Horizontal Gene Transfer and Its Association with Antibiotic Resistance in the Genus Aeromonas spp

Unveiling novel threats: Urban river isolation of Aeromonas veronii with unusual VEB-28 extended-spectrum β-lactamase and distinct mcr variants

Aeromonas spp. are frequently encountered in aquatic environments, with Aeromonas veronii emerging as an opportunistic pathogen causing a range of diseases in both humans and animals. Recent reports have raised public health concerns due to the emergence of multidrug-resistant Aeromonas spp. This is particularly noteworthy as these species have demonstrated the ability to acquire and transmit antimicrobial resistance genes (ARGs). In this study, we report the genomic and phenotypic characteristics of the A. veronii TR112 strain, which harbors a novel variant of the Vietnamese Extended-spectrum β-lactamase-encoding gene, blaVEB-28, and two mcr variants recovered from an urban river located in the Metropolitan Region of São Paulo, Brazil. A. veronii TR112 strain exhibited high minimum inhibitory concentrations (MICs) for ceftazidime (64 μg/mL), polymyxin (8 μg/mL), and ciprofloxacin (64 μg/mL). Furthermore, the TR112 strain demonstrated adherence to HeLa and Caco-2 cells within 3 h, cytotoxicity to HeLa cells after 24 h of interaction, and high mortality rates to the Galleria mellonella model. Genomic analysis showed that the TR112 strain belongs to ST257 and presented a range of ARGs conferring resistance to β-lactams (blaVEB-28, blaCphA3, blaOXA-912) and polymyxins (mcr-3 and mcr-3.6). Additionally, we identified a diversity of virulence factor-encoding genes, including those encoding mannose-sensitive hemagglutinin (Msh) pilus, polar flagella, type IV pili, type II secretion system (T2SS), aerolysin (AerA), cytotoxic enterotoxin (Act), hemolysin (HlyA), hemolysin III (HlyIII), thermostable hemolysin (TH), and capsular polysaccharide (CPS). In conclusion, our findings suggest that A. veronii may serve as an environmental reservoir for ARGs and virulence factors, highlighting its importance as a potential pathogen in public health.

One Health-based management for sustainably mitigating tetracycline-resistant Aeromonas hydrophila-induced health risk

Aeromonas hydrophila has ability to spread tetracycline resistance (tetR) under stresses of oxytetracycline (OTC), one of the most important antibiotics in aquaculture industry. Even though environmental reservoir of Aeromonas allows it to be at interfaces across One Health components, a robust modelling framework for rigorously assessing health risks is currently lacking. We proposed a One Health-based approach and leveraged recent advances in quantitative microbial risk assessment appraised by available dataset to interpret interactions at the human-animal-environment interfaces in various exposure scenarios. The dose-response models were constructed considering the effects on mortality for aquaculture species and tetR genes transfer for humans. A scenario-specific risk assessment on pond species-associated A. hydrophila infection and human gut-associated tetR genes transfer was examined. Risk-based control strategies were involved to test their effectiveness. We showed that farmed shrimp exposed to tetracycline-resistant A. hydrophila in OTC-contaminated water experienced higher infection risk (relative risk: 1.25-1.34). The tetR genes transfer risk for farmers in shrimp ponds (∼2 × 10-4) and swimmers in coastal areas (∼4 × 10-6) during autumn exceeded acceptable risk (10-6). This cautionary finding underscores the importance of accounting for monitoring, assessing, and mitigating occupational health hazards among workers in shrimp farming sectors within future One Health-based strategies for managing water infection risks. We recommend that OTC emission rate together with A. hydrophila concentration should be reduced by up to 70-99% to protect human, farmed shrimp, and environmental health. Our predictive framework can be adopted for other systems and be used as a "risk detector" for assessing tetR-related health risks that invoke potential risk management on addressing sustainable mitigation on offsetting residual OTC emission and tetR genes spread in a species-human-environmental health system.

Bacterial hosts of clinically significant beta-lactamase genes in Croatian wastewaters

Wastewater treatment plants (WWTPs) provide a suitable environment for the interaction of antibiotic resistant bacteria and antibiotic-resistance genes (ARGs) from human, animal, and environmental sources. The aim was to study the influent and effluent of two WWTPs in Croatia to identify bacterial hosts of clinically important beta-lactamase genes (blaTEM, blaVIM, blaOXA-48-like) and observe how their composition changes during the treatment process. A culture-independent epicPCR (Emulsion, Paired isolation and Concatenation Polymerase Chain Reaction) was used to identify the ARG hosts, and 16S rRNA amplicon sequencing to study the entire bacterial community. Different wastewater sources contributed to the significant differences in bacterial composition of the wastewater between the two WWTPs studied. A total of 167 genera were detected by epicPCR, with the Arcobacter genus, in which all ARGs studied were present, dominating in both WWTPs. In addition, the clinically important genera Acinetobacter and Aeromonas contained all ARGs examined. The blaOXA-48-like gene had the highest number of hosts, followed by blaVIM, while blaTEM had the narrowest host range. Based on 16S rRNA gene sequencing, ARG hosts were detected in both abundant and rare taxa. The number of hosts carrying investigated ARGs was reduced by wastewater treatment. EpicPCR provided valuable insights into the bacterial hosts of horizontally transmissible beta-lactamase genes in Croatian wastewater.

Genomic characterization of Aeromonas spp. isolates from striped catfish with motile Aeromonas septicemia and human bloodstream infections in Vietnam

Aeromonas spp. are commonly found in the aquatic environment and have been responsible for motile Aeromonas septicemia (MAS) in striped catfish, resulting in significant economic loss. These organisms also cause a range of opportunistic infections in humans with compromised immune systems. Here, we conducted a genomic investigation of 87 Aeromonas isolates derived from diseased catfish, healthy catfish and environmental water in catfish farms affected by MAS outbreaks in eight provinces in Mekong Delta (years: 2012-2022), together with 25 isolates from humans with bloodstream infections (years: 2010-2020). Genomics-based typing method precisely delineated Aeromonas species while traditional methods such as aerA PCR and MALDI-TOF were unable identify A. dhakensis. A. dhakensis was found to be more prevalent than A. hydrophila in both diseased catfish and human infections. A. dhakensis sequence type (ST) 656 followed by A. hydrophila ST251 were the predominant virulent species-lineages in diseased catfish (43.7 and 20.7 %, respectively), while diverse STs were found in humans with bloodstream infections. There was evidence of widespread transmission of ST656 and ST251 on striped catfish in the Mekong Delta region. ST656 and ST251 isolates carried a significantly higher number of acquired antimicrobial resistance (AMR) genes and virulence factors in comparison to other STs. They, however, exhibited several distinctions in key virulence factors (i.e. lack of type IV pili and enterotoxin ast in A. dhakensis), AMR genes (i.e. presence of imiH carbapenemase in A. dhakensis), and accessory gene content. To uncover potential conserved proteins of Aeromonas spp. for vaccine development, pangenome analysis has unveiled 2202 core genes between ST656 and ST251, of which 78 proteins were in either outer membrane or extracellular proteins. Our study represents one of the first genomic investigations of the species distribution, genetic landscape, and epidemiology of Aeromonas in diseased catfish and human infections in Vietnam. The emergence of antimicrobial resistant and virulent A. dhakensis strains underscores the needs of enhanced genomic surveillance and strengthening vaccine research and development in preventing Aeromonas diseases in catfish and humans, and the search for potential vaccine candidates could focus on Aeromonas core genes encoded for membrane and secreted proteins.

Characterization of biofilm formation and multi-drug resistance among Pseudomonas aeruginosa isolated from hospital wastewater in Dhaka, Bangladesh

Hospital wastewater has been identified as a hotspot for the emergence and transmission of multidrug-resistant (MDR) pathogens that present a serious threat to public health. Therefore, we investigated the current status of antibiotic resistance as well as the phenotypic and genotypic basis of biofilm formation in Pseudomonas aeruginosa from hospital wastewater in Dhaka, Bangladesh. The disc diffusion method and the crystal violet assay were performed to characterize antimicrobial resistance and biofilm formation, respectively. Biofilm and integron-associated genes were amplified by the polymerase chain reaction. Isolates exhibited varying degrees of resistance to different antibiotics, in which >80% of isolates showed sensitivity to meropenem, amikacin, and gentamicin. The results indicated that 93.82% of isolates were MDR and 71 out of 76 MDR isolates showed biofilm formation activities. We observed the high prevalence of biofilm-related genes, in which algD+pelF+pslD+ (82.7%) was found to be the prevalent biofilm genotypic pattern. Sixteen isolates (19.75%) possessed class 1 integron (int1) genes. However, statistical analysis revealed no significant association between biofilm formation and multidrug resistance (χ2 = 0.35, P = 0.55). Taken together, hospital wastewater in Dhaka city may act as a reservoir for MDR and biofilm-forming P. aeruginosa, and therefore, the adequate treatment of wastewater is recommended to reduce the occurrence of outbreaks.

The presence of virulence factor genes downregulates uterine AQP3 and alters glutathione peroxidase activity and uterine histopathology in canine pyometra

Present study was designed to evaluate the role of virulence factor genes (papG, cnf1 and hylA) in the pathogenesis of canine pyometra. Antimicrobial susceptibility test and detection of virulence genes were performed Escherichia coli (E. coli) detected in uterine swab samples. Animals were divided into two groups based on the presence (VF+, n:14) or absence (VF-, n:7) of the virulence factor genes papG, cnf1 and hylA. Blood and tissue glutathione peroxidase activity, uterine histopathologic analysis and AQP3, ESR1, PGR, OXTR gene expressions were determined in both groups. Statistical analyses were performed using Stata version 15.1. All E. coli isolates were susceptible to amikacin, whereas resistant to ampicillin, amoxicillin/clavulanic acid and lincomycin. None of the isolates were susceptible to cefotaxime. E. coli isolates had at least one virulence gene. The most prevalent gene was fimH (100%), followed by fyuA (95.8%), usp (83.3%), sfa (75%), cnf1 and hlyA (70.8%) genes. Blood GPx activity was greater in VF+ animals. On the other hand, uterine tissue GPx activity was lower in VF+ group compared to the control group. Expression levels of AQP3 were upregulated more than fivefold in VF-dogs compared to the control group. In addition, AQP3 expression levels were found approximately threefold higher in VF (-) than VF (+) group (p < .05). Varying degree of inflammation noted for all animals with pyometra, but the presence of bacteria noted only in VF+ animals. In conclusion, the presence of virulence factor genes does not play a role in the histopathological degree of inflammation, the presence of bacteria was found to vary. Serum GPx activity increased in VF+ animals. While the hormone receptor expressions were similar, AQP expression was upregulated in the absence of virulence factor genes.

Emerging challenges in antimicrobial resistance: implications for pathogenic microorganisms, novel antibiotics, and their impact on sustainability

Overuse of antibiotics is accelerating the antimicrobial resistance among pathogenic microbes which is a growing public health challenge at the global level. Higher resistance causes severe infections, high complications, longer stays at hospitals and even increased mortality rates. Antimicrobial resistance (AMR) has a significant impact on national economies and their health systems, as it affects the productivity of patients or caregivers due to prolonged hospital stays with high economic costs. The main factor of AMR includes improper and excessive use of antimicrobials; lack of access to clean water, sanitation, and hygiene for humans and animals; poor infection prevention and control measures in hospitals; poor access to medicines and vaccines; lack of awareness and knowledge; and irregularities with legislation. AMR represents a global public health problem, for which epidemiological surveillance systems have been established, aiming to promote collaborations directed at the well-being of human and animal health and the balance of the ecosystem. MDR bacteria such as E. coli, Staphylococcus aureus, Pseudomonas aeruginosa, Enterococcus spp., Acinetobacter spp., and Klebsiella pneumonia can even cause death. These microorganisms use a variety of antibiotic resistance mechanisms, such as the development of drug-deactivating targets, alterations in antibiotic targets, or a decrease in intracellular antibiotic concentration, to render themselves resistant to numerous antibiotics. In context, the United Nations issued the Sustainable Development Goals (SDGs) in 2015 to serve as a worldwide blueprint for a better, more equal, and more sustainable existence on our planet. The SDGs place antimicrobial resistance (AMR) in the context of global public health and socioeconomic issues; also, the continued growth of AMR may hinder the achievement of numerous SDGs. In this review, we discuss the role of environmental pollution in the rise of AMR, different mechanisms underlying the antibiotic resistance, the threats posed by pathogenic microbes, novel antibiotics, strategies such as One Health to combat AMR, and the impact of resistance on sustainability and sustainable development goals.

Nosocomial infections by diverse carbapenemase-producing Aeromonas hydrophila associated with combination of plumbing issues and heat waves

BACKGROUND

Aquatic opportunistic pathogen Aeromonas hydrophila, known to persist in low-nutrient chlorinated waters, can cause life-threatening infections. Two intensive care units experienced a cluster of Aeromonas infections following outdoor temperature spikes coinciding with recurrent plumbing issues, with fatalities due to severe underlying comorbidities co-occurring with extensively-drug resistant (XDR) Aeromonas.

METHODS

We investigated this cluster using whole genome sequencing to assess genetic relatedness of isolates and identify antimicrobial resistance determinants. Three A. hydrophila were isolated from patients staying in or adjacent to rooms with plumbing issues during or immediately after periods of elevated outdoor temperatures. Sinks and faucets were swabbed for culture.

RESULTS

All A. hydrophila clinical isolates exhibited carbapenem resistance but were not genetically related. Diverse resistance determinants corresponding to extensively-drug resistant were found, including co-occurring KPC-3 and VIM-2, OXA-232, and chromosomal CphA-like carbapenemase genes, contributing to major treatment challenges. All 3 patients were treated with multiple antibiotic regimens to overcome various carbapenemase classes and expired due to underlying comorbidities. Environmental culture yielded no Aeromonas.

CONCLUSIONS

While the investigation revealed no singular source of contamination, it supports a possible link between plumbing issues, elevated outdoor temperatures and incidence of nosocomial Aeromonas infections. The diversity of carbapenemase genes detected in these wastewater-derived Aeromonas warrants heightened infection prevention precautions during periods of plumbing problems especially with heat waves.

The role and potential of computer-aided drug discovery strategies in the discovery of novel antimicrobials

Antimicrobial resistance (AMR) has become more of a concern in recent decades, particularly in infections associated with global public health threats. The development of new antibiotics is crucial to ensuring infection control and eradicating AMR. Although drug discovery and development are essential processes in the transformation of a drug candidate from the laboratory to the bedside, they are often very complicated, expensive, and time-consuming. The pharmaceutical sector is continuously innovating strategies to reduce research costs and accelerate the development of new drug candidates. Computer-aided drug discovery (CADD) has emerged as a powerful and promising technology that renews the hope of researchers for the faster identification, design, and development of cheaper, less resource-intensive, and more efficient drug candidates. In this review, we discuss an overview of AMR, the potential, and limitations of CADD in AMR drug discovery, and case studies of the successful application of this technique in the rapid identification of various drug candidates. This review will aid in achieving a better understanding of available CADD techniques in the discovery of novel drug candidates against resistant pathogens and other infectious agents.

The CRISPR-Cas system in clinical strains of Acinetobacter baumannii: an in-silico analysis

Acinetobacter baumannii is a relevant bacterium due to its high-resistance profile. It is well known that antimicrobial resistance is primarily linked to mutations and the acquisition of external genomic material, such as plasmids or phages, to which the Clustered Regularly Interspaced Short Palindromic Repeats associated with Cas proteins, or CRISPR-Cas, system is related. It is known that the system can influence the acquisition of foreign genetic material and play a role in various physiological pathways. In this study, we conducted an in-silico analysis using 91 fully assembled genomes of clinical strains obtained from the NCBI database. Among the analyzed genomes, the I-F1 subtype of the CRISPR-Cas system was detected showcasing variations in architecture and phylogeny. Using bioinformatic tools, we determined the presence, distribution, and specific characteristics of the CRISPR-Cas system. We found a possible association of the system with resistance genes but not with virulence determinants. Analysis of the system's components, including spacer sequences, suggests its potential role in protecting against phage infections, highlighting its protective function.

Detection of chromosome-mediated blaNDM-1-carrying Aeromonas spp. in the intestinal contents of fresh water river fish in Ho Chi Minh City, Vietnam

The spread of antibiotic-resistant bacteria is a global problem that should be addressed through the perspective of the "one health" concept. The purpose of this study was to determine the contamination rate of antibiotic-resistant Aeromonas spp. in fresh water river fish purchased from a fish market in Vietnam. We then defined the pattern of antibiotic resistance to assess antibiotic-resistant contamination. Antibiotic-resistant Aeromonas spp. were detected in the intestinal contents of 32 of 80 fish. blaNDM-1 was detected in seven strains. Extended-spectrum β-lactamase and AmpC β-lactamase-related genes were detected in 28 strains, including blaCTX-M-55, blaCTX-M-15, blaCTX-M-1, and blaDHA,blaFOX, and blaMOX. The blaNDM-1 detected in the seven Aeromonas spp. strains were found chromosomally. This finding suggests that the blaNDM gene is stable in the natural environment and may spread widely into animals and humans via Aeromonas spp. with a transposon. Our results suggest the importance of continuing to monitor carbapenemase genes in Aeromonas spp. to evaluate the possibility that they may spread in other Enterobacterales, and to elucidate the mechanism of spread.

Uncovering the hidden threat: The widespread presence of chromosome-borne accessory genetic elements and novel antibiotic resistance genetic environments in Aeromonas

The emergence of antibiotic-resistant Aeromonas strains in clinical settings has presented an escalating burden on human and public health. The dissemination of antibiotic resistance in Aeromonas is predominantly facilitated by chromosome-borne accessory genetic elements, although the existing literature on this subject remains limited. Hence, the primary objective of this study is to comprehensively investigate the genomic characteristics of chromosome-borne accessory genetic elements in Aeromonas. Moreover, the study aims to uncover novel genetic environments associated with antibiotic resistance on these elements. Aeromonas were screened from nonduplicated strains collected from two tertiary hospitals in China. Complete sequencing and population genetics analysis were performed. BLAST analysis was employed to identify related elements. All newly identified elements were subjected to detailed sequence annotation, dissection, and comparison. We identified and newly designated 19 chromosomal elements, including 18 integrative and mobilizable elements (IMEs) that could be classified into four categories: Tn6737-related, Tn6836-related, Tn6840-related, and Tn6844a-related IMEs. Each class exhibited a distinct pattern in the types of resistance genes carried by the IMEs. Several novel antibiotic resistance genetic environments were uncovered in these elements. Notably, we report the first identification of the blaOXA-10 gene and blaVEB-1 gene in clinical A. veronii genome, the first presence of a tetA(E)-tetR(E) resistance gene environment within the backbone region in IMEs, and a new mcr-3.15 resistance gene environment. The implications of these findings are substantial, as they provide new insights into the evolution, structure, and dissemination of chromosomal-borne accessory elements.

Identification and characterization of motile Aeromonas spp. isolated from farmed Nile tilapia (Oreochromis niloticus) in the Philippines

AIMS

Motile Aeromonas septicaemia (MAS) caused by motile Aeromonas species is an important disease in farmed freshwater fish due to intensification of culture and improper farm practices. This study characterized and profiled motile Aeromonas species recovered from clinically sick tilapia farmed in the Philippines, with a view to identifying targeted disease prevention and control measures against MAS in farmed tilapia species.

METHODS AND RESULTS

Sixteen isolates from diseased farmed Nile tilapia were identified as Aeromonas veronii (n = 14), Aeromonas caviae (n = 1), and Aeromonas dhakensis (n = 1). Five biochemical profiles using API 20E were exhibited by the A. veronii strains giving an unreliable identification. A high level of agreement was observed in identifying the Aeromonas strains using 16S rRNA and rpoD gene sequencing, although the latter has a higher discriminatory value. Three or more virulence genes dominated by cytotoxic enterotoxin act and aerolysin aer were detected. Different genotypes based on virulence gene clustering suggested varied mechanisms used by Aeromonas to colonize and infect or to mutualistically co-exist with the fish. Acquired multiple antibiotic resistance was found in a single A. veronii isolate. All were susceptible to enrofloxacin, oxolinic acid, florfenicol, and chloramphenicol. Tetracycline and sulfonamide resistances and class 1 integron were detected in three A. veronii isolates.

CONCLUSION

Several strains of motile aeromonads, especially A. veronii, which have varied genotypes based on virulence, biochemical profile, and antibiotic resistance, are involved in MAS in natural disease outbreaks in farmed Nile tilapia in the Philippines.

Origin of Antibiotics and Antibiotic Resistance, and Their Impacts on Drug Development: A Narrative Review

Antibiotics have revolutionized medicine, saving countless lives since their discovery in the early 20th century. However, the origin of antibiotics is now overshadowed by the alarming rise in antibiotic resistance. This global crisis stems from the relentless adaptability of microorganisms, driven by misuse and overuse of antibiotics. This article explores the origin of antibiotics and the subsequent emergence of antibiotic resistance. It delves into the mechanisms employed by bacteria to develop resistance, highlighting the dire consequences of drug resistance, including compromised patient care, increased mortality rates, and escalating healthcare costs. The article elucidates the latest strategies against drug-resistant microorganisms, encompassing innovative approaches such as phage therapy, CRISPR-Cas9 technology, and the exploration of natural compounds. Moreover, it examines the profound impact of antibiotic resistance on drug development, rendering the pursuit of new antibiotics economically challenging. The limitations and challenges in developing novel antibiotics are discussed, along with hurdles in the regulatory process that hinder progress in this critical field. Proposals for modifying the regulatory process to facilitate antibiotic development are presented. The withdrawal of major pharmaceutical firms from antibiotic research is examined, along with potential strategies to re-engage their interest. The article also outlines initiatives to overcome economic challenges and incentivize antibiotic development, emphasizing international collaborations and partnerships. Finally, the article sheds light on government-led initiatives against antibiotic resistance, with a specific focus on the Middle East. It discusses the proactive measures taken by governments in the region, such as Saudi Arabia and the United Arab Emirates, to combat this global threat. In the face of antibiotic resistance, a multifaceted approach is imperative. This article provides valuable insights into the complex landscape of antibiotic development, regulatory challenges, and collaborative efforts required to ensure a future where antibiotics remain effective tools in safeguarding public health.

Polyinfection in Fish Aeromoniasis: A Study of Co-Isolated Aeromonas Species in Aeromonas veronii Outbreaks

We studied the phenotypic and genomic characteristics related to the virulence and antibiotic resistance of two Aeromonas strains, which were co-isolated before an outbreak of Aeromonas veronii among diseased seabass on Agathonisi Island, Greece, in April 2015. The first strain, AG2.13.2, is a potentially pathogenic mesophilic variant of Aeromonas salmonicida, and the second, AG2.13.5, corresponds to an Aeromonas rivipollensis related to A. rivipollensis KN-Mc-11N1 with an ANI value of 97.32%. AG2.13.2 lacks the type III secretion system just like other mesophilic strains of A. salmonicida. This characteristic has been associated with lower virulence. However, the genome of AG2.13.2 contains other important virulence factors such as type II and type VI secretion systems, and toxins such as rtxA, aerolysin aer/act, and different types of hemolysins. The strain also carries several genes associated with antibiotic resistance such as the tetE efflux pump, and exhibits resistance to tetracycline, ampicillin, and oxolinic acid. In an in vivo challenge test with gilthead seabream larvae, the A. veronii bv sobria strain AG5.28.6 exhibited the highest virulence among all tested strains. Conversely, both A. salmonicida and A. rivipollensis showed minimal virulence when administered alone. Interestingly, when A. veronii bv sobria AG5.28.6 was co-administered with A. rivipollensis, the larvae survival probability increased compared to those exposed to A. veronii bv sobria AG5.28.6 alone. This finding indicates an antagonistic interaction between A. veronii bv sobria AG5.28.6 and A. rivipollensis AG2.13.5. The co-administration of A. veronii bv sobria AG5.28.6 with Aeromonas salmonicida did not yield distinct survival probabilities. Our results validate that the primary pathogen responsible for European seabass aeromoniasis is Aeromonas veronii bv sobria.

Regulation Transcriptional of Antibiotic Resistance Genes (ARGs) in Bacteria Isolated from WWTP

The incidence of antibiotics and transcriptional regulation of ARGs in isolated bacteria from wastewater needs to be explored. By HPLC, in samples of untreated wastewater, ampicillin (49.74 ± 5.70 µg/mL), chloramphenicol (0.60 ± 0.03 µg/mL), tylosin (72.95 ± 2.03 µg/mL), and oxytetracycline (0.22 ± 0.01 µg/mL) was determined. Through metagenomic analysis identified 58 bacterial species belonging to 9 phyla and at least 14 species have shown resistance to a variety of antibiotics. Twenty-two bacterial isolates were proved to be resistant to fifteen antibiotics of new generation and used in medical research to combat infectious diseases. Fourteen strains were shown to harbor plasmids in size ranges of 2-5 Kb, 6-10 Kb and plasmids with size greater than 10 Kb. By quantitative PCR it was possible to identify genes sul, qnr, cat1, aadA1, and sat-1 gene were shown to be present in gDNA samples from treated and untreated samples of wastewater and by relative expression analysis, differential expression of cat1, ermB, act, and tetA genes was demonstrated in strains that showed identity with Escherichia coli, Bacteroides fragilis, and Salmonella thyphi, and that were stressed with different concentrations of antibiotics. The presence of ARGs in untreated water samples, as well as in bacterial isolates, was indicative that in these habitats there are microorganisms that can resist β-lactams, aminoglycosides, tetracyclines, sulfonamides, and quinolones.

An Overview of Preventive Strategies and the Role of Various Organizations in Combating Antimicrobial Resistance

The rise of antimicrobial resistance (AMR) is a major global public health threat due to excessive and inappropriate use of antibiotics and is responsible for prolonged illness, longer hospital stays, and economic burden to society. This article aims to review the factors, role of antimicrobial stewardship, preventive strategies, and role of various organizations in combating AMR. Three major factors of AMR are inappropriate and excessive utilization of antibiotics, nonadherence to infection control measures, and the emergence of pathogens that are resistant to multiple drugs. Antimicrobial stewardship initiatives play a vital role in promoting judicious and targeted utilization of antimicrobials, thereby safeguarding their efficacy and mitigating the emergence of resistance. Implementing such programs optimizes patient outcomes by ensuring that individuals receive the most suitable therapeutic interventions. International organizations have a vital role to play in addressing AMR by promoting the responsible use of antimicrobials, developing new drugs, and improving surveillance systems. As AMR's impact grows, it is critical to take a collaborative and interdisciplinary approach to mitigate its consequences effectively.

One Health and Global Health View of Antimicrobial Susceptibility through the "Eye" of Aeromonas: Systematic Review and Meta-Analysis

Antimicrobial resistance (AMR) is one of the most pressing public health concerns; therefore, it is imperative to advance our understanding of the factors influencing AMR from Global and One Health perspectives. To address this, Aeromonas populations were identified using 16S rRNA gene libraries among human, agriculture, aquaculture, drinking water, surface water, and wastewater samples, supporting its use as indicator bacteria to study AMR. A systematic review and meta-analysis was then performed from Global and One Health perspectives, including data from 221 articles describing 15 891 isolates from 57 countries. The interconnectedness of different environments was evident as minimal differences were identified between sectors among 21 different antimicrobials. However, resistance to critically important antibiotics (aztreonam and cefepime) was significantly higher among wastewater populations compared with clinical isolates. Additionally, isolates from untreated wastewater typically exhibited increased AMR compared with those from treated wastewater. Furthermore, aquaculture was associated with increased AMR to ciprofloxacin and tetracycline compared with wild-caught seafood. Using the World Health Organization AWaRe classifications, countries with lower consumption of "Access" compared to "Watch" drugs from 2000 to 2015 demonstrated higher AMR levels. The current analysis revealed negative correlations between AMR and anthropogenic factors, such as environmental performance indices and socioeconomic standing. Environmental health and sanitation were two of the environmental factors most strongly correlated with AMR. The current analysis highlights the negative impacts of "Watch" drug overconsumption, anthropogenic activity, absence of wastewater infrastructure, and aquaculture on AMR, thus stressing the need for proper infrastructure and global regulations to combat this growing problem.

Plasmid permissiveness of wastewater microbiomes can be predicted from 16S rRNA sequences by machine learning

MOTIVATION

Wastewater treatment plants (WWTPs) harbor a dense and diverse microbial community. They constantly receive antimicrobial residues and resistant strains, and therefore provide conditions for horizontal gene transfer (HGT) of antimicrobial resistance (AMR) determinants. This facilitates the transmission of clinically important genes between, e.g. enteric and environmental bacteria, and vice versa. Despite the clinical importance, tools for predicting HGT remain underdeveloped.

RESULTS

In this study, we examined to which extent water cycle microbial community composition, as inferred by partial 16S rRNA gene sequences, can predict plasmid permissiveness, i.e. the ability of cells to receive a plasmid through conjugation, based on data from standardized filter mating assays using fluorescent bio-reporter plasmids. We leveraged a range of machine learning models for predicting the permissiveness for each taxon in the community, representing the range of hosts a plasmid is able to transfer to, for three broad host-range resistance IncP plasmids (pKJK5, pB10, and RP4). Our results indicate that the predicted permissiveness from the best performing model (random forest) showed a moderate-to-strong average correlation of 0.49 for pB10 [95% confidence interval (CI): 0.44-0.55], 0.43 for pKJK5 (0.95% CI: 0.41-0.49), and 0.53 for RP4 (0.95% CI: 0.48-0.57) with the experimental permissiveness in the unseen test dataset. Predictive phylogenetic signals occurred despite the broad host-range nature of these plasmids. Our results provide a framework that contributes to the assessment of the risk of AMR pollution in wastewater systems.

AVAILABILITY AND IMPLEMENTATION

The predictive tool is available as an application at https://github.com/DaneshMoradigaravand/PlasmidPerm.

The Effects of Preservatives on Antibiotic- and Preservative-Resistant Microbes and Nitrogen/Sulfur Cycle Associated Microbial Communities in Freshwater River Sediments

The intensive use of benzoic acid (BA), 4-hydroxybenzoic acid (HB), and dehydroacetate (DHA) as additives and preservatives in cosmetics and foods causes emerging environmental pollutions. Anthropogenic releases of BA, HB and DHA are primarily emissions into water and soil. However, few studies investigate the effects of BA, HB and DHA on microbial communities in freshwater river sediments. The aim of this study is to reveal the effects of BA, HB and DHA on microbial communities in freshwater river sediments. Tetracycline-, sulfamethoxazole- and preservative-resistant microbes were increased in the river sediments treated with BA, HB and DHA. The relative abundances of methanogen- and xenobiotic-degradation-associated microbial communities were also increased in the BA-, HB- and DHA-treated sediments. The relative abundance of four nitrogen cycle associated microbial groups (anammox, nitrogen fixation, denitrification, and dissimilatory nitrate reduction) were increased after the eighth week in the BA-, HB- and DHA-treated sediments. For the sulfur cycle, the relative abundance of thiosulfate oxidation associated microbial communities were increased after the eighth week in the BA-, HB- and DHA-treated sediments. Results of this study provide insight into the effects of BA, HB and DHA on antibiotic resistance, nitrogen cycle, sulfur cycle, drug resistance and methane production in freshwater aquatic environments.

Genomic Characterization of Aeromonas veronii Provides Insights into Taxonomic Assignment and Reveals Widespread Virulence and Resistance Genes throughout the World

Aeromonas veronii is a Gram-negative bacterial species that causes disease in fish and is nowadays increasingly recurrent in enteric infections of humans. This study was performed to characterize newly sequenced isolates by comparing them with complete genomes deposited at the NCBI (National Center for Biotechnology Information). Nine isolates from fish, environments, and humans from the São Francisco Valley (Petrolina, Pernambuco, Brazil) were sequenced and compared with complete genomes available in public databases to gain insight into taxonomic assignment and to better understand virulence and resistance profiles of this species within the One Health context. One local genome and four NCBI genomes were misidentified as A. veronii. A total of 239 virulence genes were identified in the local genomes, with most encoding adhesion, motility, and secretion systems. In total, 60 genes involved with resistance to 22 classes of antibiotics were identified in the genomes, including mcr-7 and cphA. The results suggest that the use of methods such as ANI is essential to avoid misclassification of the genomes. The virulence content of A. veronii from local isolates is similar to those complete genomes deposited at the NCBI. Genes encoding colistin resistance are widespread in the species, requiring greater attention for surveillance systems.

Impact of antibiotics on gut microbiome composition and resistome in the first years of life in low- to middle-income countries: A systematic review

BACKGROUND

Inappropriate antimicrobial usage is a key driver of antimicrobial resistance (AMR). Low- and middle-income countries (LMICs) are disproportionately burdened by AMR and young children are especially vulnerable to infections with AMR-bearing pathogens. The impact of antibiotics on the microbiome, selection, persistence, and horizontal spread of AMR genes is insufficiently characterized and understood in children in LMICs. This systematic review aims to collate and evaluate the available literature describing the impact of antibiotics on the infant gut microbiome and resistome in LMICs.

METHODS AND FINDINGS

In this systematic review, we searched the online databases MEDLINE (1946 to 28 January 2023), EMBASE (1947 to 28 January 2023), SCOPUS (1945 to 29 January 2023), WHO Global Index Medicus (searched up to 29 January 2023), and SciELO (searched up to 29 January 2023). A total of 4,369 articles were retrieved across the databases. Duplicates were removed resulting in 2,748 unique articles. Screening by title and abstract excluded 2,666 articles, 92 articles were assessed based on the full text, and 10 studies met the eligibility criteria that included human studies conducted in LMICs among children below the age of 2 that reported gut microbiome composition and/or resistome composition (AMR genes) following antibiotic usage. The included studies were all randomized control trials (RCTs) and were assessed for risk of bias using the Cochrane risk-of-bias for randomized studies tool. Overall, antibiotics reduced gut microbiome diversity and increased antibiotic-specific resistance gene abundance in antibiotic treatment groups as compared to the placebo. The most widely tested antibiotic was azithromycin that decreased the diversity of the gut microbiome and significantly increased macrolide resistance as early as 5 days posttreatment. A major limitation of this study was paucity of available studies that cover this subject area. Specifically, the range of antibiotics assessed did not include the most commonly used antibiotics in LMIC populations.

CONCLUSION

In this study, we observed that antibiotics significantly reduce the diversity and alter the composition of the infant gut microbiome in LMICs, while concomitantly selecting for resistance genes whose persistence can last for months following treatment. Considerable heterogeneity in study methodology, timing and duration of sampling, and sequencing methodology in currently available research limit insights into antibiotic impacts on the microbiome and resistome in children in LMICs. More research is urgently needed to fill this gap in order to better understand whether antibiotic-driven reductions in microbiome diversity and selection of AMR genes place LMIC children at risk for adverse health outcomes, including infections with AMR-bearing pathogens.

Prevalence of the blaCTX-M and blaTEM genes among extended-spectrum beta lactamase-producing Escherichia coli isolated from broiler chickens in Indonesia

Introduction

Infections of humans and animals by multidrug resistant bacteria are increasing because of the inappropriate use of antibiotics. Disease management may be more challenging if Escherichia coli produce extended-spectrum beta-lactamase (ESBL), which could cause resistance to aztreonam and third-generation cephalosporins. This study was aimed at determining the prevalence of the blaCTX-M and blaTEM genes among ESBL-producing E. coli isolated from broiler chickens in Indonesia.

Material and Methods

A total of 115 broiler cloacal swab samples were obtained from 22 farms and studied for the presence of E. coli. The isolates were identified using approved standard methods and were purified on eosin methylene blue agar media. The E. coli isolates were subjected to sensitivity testing using beta-lactam antibiotics, and ESBL production was confirmed by a double-disc synergy test. The presence of the blaCTX-M and blaTEM genes was identified using a PCR.

Results

It was found that 99/115 (86.1%) of the isolated E. coli were resistant to beta-lactam antibiotics and 34/115 (29.6%) of them were phenotypically detected to be ESBL producers. Of the 34 isolates that were confirmed ESBL producers, 32/34 (94.1%) of them harboured the blaCTX-M and 13/34 (38.2%) the blaTEM genes. The blaCTX-M and blaTEM genes were detected together in 12/34 (35.3%) isolates.

Conclusion

This study discovered that broiler chickens are possible reservoirs of ESBL-producing E. coli that may infect humans. Thus, a committed public health education campaign is recommended in order to mitigate the potential threat to human health.

Antibiotic Resistance in Selected Emerging Bacterial Foodborne Pathogens-An Issue of Concern?

Antibiotic resistance (AR) and multidrug resistance (MDR) have been confirmed for all major foodborne pathogens: Campylobacter spp., Salmonella spp., Escherichia coli and Listeria monocytogenes. Of great concern to scientists and physicians are also reports of antibiotic-resistant emerging food pathogens-microorganisms that have not previously been linked to food contamination or were considered epidemiologically insignificant. Since the properties of foodborne pathogens are not always sufficiently recognized, the consequences of the infections are often not easily predictable, and the control of their activity is difficult. The bacteria most commonly identified as emerging foodborne pathogens include Aliarcobacter spp., Aeromonas spp., Cronobacter spp., Vibrio spp., Clostridioides difficile, Escherichia coli, Mycobacterium paratuberculosis, Salmonella enterica, Streptocccus suis, Campylobacter jejuni, Helicobacter pylori, Listeria monocytogenes and Yersinia enterocolitica. The results of our analysis confirm antibiotic resistance and multidrug resistance among the mentioned species. Among the antibiotics whose effectiveness is steadily declining due to expanding resistance among bacteria isolated from food are β-lactams, sulfonamides, tetracyclines and fluoroquinolones. Continuous and thorough monitoring of strains isolated from food is necessary to characterize the existing mechanisms of resistance. In our opinion, this review shows the scale of the problem of microbes related to health, which should not be underestimated.

Metagenomic Insights for Antimicrobial Resistance Surveillance in Soils with Different Land Uses in Brazil

Land-use conversion changes soil properties and their microbial communities, which, combined with the overuse of antibiotics in human and animal health, promotes the expansion of the soil resistome. In this context, we aimed to profile the resistome and the microbiota of soils under different land practices. We collected eight soil samples from different locations in the countryside of São Paulo (Brazil), assessed the community profiles based on 16S rRNA sequencing, and analyzed the soil metagenomes based on shotgun sequencing. We found differences in the communities' structures and their dynamics that were correlated with land practices, such as the dominance of Staphylococcus and Bacillus genera in agriculture fields. Additionally, we surveyed the abundance and diversity of antibiotic resistance genes (ARGs) and virulence factors (VFs) across studied soils, observing a higher presence and homogeneity of the vanRO gene in livestock soils. Moreover, three β-lactamases were identified in orchard and urban square soils. Together, our findings reinforce the importance and urgency of AMR surveillance in the environment, especially in soils undergoing deep land-use transformations, providing an initial exploration under the One Health approach of environmental levels of resistance and profiling soil communities.

SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies

High-throughput genome sequencing technologies enable the investigation of complex genetic interactions, including the horizontal gene transfer of plasmids and bacteriophages. However, identifying these elements from assembled reads remains challenging due to genome sequence plasticity and the difficulty in assembling complete sequences. In this study, we developed a classifier, using random forest, to identify whether sequences originated from bacterial chromosomes, plasmids, or bacteriophages. The classifier was trained on a diverse collection of 23,211 chromosomal, plasmid, and bacteriophage sequences from hundreds of bacterial species. In order to adapt the classifier to incomplete sequences, each complete sequence was subsampled into 5,000 nucleotide fragments and further subdivided into k-mers. This three-class classifier succeeded in identifying chromosomes, plasmids, and bacteriophages using k-mer distributions of complete and partial genome sequences, including simulated metagenomic scaffolds with minimum performance of 0.939 area under the receiver operating characteristic curve (AUC). This classifier, implemented as SourceFinder, has been made available as an online web service to help the community with predicting the chromosomal, plasmid, and bacteriophage sources of assembled bacterial sequence data (https://cge.food.dtu.dk/services/SourceFinder/). IMPORTANCE Extra-chromosomal genes encoding antimicrobial resistance, metal resistance, and virulence provide selective advantages for bacterial survival under stress conditions and pose serious threats to human and animal health. These accessory genes can impact the composition of microbiomes by providing selective advantages to their hosts. Accurately identifying extra-chromosomal elements in genome sequence data are critical for understanding gene dissemination trajectories and taking preventative measures. Therefore, in this study, we developed a random forest classifier for identifying the source of bacterial chromosomal, plasmid, and bacteriophage sequences.

Identification of Key Genes during Ca2+-Induced Genetic Transformation in Escherichia coli by Combining Multi-Omics and Gene Knockout Techniques

The molecular mechanism of the Ca²⁺-mediated formation of competent cells in Escherichia coli remains unclear. In this study, transcriptome and proteomics techniques were used to screen genes in response to Ca²⁺ treatment. A total of 333 differentially expressed genes (317 upregulated and 16 downregulated) and 145 differentially expressed proteins (54 upregulated and 91 downregulated) were obtained. These genes and proteins are mainly enriched in cell membrane components, transmembrane transport, and stress response-related functional terms. Fifteen genes with these functions, including yiaW, ygiZ, and osmB, are speculated to play a key role in the cellular response to Ca²⁺. Three single-gene deletion strains were constructed with the Red homologous recombination method to verify its function in genetic transformation. The transformation efficiencies of yiaW, ygiZ, and osmB deletion strains for different-size plasmids were significantly increased. None of the three gene deletion strains changed in size, which is one of the main elements of microscopic morphology, but they exhibited different membrane permeabilities and transformation efficiencies. This study demonstrates that Ca²⁺-mediated competence formation in E. coli is not a simple physicochemical process and may involve the regulation of genes in response to Ca²⁺. This study lays the foundation for further in-depth analyses of the molecular mechanism of Ca²⁺-mediated transformation. IMPORTANCE Using transcriptome and proteome techniques and association analysis, we identified several key genes involved in the formation of Ca²⁺-mediated E. coli DH5α competent cells. We used Red homologous recombination technology to construct three single-gene deletion strains and found that the transformation efficiencies of yiaW, ygiZ, and osmB deletion strains for different-size plasmids were significantly increased. These results proved that the genetic transformation process is not only a physicochemical process but also a reaction process involving multiple genes. These results suggest ways to improve the horizontal gene transfer mechanism of foodborne microorganisms and provide new ideas for ensuring the safety of food preservation and processing.

Evaluating the Role of Wastewaters as Reservoirs of Antibiotic-Resistant ESKAPEE Bacteria Using Phenotypic and Molecular Methods

Introduction

Methodology

Results

Conclusion

Prevalence, Antimicrobial Susceptibility and Resistance Gene Detection in Bacteria Isolated from Goldfish and Tiger Barb from Ornamental Fish Farms of Tamil Nadu

This study aims to determine the antimicrobial resistance (AMR) pattern in freshwater ornamental cyprinids, such as Goldfish and Tiger barb. Molecular characterization of bacterial isolates confirmed the presence of 7 bacterial isolates in Goldfish and 6 in Tiger barb. Antimicrobial susceptibility test using 36 antibiotics revealed a higher resistance pattern for bacitracin, rifampicin, trimethoprim, cefalexin, ampicillin, amoxicillin, nalidixic acid and nitrofurantoin. Sulphafurazole, norfloxacin and ciprofloxacin were effective against all the bacterial isolates derived from Goldfish and Tiger barb. Most bacterial isolates exhibited > 0.2 multi-drug resistance index (MDR), indicating the severity of antibiotic use in the culture system. The finding of the present study suggests that ornamental fish may act as the reservoir of MDR bacteria and dissemination of resistance genes to clinical and human commensal bacteria through horizontal gene transfer.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-022-01023-y.

Aerolysin gene characterization and antimicrobial resistance profile of Aeromonas hydrophila isolated from milkfish (Chanos chanos) in Gresik, Indonesia

Background and Aim: Motile Aeromonas septicemia is a crucial disease in freshwater fish. Aeromonas hydrophila is a disease agent associated with sporadic fish mortality, food safety, and public health. This study aimed to estimate the prevalence and the presence of the aerolysin gene and antimicrobial resistance profile of A. hydrophila isolated from milkfish in Gresik, Indonesia. Materials and Methods: A total of 153 milkfish gill samples were collected from 16 locations in Gresik and then cultured and identified using biochemical tests. The aerolysin gene was investigated using a polymerase chain reaction, and antimicrobial resistance profiles of the recovered isolates were investigated. Results: Of the 153 examined samples, 35 (22.9%) were confirmed positive for A. hydrophila and 22 (62.9%) presented the aerolysin gene. The recovered isolates were resistant to the following antibiotics: Amoxicillin (62.9%), tetracycline (60%), streptomycin (54.3%), cefotaxime (51.4%), gentamycin (31.4%), kanamycin (28.6%), erythromycin (25.7%), chloramphenicol (20%), and trimethoprim (14.3%). Meanwhile, only ciprofloxacin, nalidixic acid, and imipenem were indicated as susceptible. Conclusion: The presence of the aerolysin gene is vital in determining the virulence of A. hydrophila. The study results indicated a high aerolysin gene prevalence. In addition, this study emphasized antibiotic use monitoring, food safety improvement, and negative impact reduction on human health and the environment.

Raw Meat Contaminated with Cephalosporin-Resistant Enterobacterales as a Potential Source of Human Home Exposure to Multidrug-Resistant Bacteria

The prevalence of cephalosporine-resistant (3GC-R) strains among United States community-related research samples ranged from 5.6 to 10.8%, while, in the European countries, it was 1.2% to 10.1%. Several studies suggest that meat of animal origin could be one of the reservoirs of 3GC-R bacteria. Here, 86 raw meat samples (turkey, pork, chicken and beef) were collected randomly and verified for the presence of 3GC-R bacteria. The 3GC-R bacteria were isolated, identified and characterized phenotypically (antibiotic resistance, motility and biofilm) and genotypically (repetitive-sequence-based rep-PCR) to elucidate any correlations with principal component analysis (PCA). From 28 3GC-R positive samples, 41 strains were isolated, from which the majority belonged to Serratia fonticola (39%), followed by Escherichia coli (19.5%), Enterobacter cloacae (17.1%) and Klebsiella pneumoniae (14.6%). The isolates of E. coli and S. fonticola presented diverse profiles in rep-PCR. Generally, 3GC-R strains were more resistant to antibiotics used in veterinary medicine than in human medicine. PCA derived from antibiotic resistance, motility and biofilm formation of S. fonticola and E. coli strains showed that resistance to beta-lactams was separated from the resistance to other antibiotic classes. Moreover, for the S. fonticola, E. coli and En. cloacae, the type of meat can create a specific tendency towards antibiotic resistance and phenotypic characteristics for S. fonticola, while these relationships were not found for other tested species.

Detection of Virulence-Associated Genes and in vitro Gene Transfer From Aeromonas sp. Isolated From Aquatic Environments of Sub-himalayan West Bengal

Aeromonas is omnipresent in aquatic environments and cause disease within a wide host range. A total of thirty-four isolates from water samples of small fish farms were identified as Aeromonas based on biochemical characteristics and 16S rRNA gene sequence. A total of six virulent factors were analyzed which indicated 100% of isolates as beta-haemolytic and proteolytic, whereas 44.1, 38.2, and 70.6% of isolates produced DNAse, siderophore, and amylase, respectively. Studies on the occurrence of four genetic determinants of virulence factors revealed that aer/haem (haemolytic toxin) and flaA (polar flagella) genes were present in 44.1% of strains whereas ascV (type 3 secretion system) and aspA (serine protease) genes were detected in 21.5 and 8.82% of strains, respectively. Fish (Anabas testudineus) challenge studies showed that the isolate GP3 (Aeromonas veronii) bearing five virulent factors with the combination of aer/haem⁺/ascV⁺/fla⁺ genes induced severe lesions leading to 100% of mortality. In contrast, RB7 possessing four virulence factors and three genes (aer/haem⁺/ascV⁺/aspA⁺) could not produce severe lesions and any mortality indicating the absence of correlation between the virulence factors, its genes, and the pathogenicity in fishes. GP3 was cytotoxic to human liver cell line (WRL-68) in trypan blue dye exclusion assay. The 431 bp aer/haem gene of GP3 was transferable to E. coli Dh5α with a conjugational efficiency of 0.394 × 10^–4 transconjugants per recipient cell. The transfer was confirmed by PCR and by the presence of 23-kb plasmids in both donor and transconjugants. Therefore, the occurrence of mobile genetic elements bearing virulence-associated genes in Aeromonas indicates the need for periodic monitoring of the aquatic habitat to prevent disease outbreaks.

PlasmidHostFinder: Prediction of Plasmid Hosts Using Random Forest

Plasmids play a major role facilitating the spread of antimicrobial resistance between bacteria. Understanding the host range and dissemination trajectories of plasmids is critical for surveillance and prevention of antimicrobial resistance. Identification of plasmid host ranges could be improved using automated pattern detection methods compared to homology-based methods due to the diversity and genetic plasticity of plasmids. In this study, we developed a method for predicting the host range of plasmids using machine learning-specifically, random forests. We trained the models with 8,519 plasmids from 359 different bacterial species per taxonomic level; the models achieved Matthews correlation coefficients of 0.662 and 0.867 at the species and order levels, respectively. Our results suggest that despite the diverse nature and genetic plasticity of plasmids, our random forest model can accurately distinguish between plasmid hosts. This tool is available online through the Center for Genomic Epidemiology (https://cge.cbs.dtu.dk/services/PlasmidHostFinder/). IMPORTANCE Antimicrobial resistance is a global health threat to humans and animals, causing high mortality and morbidity while effectively ending decades of success in fighting against bacterial infections. Plasmids confer extra genetic capabilities to the host organisms through accessory genes that can encode antimicrobial resistance and virulence. In addition to lateral inheritance, plasmids can be transferred horizontally between bacterial taxa. Therefore, detection of the host range of plasmids is crucial for understanding and predicting the dissemination trajectories of extrachromosomal genes and bacterial evolution as well as taking effective countermeasures against antimicrobial resistance.

Tracking Klebsiella pneumoniae carbapenemase gene as an indicator of antimicrobial resistance dissemination from a hospital to surface water via a municipal wastewater treatment plant

Antibiotic-resistant bacteria originating from hospitals are ultimately discharged to municipal wastewater treatment plants (WWTP), which may serve as important reservoirs for the spread of antibiotic resistant genes. This study traced and quantified the presence of a rare but clinically relevant antimicrobial resistance gene; Klebsiella pneumoniae carbapenamase (KPC)-and the viable organisms (KPCO) which carried this gene in hospital, non-hospital wastewater discharges, various compartments within a municipal WWTP, receiving water and sediment samples. High concentration of the gene, blaKPC harbored in viable and multispecies KPCO was detected in the hospital wastewater and in the forepart stages of the WWTP, but was not detected in the final effluent following UV disinfection. KPCO were not detected in multiple non-hospital sources of wastewater discharges tested. The treatment train used in the sampled WWTP was found to help remove and reduce KPCO load. Using whole-genome sequencing, a KPC-producing Klebsiella oxytoca strain identical to strains seen in the patients and hospital environment was isolated from the downstream receiving water on one sampling event. KPCO were also found to persist in the biosolids throughout the WWTP, but were not detected in the processed compost-products made from WWTP-biosolids. This study systematically demonstrates dissemination of KPCO from hospital point source to environment via municipal WWTP. Understanding hospitals as the origin and source of spread of some of the most clinically urgent antimicrobial-resistant organisms may help direct interventions that target rate at which antibiotic resistant bacteria evolve and spread via enhancement of wastewater treatment and mitigation of dissemination at source.

Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance

Microbial communities are composed of cells of varying metabolic capacity, and regularly include auxotrophs that lack essential metabolic pathways. Through analysis of auxotrophs for amino acid biosynthesis pathways in microbiome data derived from >12,000 natural microbial communities obtained as part of the Earth Microbiome Project (EMP), and study of auxotrophic–prototrophic interactions in self-establishing metabolically cooperating yeast communities (SeMeCos), we reveal a metabolically imprinted mechanism that links the presence of auxotrophs to an increase in metabolic interactions and gains in antimicrobial drug tolerance. As a consequence of the metabolic adaptations necessary to uptake specific metabolites, auxotrophs obtain altered metabolic flux distributions, export more metabolites and, in this way, enrich community environments in metabolites. Moreover, increased efflux activities reduce intracellular drug concentrations, allowing cells to grow in the presence of drug levels above minimal inhibitory concentrations. For example, we show that the antifungal action of azoles is greatly diminished in yeast cells that uptake metabolites from a metabolically enriched environment. Our results hence provide a mechanism that explains why cells are more robust to drug exposure when they interact metabolically.

Using microbiome data analysis and a self-establishing metabolically cooperating yeast community model, the authors show that the presence of auxotrophs in a microbial community increases metabolic interactions between cells and fosters antimicrobial drug tolerance.

Sanguinarine Protects Channel Catfish against Aeromonas hydrophila Infection by Inhibiting Aerolysin and Biofilm Formation

Aeromonas hydrophila is a pathogenic bacterium that can cause serious infections both in humans and aquatic animals. Antibiotics are the main approach for fighting against the pathogen. However, the emergence of antibiotic resistance has resulted in treatment failure. Therefore, drugs with novel strategies need to be developed. Quorum sensing has been recognized as a promising method for identifying anti-virulence drugs against bacterial infections. The aim of this study was to identify novel drugs targeting quorum sensing of A. hydrophila as alternatives of antibiotics in aquaculture. Thus, hemolytic activity, biofilm formation, qPCR and experimental therapeutics assays were conducted. The results showed that sanguinarine inhibited the growth of A. hydrophila at concentrations higher than 16 μg/mL, but the production of aerolysin and biofilm formation was significantly inhibited at sub-inhibitory concentrations by disrupting the quorum sensing system. Cell viability results showed that sanguinarine could provide protection for A549 cells from aerolysin-induced cell injury. In addition, the mortality of channel catfish administered with sanguinarine at a dosage of 20 mg/kg decreased to 40%, which showed a significant decrease compared with fish in positive group. Taken together, these findings demonstrated that anti-virulence strategies can be a powerful weapon for fighting against bacterial pathogens and sanguinarine appears to be a promising candidate in the treatment of A. hydrophila infections.

Antimicrobial Resistance in Rivers: A Review of the Genes Detected and New Challenges

River ecosystems are very important parts of the water cycle and an excellent habitat, food, and drinking water source for many organisms, including humans. Antibiotics are emerging contaminants which can enter rivers from various sources. Several antibiotics and their related antibiotic resistance genes (ARGs) have been detected in these ecosystems by various research programs and could constitute a substantial problem. The presence of antibiotics and other resistance cofactors can boost the development of ARGs in the chromosomes or mobile genetic elements of natural bacteria in rivers. The ARGs in environmental bacteria can also be transferred to clinically important pathogens. However, antibiotics and their resistance genes are both not currently monitored by national or international authorities responsible for controlling the quality of water bodies. For example, they are not included in the contaminant list in the European Water Framework Directive or in the US list of Water-Quality Benchmarks for Contaminants. Although ARGs are naturally present in the environment, very few studies have focused on non-impacted rivers to assess the background ARG levels in rivers, which could provide some useful indications for future environmental regulation and legislation. The present study reviews the antibiotics and associated ARGs most commonly measured and detected in rivers, including the primary analysis tools used for their assessment. In addition, other factors that could enhance antibiotic resistance, such as the effects of chemical mixtures, the effects of climate change, and the potential effects of the coronavirus disease 2019 pandemic, are discussed. Environ Toxicol Chem 2022;41:687-714. © 2022 SETAC.

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.

Characterization of a novel broad-spectrum endolysin PlyD4 encoded by a highly conserved prophage found in Aeromonas hydrophila ST251 strains

Aeromonas hydrophila is a zoonotic pathogen that exhibits high level resistance to classic antibiotics and is a heavy burden for aquaculture industry. Lytic enzymes encoded by phages or prophages have shown potential for use against pathogenic bacteria. In this study, an intact prophage (named phAhD4) was identified from A. hydrophila D4. phAhD4 is highly conserved in all 10 published A. hydrophila sequence type (ST) 251 strains and is unique to the ST251 strains. The unique endolysin PlyD4, encoded by phAhD4, was obtained by prokaryotic expression. PlyD4 showed bactericidal activity against a broad range of bacterial species in vitro, including A. hydrophila, Aeromonas veronii, Vibrio parahemolyticus, Pseudomonas aeruginosa, and so on. Synergistically with 5 mmol/L ethylene diamine tetraacetic acid (EDTA), the ratio of the optical density at 600 nm (OD₆₀₀) of PlyD4 treatment versus the OD₆₀₀ with no PlyD4 treatment for most tested strains decreased from 1 to 0.1-0.8 within 2 h. PlyD4 exhibited optimal activity at 28 °C and maintained high activity over a wide pH range (pH 6-10). Divalent metal ions conferred significant enhancement to PlyD4 lytic activity at low concentrations (0.1 mmol/L). In vivo, a 4.5 μg dose of PlyD4 protected 75.0% (15/20) of zebrafish in a bacteremia model of A. hydrophila D4 infection. These results indicated that PlyD4 was an effective therapeutic agent against multiple aquaculture-related pathogens. To the best of our knowledge, this study is the first to report on an A. hydrophila prophage endolysin that exerts antibacterial activity against a broad range of pathogens. KEY POINTS: • The prophage phAhD4 is highly conserved in 10 published A. hydrophila ST251 strains. • PlyD4 exerts antibacterial activity against multiple aquaculture-related pathogens. • PlyD4 conferred protection against A. hydrophila infection in a zebrafish model.

The war against bacteria, from the past to present and beyond

INTRODUCTION

The human defense against microorganisms dates back to the ancient civilizations, with attempts to use substances from vegetal, animal, or inorganic origin to fight infections. Today, the emerging threat of multidrug-resistant bacteria highlights the consequences of antibiotics inappropriate use, and the urgent need for novel effective molecules.

METHODS AND MATERIALS

We extensively researched on more recent data within PubMed, Medline, Web of Science, Elsevier's EMBASE, Cochrane Review for the modern pharmacology in between 1987 - 2021. The historical evolution included a detailed analysis of past studies on the significance of medical applications in the ancient therapeutic field.

AREAS COVERED

We examined the history of antibiotics development and discovery, the most relevant biochemical aspects of their mode of action, and the biomolecular mechanisms conferring bacterial resistance to antibiotics.

EXPERT OPINION

The list of pathogens showing low sensitivity or full resistance to most currently available antibiotics is growing worldwide. Long after the 'golden age' of antibiotic discovery, the most novel molecules should be carefully reserved to treat serious bacterial infections of susceptible bacteria. A correct diagnostic and therapeutic procedure can slow down the spreading of nosocomial and community infections sustained by multidrug-resistant bacterial strains.

Antimicrobial Resistance and Inorganic Nanoparticles

Antibiotics are being less effective, which leads to high mortality in patients with infections and a high cost for the recovery of health, and the projections that are had for the future are not very encouraging which has led to consider antimicrobial resistance as a global health problem and to be the object of study by researchers. Although resistance to antibiotics occurs naturally, its appearance and spread have been increasing rapidly due to the inappropriate use of antibiotics in recent decades. A bacterium becomes resistant due to the transfer of genes encoding antibiotic resistance. Bacteria constantly mutate; therefore, their defense mechanisms mutate, as well. Nanotechnology plays a key role in antimicrobial resistance due to materials modified at the nanometer scale, allowing large numbers of molecules to assemble to have a dynamic interface. These nanomaterials act as carriers, and their design is mainly focused on introducing the temporal and spatial release of the payload of antibiotics. In addition, they generate new antimicrobial modalities for the bacteria, which are not capable of protecting themselves. So, nanoparticles are an adjunct mechanism to improve drug potency by reducing overall antibiotic exposure. These nanostructures can overcome cell barriers and deliver antibiotics to the cytoplasm to inhibit bacteria. This work aims to give a general vision between the antibiotics, the nanoparticles used as carriers, bacteria resistance, and the possible mechanisms that occur between them.

Aeromonas: the multifaceted middleman in the One Health world

Aeromonas is at the interface of all the One Health components and represents an amazingly sound test case in the One Health approach, from economic loss in aquaculture tochallenges related to antibiotic-resistant bacteria selected from the environment. In human health, infections following leech therapy is an outstanding example of such One Health challenges. Aeromonads are not only ubiquitous environmental bacteria, able to rapidly colonize and cause opportunistic infections in humans and animals, they are also capable of promoting interactions and gene exchanges between the One Health components. This makes this genus a key amplifier of genetic transfer, especially of antibiotic resistance genes.

Antimicrobial Resistance in Equine Reproduction

Bacteria develop resistance to antibiotics following low-level "background" exposure to antimicrobial agents as well as from exposure at therapeutic levels during treatment for bacterial infections. In this review, we look specifically at antimicrobial resistance (AMR) in the equine reproductive tract and its possible origin, focusing particularly on antibiotics in semen extenders used in preparing semen doses for artificial insemination. Our review of the literature indicated that AMR in the equine uterus and vagina were reported worldwide in the last 20 years, in locations as diverse as Europe, India, and the United States. Bacteria colonizing the mucosa of the reproductive tract are transferred to semen during collection; further contamination of the semen may occur during processing, despite strict attention to hygiene at critical control points. These bacteria compete with spermatozoa for nutrients in the semen extender, producing metabolic byproducts and toxins that have a detrimental effect on sperm quality. Potential pathogens such as Klebsiella pneumoniae, Escherichia coli, and Pseudomonas aeruginosa may occasionally cause fertility issues in inseminated mares. Antibiotics are added during semen processing, according to legislation, to impede the growth of these microorganisms but may have a detrimental effect on sperm quality, depending on the antimicrobial agent and concentration used. However, this addition of antibiotics is counter to current recommendations on the prudent use of antibiotics, which recommend that antibiotics should be used only for therapeutic purposes and after establishing bacterial sensitivity. There is some evidence of resistance among bacteria found in semen samples. Potential alternatives to the addition of antibiotics are considered, especially physical removal separation of spermatozoa from bacteria. Suggestions for further research with colloid centrifugation are provided.

Investigation into the prevalent CRISPR-Cas systems among the Aeromonas genus

Clustered regularly interspaced short palindromic repeats (CRISPR) is a prokaryotic adaptive immune system that checks invasion by mobile genetic elements through nuclease targeting. In this study, we investigated the occurrence, diversity, and features of the CRISPR system in the genus Aeromonas using bioinformatics tools. Only 13 out of 122 complete genomes (10.66%) of the genus Aeromonas from the NCBI GenBank database harbored the CRISPR system. The Type I-F system was the most prevalent CRISPR system among the Aeromonads, followed by the Type I-E system. Only one strain harbored a Type I-C CRISPR system. Among the Aeromonads, Aeromonas caviae (22.7%) and Aeromonas veronii (20%) had a higher prevalence rate of the complete CRISPR system. The analysis of direct repeat (DR) sequences showed that all could form stable RNA secondary structures. A phylogenetic tree generated for the Cas1 protein classified CRISPR subtypes into three distinct clusters. Among the 748 spacers investigated, 41.98% and 17.25% showed perfect homology to phage and plasmid sequences, respectively. Some arrays had duplicated spacers. The CRISPR loci are closely linked to antibiotic resistance genes in most strains. Collectively, our results would contribute to research on antibiotic resistance in the Aeromonas group, and provide new insights into the diversity and evolution of the CRISPR-Cas system.

A review on non-thermal plasma treatment of water contaminated with antibiotics

Large amounts of antibiotics are produced and consumed worldwide, while wastewater treatment is still rather inefficient, leading to considerable water contamination. Concentrations of antibiotics in the environment are often sufficiently high to exert a selective pressure on bacteria of clinical importance that increases the prevalence of resistance. Since the drastic reduction in the use of antibiotics is not envisaged, efforts to reduce their input into the environment by improving treatment of contaminated wastewater is essential to limit uncontrollable spread of antibiotic resistance. This paper reviews recent progress on the use of non-thermal plasma for the degradation of antibiotics in water. The target compounds removal, the energy efficiency and the mineralization are analyzed as a function of discharge configuration and the most important experimental parameters. Various ways to improve the plasma process efficiency are addressed. Based on the identified reaction intermediates, degradation pathways are proposed for various classes of antibiotics and the degradation mechanisms of these chemicals under plasma conditions are discussed.

Detection of mobile genetic elements in multidrug-resistant Klebsiella pneumoniae isolated from different infection sites in Hamadan, west of Iran

Objective

Klebsiella pneumoniae is one of most opportunistic pathogens that can be related to nosocomial infections. Increased acquisitions of multidrug resistance in this bacterium as well as the transfer of genes to other strains have caused concern. Integrons play key role in the acquisition and the spread of resistance genes. The aim of this study was evaluated the frequency of resistance genes sulI, sulII, tetA, tetB, class I (intI gene), class II integrons (intII gene) and the association between multidrug resistance and the presence of integrons in K. pneumoniae.

Results

Antibiotics susceptibility test was performed on 126 of K. pneumoniae isolates. Also, DNA extraction was done and genes were detected using PCR method. In this study, 67 isolates (53%), carrying both the sulI and sulII genes. Forty-five percent tetracycline-resistant isolates were tetA or tetB positive. The prevalence of intI gene was 96%, while only sixteen isolate harboring intII gene (12.5%). Our results showed the high prevalence of integrons in MDR K. pneumoniae, indicating the important role of these genes in the transmission of antibiotic resistance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13104-021-05748-9.

Outer Membrane Vesicles Derived from Klebsiella pneumoniae Are a Driving Force for Horizontal Gene Transfer

Gram-negative bacteria release Outer Membrane Vesicles (OMVs) into the extracellular environment. Recent studies recognized these vesicles as vectors to horizontal gene transfer; however, the parameters that mediate OMVs transfer within bacterial communities remain unclear. The present study highlights for the first time the transfer of plasmids containing resistance genes via OMVs derived from Klebsiella pneumoniae (K. pneumoniae). This mechanism confers DNA protection, it is plasmid copy number dependent with a ratio of 3.6 times among high copy number plasmid (pGR) versus low copy number plasmid (PRM), and the transformation efficiency was 3.6 times greater. Therefore, the DNA amount in the vesicular lumen and the efficacy of horizontal gene transfer was strictly dependent on the identity of the plasmid. Moreover, the role of K. pneumoniae-OMVs in interspecies transfer was described. The transfer ability was not related to the phylogenetic characteristics between the donor and the recipient species. K. pneumoniae-OMVs transferred plasmid to Escherichia coli, Salmonella enterica, Pseudomonas aeruginosa and Burkholderia cepacia. These findings address the pivotal role of K. pneumoniae-OMVs as vectors for antimicrobial resistance genes spread, contributing to the development of antibiotic resistance in the microbial communities.

Strategies to combat antimicrobial resistance in Indian scenario

Antimicrobial resistance (AMR) is one of the major public health crisis recognised globally. Microbial infections cause significant productivity losses in animals and humans. In livestock, these microbial infections reduce the growth rates and fertility, diminish production of meat and milk, and occasionally lead to mortality, and are therefore, a major concern for animal welfare. In the dearth of alternative prophylactic measures, antibiotics remain the principal tool for their management. Once an antibiotic is used rampantly, resistance against it is inevidently seen in the microbe population and the hunt for a new drug grows. Discovery and development of a new antimicrobial drug is a time taking and expensive procedure with limited assurance of success. As a result, the past few decades have witnessed only a very few new classes of antibiotics. If the AMR can be restricted or reverted, the success rate of antimicrobial therapy can be boosted and many public health issues be avoided. All these ask for a comprehensive plan to prevent or reduce the antimicrobial resistance and economic losses to the animal husbandry sector. The present review provides an overview of AMR in India, mechanism of its occurrence and the possible roadmap to combat the emerging threat of AMR in Indian scenario.