthy and hypertrophic states of tonsils and may provide new directions for future researches in the specific role of oral microbiota in the etiology of tonsil diseases.

Lead and Chromium Immobilization Process Subjected to Different Freeze-Thaw Treatments in Soils of the Northeastern Qinghai-Tibet Plateau

The freeze-thaw cycle is one of the important processes that affected heavy metal behaviors in soil. However, information regarding the adsorption and desorption behavior of heavy metals in soils under different freeze-thaw conditions is relatively less. Therefore, different freeze-thaw conditions including unfrozen, 15 freeze-thaw cycles at 60% water content, and 15 freeze-thaw cycles at 100% water content were investigated. Then the adsorption and desorption behaviors of Pb and Cr in freeze-thaw soils were studied. Results showed the Pb and Cr adsorption amount mostly decreased with increasing water-soil ratio, and the soil performance of Pb and Cr adsorption at same water-soil ratios showed variation under different freeze-thaw conditions. The Pb isothermal adsorption was higher for most freeze-thaw treatments compared to the control. The soil performance of Cr isothermal adsorption showed variation under different freeze-thaw conditions. Most electrostatic binding of Pb and Cr were stronger under unfrozen and freeze-thaw conditions than unfrozen conditions. Most Pb and Cr adsorption kinetics patterns of freeze-thaw treated soils were rapid than unfrozen conditions. These results implied that freeze-thaw cycles could change the soil adsorption and desorption patterns of Pb and Cr. Therefore, further studies are urgently needed to investigate Pb and Cr immobilization mechanisms in soils during freeze-thaw cycles. Hence, these findings provided useful information on Pb and Cr immobilization process in soils that underwent freeze-thaw cycles to offer an additional insight into predicting Pb and Cr behaviors in cold and freezing environments.

Anthropogenic Modifications to Estuaries Facilitate the Invasion of Non-Native Species

New observations of non-indigenous species (NIS) in coastal waters, such as the Gulf of Cadiz (Spain) have increased since 1980 and more or less exponentially in the last five years. Ballast water has become the most significant pathway for unintentional introductions of NIS into marine ecosystems. For example, the marine larvae of crustacean decapods that inhabit the water column could be transported in ballast water. Although elevated concentrations of metals are toxic to many marine organisms, some of them have evolved effective detoxification, or avoidance mechanisms making it possible to consider they have a superior ability to withstand exposures to these toxicants. In this text, we try to reinforce the hypothesis that anthropogenic modifications (such as chemical alterations and modified environments) benefit NIS with broad environmental tolerances. Taking these risks into account, a reinforcement of efficient Ballast Water Management Systems to respond to today’s challenging environmental conditions is discussed.

Antimicrobial Ceramic Filters for Water Bio-Decontamination

Bio-contamination of water through biofouling, which involves the natural colonization of submerged surfaces by waterborne organisms, is a global socio-economic concern, allied to premature materials bio-corrosion and high human health risks. Most effective strategies release toxic and persistent disinfectant compounds into the aquatic medium, causing environmental problems and leading to more stringent legislation regarding their use. To minimize these side effects, a newly non-biocide-release coating strategy suitable for several polymeric matrices, namely polydimethylsiloxane and polyurethane (PU)-based coatings, was used to generate antimicrobial ceramic filters for water bio-decontamination. The best results, in terms of antimicrobial activity and biocide release, showed an expressed delay and a decrease of up to 66% in the population of methicillin-resistant Staphylococcus aureus bacteria on ceramic filters coated with polyurethane (PU)-based coatings containing grafted Econea biocide, and no evidence of biocide release after being submerged for 45 days in water. Biocidal PU-based surfaces were also less prone to Enterococcus faecalis biofilm formation under flow conditions with an average reduction of 60% after 48 h compared to a pristine PU-based surface. Biocidal coated filters show to be a potential eco-friendly alternative for minimizing the environmental risks associated with biofouling formation in water-based industrial systems.

Occurrence of emerging sulfonamide resistance (sul1 and sul2) associated with mobile integrons-integrase (intI1 and intI2) in riverine systems

Global use of antibiotics has exceedingly enhanced in agricultural, veterinary and prophylactic human use in recent days. Hence, these antibiotics can easily be found in the environment. This study revealed the occurrence of emerging MDR and ESBL producing strains, pollution profile, and factors integrons (intI1 and intI2) and environmental factors associated, in the riverine systems under different ecological and geo-climatic zones were investigated. The samples were collected based on anthropogenic intervention such as discharge of domestic wastes, industrial wastes, hospital, and municipal wastes. Among 160bacterial morphotypes, 121 (75.62%) exhibited MDR trait with maximum resistance towards lincosamide (CD = 71.3%), beta-lactams (P = 70.6%; AMX = 66.3%), cephalosporin (CZ = 60.6%; CXM = 34.4%), sulfonamide (COT = 50.6%; TR = 43.8%) followed by macrolide (E = 29.4%), tetracycline (TET = 18.8%), aminoglycosides (S = 18.8%; GEN = 6.3%), fluoroquinolones (NX = 18.1%; OF = 4.4%) and carbapenem (IPM = 5.0%). IntI1 gene was detected in 73 (60.3%) of isolates, whereas intI2 was found in 11 (9.09%) isolates. Eight (6.61%) isolates carried both integron genes (intI1 and intI2). sul1 and dfrA1 genes were detected in 53 (72.6%) and 63 (86.3%) isolates, respectively. A total of 103 (85.1%) were found ESBL positive with the presence of ESBL genes in 100 (97.08%) isolates. In riverine systems most prevalent ESBL gene blaTEM (93.0%) was detected alone as well as in combination with bla genes. The data can be utilized for public awareness and regulation of guidelines by local governing bodies as an alarming threat to look-out against the prevalent resistance in environment thereby assisting in risk management during epidemics. This study is a comprehensive investigation of emerging antibiotic pollutants and its resistance in bacteria associated with factors integrons-integrase responsible for its dissemination. It may also assist in global surveillance of antibiotic resistance and policies to curtail unnecessary antibiotic use.