Multidrug-resistance in methicillin-resistant Staphylococcus aureus (MRSA) isolated from a subtropical river contaminated by nearby livestock industries

The escalating threat of human-associated infectious bacteria in surface aquatic resources: Insights into prevalence, antibiotic resistance, survival mechanisms, detection, and prevention strategies

Anthropogenic activities and climate change profoundly impact water quality, leading to a concerning increase in the prevalence and abundance of bacterial pathogens across diverse aquatic environments. This rise has resulted in a growing challenge concerning the safety of water sources, particularly surface waters and marine environments. This comprehensive review delves into the multifaceted challenges presented by bacterial pathogens, emphasizing threads to human health within ground and surface waters, including marine ecosystems. The exploration encompasses the intricate survival mechanisms employed by bacterial pathogens and the proliferation of antimicrobial resistance, largely driven by human-generated antibiotic contamination in aquatic systems. The review further addresses prevalent pathogenic bacteria, elucidating associated risk factors, exploring their eco-physiology, and discussing the production of potent toxins. The spectrum of detection techniques, ranging from conventional to cutting-edge molecular approaches, is thoroughly examined to underscore their significance in identifying and understanding waterborne bacterial pathogens. A critical aspect highlighted in this review is the imperative for real-time monitoring of biomarkers associated with waterborne bacterial pathogens. This monitoring serves as an early warning system, facilitating the swift implementation of action plans to preserve and protect global water resources. In conclusion, this comprehensive review provides fresh insights and perspectives, emphasizing the paramount importance of preserving the quality of aquatic resources to safeguard human health on a global scale.

Recent development and fighting strategies for lincosamide antibiotic resistance

SUMMARYLincosamides constitute an important class of antibiotics used against a wide range of pathogens, including methicillin-resistant Staphylococcus aureus. However, due to the misuse of lincosamide and co-selection pressure, the resistance to lincosamide has become a serious concern. It is urgently needed to carefully understand the phenomenon and mechanism of lincosamide resistance to effectively prevent and control lincosamide resistance. To date, six mobile lincosamide resistance classes, including lnu, cfr, erm, vga, lsa, and sal, have been identified. These lincosamide resistance genes are frequently found on mobile genetic elements (MGEs), such as plasmids, transposons, integrative and conjugative elements, genomic islands, and prophages. Additionally, MGEs harbor the genes that confer resistance not only to antimicrobial agents of other classes but also to metals and biocides. The ultimate purpose of discovering and summarizing bacterial resistance is to prevent, control, and combat resistance effectively. This review highlights four promising strategies, including chemical modification of antibiotics, the development of antimicrobial peptides, the initiation of bacterial self-destruct program, and antimicrobial stewardship, to fight against resistance and safeguard global health.

Bioaerosolization behaviour of potential pathogenic microorganisms from wastewater treatment plants: Occurrence profile, social function and health risks

Wastewater treatment plants (WWTPs) are the leading sources of potential pathogenic bioaerosol that cause non-negligible health risks. However, bioaerosolization behaviour of potential pathogenic microorganisms (PPMs) migrating from wastewater to the atmosphere is still unclear. This study investigated the occurrence profile of PPMs in wastewater, sludge and bioaerosol, then analyzed bioaerosolization level, impact factors and social function. Staphylococcus aureus was selected as the target due to its pathogenicity, and the health risks of workers, engineers and researchers wearing various masks (N90, N95 and medical masks) were evaluated. The results showed that there were 38 and 64 PPMs in bioaerosol from plant A and B. Streptomyces in plant A (average bioaerosolization index, BI= 237.71) and Acinetobacter in plant B (average BI = 505.88) were more likely to migrate from wastewater to the atmosphere forming bioaerosol. Environmental factors (relative humidity, wind speed and temperature) affected both BI and microbial species of PPMs in different ways. PPMs related to fermentation, aerobic chemoheterotrophy, and chemoheterotrophy are the most abundant. Meanwhile microbial networks from plants A and B showed that PPMs were well-connected. Emission level of Staphylococcus aureus bioaerosol can reach 980 ± 309.19 CFU/m3 in plant A and 715.55 ± 44.17 CFU/m3 in plant B. For three exposure population, disease burden (DB) and annual probability infection (Py) of Staphylococcus aureus bioaerosol in two plants were both higher than the U.S.EPA benchmark (10-4 DALYs pppy). All three masks (N90,N95 and medical masks) can decrease Py and DB by at least one order of magnitude. This study illustrated the bioaerosolization behaviour of PPMs comprehensively, which provides a scientific basis for exposure risk prevention and control.

Sub-MIC streptomycin and tetracycline enhanced Staphylococcus aureus Guangzhou-SAU749 biofilm formation, an in-depth study on transcriptomics

Staphylococcus aureus is a major human pathogen, a potential "Super-bug" and a typical biofilm forming bacteria. With usage of large amount of antibiotics, the residual antibiotics in clinical settings further complicate the colonization, pathogenesis and resistance of S. aureus. This study aimed at investigating the phenotypical and global gene expression changes on biofilm formation of a clinical S. aureus isolate treated under different types of antibiotics. Firstly, an isolate Guangzhou-SAU749 was selected from a large sale of previously identified S. aureus isolates, which exhibited weak biofilm formation in terms of biomass and viability. Secondly, 9 commonly prescribed antibiotics for S. aureus infections treatment, together with 10 concentrations ranging from 1/128 to 4 minimum inhibitory concentration (MIC) with 2-fold serial dilution, were used as different antibiotic stress conditions. Then, biofilm formation of S. aureus Guangzhou-SAU749 at different stages including 8 h, 16 h, 24 h, and 48 h, was tested by crystal violet and MTS assays. Thirdly, the whole genome of S. aureus Guangzhou-SAU749 was investigated by genome sequencing on PacBio platform. Fourthly, since enhancement of biofilm formation occurred when treated with 1/2 MIC tetracycline (TCY) and 1/4 MIC streptomycin (STR) since 5 h, the relevant biofilm samples were selected and subjected to RNA-seq and bioinformatics analysis. Last, expression of two component system (TCS) and biofilm associated genes in 4 h, 8 h, 16 h, 24 h, and 48 h sub-MIC TCY and STR treated biofilm samples were performed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Although most antibiotics lowered the biomass and cell viability of Guangzhou-SAU749 biofilm at concentrations higher than MIC, certain antibiotics including TCY and STR promoted biofilm formation at sub-MICs. Additionally, upon genome sequencing, RNA-seq and RT-qPCR on biofilm samples treated with sub-MIC of TCY and STR at key time points, genes lytR, arlR, hssR, tagA, clfB, atlA and cidA related to TCS and biofilm formation were identified to contribute to the enhanced biofilm formation, providing a theoretical basis for further controlling on S. aureus biofilm formation.

Global patterns and correlates in the emergence of antimicrobial resistance in humans

Antimicrobial resistance (AMR) is a critical global health threat, and drivers of the emergence of novel strains of antibiotic-resistant bacteria in humans are poorly understood at the global scale. We examined correlates of AMR emergence in humans using global data on the origins of novel strains of AMR bacteria from 2006 to 2017, human and livestock antibiotic use, country economic activity and reporting bias indicators. We found that AMR emergence is positively correlated with antibiotic consumption in humans. However, the relationship between AMR emergence and antibiotic consumption in livestock is modified by gross domestic product (GDP), with only higher GDP countries showing a slight positive association, a finding that differs from previous studies on the drivers of AMR prevalence. We also found that human travel may play a role in AMR emergence, likely driving the spread of novel AMR strains into countries where they are subsequently detected for the first time. Finally, we used our model to generate a country-level map of the global distribution of predicted AMR emergence risk, and compared these findings against reported AMR emergence to identify gaps in surveillance that can be used to direct prevention and intervention policies.

The presence of antibiotics and multidrug-resistant Staphylococcus aureus reservoir in a low-order stream spring in central Brazil

The disposal of industrial effluents strongly influences low-order streams, which makes them fragile ecosystems that can be impacted by contamination. In central Brazil, the Extrema River spring targets the dumping of pharmaceutical products from the surrounding industries. So, this work aimed to investigate the presence of antibiotics in Extrema River spring samples and the isolation of Staphylococcus aureus, a potential multidrug-resistant bacteria, verifying the antimicrobial resistance profile of these isolates. Three campaigns were carried out in different locals (P1-P3) between October and December 2021, in the dry and rainy seasons. The high-performance liquid chromatography-tandem mass spectrometry (LCMS) approach indicated the presence of sulfamethoxazole (≥ 1 ng/L), metronidazole (< 0.5 ng/L), and chloramphenicol (< 5 ng/L) in the water samples in November (rainy season). S. aureus was isolated in P1 (n = 128), P2 (n = 168), and P3 (n = 36), with greater resistance to trimethoprim-sulfamethoxazole (90%), clindamycin (70%), and gentamicin (60%). The presence of antibiotics in the Extrema River spring may cause S. aureus antibiotic resistance development. The presence of antibiotics and the high percentage of isolated multidrug-resistant S. aureus in the Extrema River spring cause concern and indicate the clandestine dumping of effluents from nearby pharmaceutical industries. Since preserving the springs of low-order streams is important for the environment and public health, we encourage monitoring the wastewater from Extrema River's nearby pharmaceutical industries and preserving the spring of this river.

Molecular epidemiological characteristics and genetic evolutionary relationships of methicillin-resistant Staphylococcus aureus of different avian origins in Qingdao, China, using whole-genome sequencing

Introduction

To understand the prevalence of avian methicillin-resistant Staphylococcus aureus (MRSA) and the current status of drug resistance in Qingdao, a comprehensive molecular epidemiological investigation and analysis of evolutionary relationships of MRSA isolates from broiler and layer chickens and waterfowl was conducted.

Material and Methods

One hundred and two avian MRSA strains were identified by multi-locus sequence typing, staphylococcal protein A (spa) and staphylococcal cassette chromosome mec (SCCmec) typing, and whole-genome sequencing.

Results

The sequence type (ST) 9-t899-SCCmec IVb type represented the highest proportion of avian-derived MRSA strains (71.57%), with ST398 type strains occasionally observed in broilers and waterfowl. The poultry-derived MRSA strains were all resistant to eight or more antimicrobials. Avian-derived MRSA strains carried 20 resistance genes, 109 virulence genes and 10 plasmids. Strains carrying the cfr oxazolidinone resistance gene were occasionally seen in broiler- and layer-derived MRSA. Single nucleotide polymorphism (SNP) core genome evolution and locus difference analysis showed that the closest strains were all of ST9-t899 type (to which also affiliated the highest number of strains) and this type occurred on all three kinds of poultry farm, but the SNP difference loci between strains of the same type ranged from 0 to 1472.

Conclusion

The dominant type of MRSA from different poultry sources in Qingdao is ST9-t899-SCCmec IVb, which is commonly resistant to a variety of antimicrobial drugs and carries a variety of resistance genes and a large number of virulence genes. Sequence type 9-t899 type is widely spread among the three kinds of poultry investigated, but there are differences in affiliations.

Synergistic Antibiotic Activity of Ricini Semen Extract with Oxacillin against Methicillin-Resistant Staphylococcus aureus

Resistant bacteria are emerging as a critical problem in the treatment of bacterial infections by neutralizing antibiotic activity. The development of new traditional mechanisms of antibiotics is not the optimal solution. A more reasonable approach may be to use relatively safe, plant-based compounds in combination with conventional antibiotics in an effort to increase their efficacy or restore their activity against resistant bacteria. We present our study of mixing Ricini Semen extract, or its constituent fatty acids, with oxacillin and testing the effects of each on the growth of methicillin-resistant Staphylococcus aureus. Changes in the cell membrane fluidity of methicillin-resistant S. aureus were found to be a major component of the mechanism of synergistic antibiotic activity of Ricini Semen extract and its constituent fatty acids. In our model, changes in cellular membrane fluidity disrupted the normal function of bacterial signaling membrane proteins BlaR1 and MecR1, which are known to detect oxacillin, and resulted in the incomplete expression of penicillin-binding proteins 2a and β-lactamase. Utilizing the mechanism presented in this study presents the possibility of developing a method for treating antibiotic-resistant bacteria using traditional antibiotics with plant-based compounds.

Resistome Diversity and Dissemination of WHO Priority Antibiotic Resistant Pathogens in Lebanese Estuaries

Anthropogenic pressure is known to be a key driver of antimicrobial resistance (AMR) dissemination in the environment. Especially in lower income countries, with poor infrastructure, the level of AMR dissemination is high. Therefore, we assessed the levels and diversity of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in Lebanese rivers at estuaries’ sites (n = 72) of the Mediterranean Sea in spring 2017 and winter 2018. Methods: A combined approach using culture techniques and high throughput qPCR were applied to identify ARB and ARGs in rivers along the Lebanese coast. Results: Multidrug-resistant Gram-negative (Enterobacterales and Pseudomonas spp.) and Gram-positive bacterial pathogens were isolated. Levels of ARGs were highest in the winter campaign and areas with high anthropogenic activities and population growth with an influx of refugees. Conclusion: Qualitative analysis of ARB and the analysis of the Lebanese estuaries’ resistome revealed critical levels of contamination with pathogenic bacteria and provided significant information about the spread of ARGs in anthropogenically impacted estuaries.

Prevalence, virulence-gene profiles, antimicrobial resistance, and genetic diversity of human pathogenic Aeromonas spp. from shellfish and aquatic environments

Aeromonas are found in various habitats, particularly in aquatic environments. This study examined the presence of the most common human pathogenic Aeromonas species (Aeromonas caviae, A. hydrophila, and A. veronii) in surface water, sea water, and shellfish. The detection rates in fishing harbour seawater, shellfish farming seawater, and a river basin were 33.3%, 26.4%, and 29.4%, respectively, and high prevalence was observed in summer. The detection rates in shellfish procured from a fish market and shellfish farm were 34.9% and 13.3%, respectively. The most abundant species of human pathogenic Aeromonas detected via water sampling was A. caviae, whereas that obtained via shellfish sampling was A. veronii. The prevalence of human pathogenic Aeromonas in river water was lower in fishing harbours and in the estuary shellfish farming area. Here, 25 isolates of human pathogenic Aeromonas species were isolated from 257 samples and divided among 16 virulence profiles. The high virulence gene-carrying isolates (more than six genes) belonged to A. hydrophila. The shellfish-sourced isolates had the highest detection rates of act, aerA, and fla genes than of other virulence genes, and vice versa for seawater-sourced isolates. The Aeromonas isolates showed high levels of resistance to ampicillin-sulbactam; however, none were resistant to cefepime, ciprofloxacin, or gentamicin. The incidence of multiple drug resistance (MDR) in Aeromonas isolates was 20%. In this study, phylogenetic analysis with 16S rRNA sequencing, biochemical tests and enterobacterial repetitive intergenic consensus-polymerase chain reaction fingerprinting facilitated the distinct categorisation of three species of human pathogenic Aeromonas isolates. In addition, A. veronii isolates from the same geographical area were also concentrated in the same cluster. This study provides information on the risk of infection by Aeromonas with MDR and multiple virulence genes isolated from shellfish and aquatic environments.

Molecular Evaluation of Traditional Chicken Farm-Associated Bioaerosols for Methicillin-Resistant Staphylococcus aureus Shedding

The outbreak of airborne pathogens, such as methicillin-resistant Staphylococcus aureus (MRSA) through bioaerosol, and their molecular characterization around domestic poultry farming areas, was not completely understood. This imposes risk of a MRSA-associated health threat for the relevant livestock food production units. To address this issue, the present study investigated the role of bioaerosol in transmitting MRSA strains in poultry house settings by combining molecular typing, phylogenetic classification, antibiotic susceptibility, and virulence gene distribution patterns. The present study highlights that all 18 bioaerosol and stool samples collected were MRSA positive, with a unique set of virulence factors. Out of 57 isolated MRSA isolates, 68.4% and 19.3% consisted of SCCmec I and IV elements, respectively, which are commonly linked with hospital-acquired and livestock-associated MRSA strains. It is worth noting that the exfoliative toxin eta and etb genes were carried by 100% and 70.2% of all isolates, respectively. Only 17.5% of strains showed the presence of enterotoxin entC. These MRSA isolates were resistant to chloramphenicol (C), ciprofloxacin (CIP), clindamycin (DA), erythromycin (E), and tetracycline (T), signifying their multi-drug resistance traits. A cluster of phylogenetic analysis described that 80.7% and 15.8% of total isolates belonged to Staphylococcus aureus protein A (spa) type t002 and t548. Whereas 3.5% were reflected as a new spa type. Additionally, as per the chi-squared test score value, these two spa types (t002 and t548) have a distribution correlation with HA-MRSA and LA-MRSA in all the samples (p < 0.005, chi-squared test; degree of freedom = 1). Ultimately, this study highlights the prevalence of MRSA colonization in the conventional poultry farm environment, showing the risk of bioaerosol transmission, which needs epidemiological attention and prevention strategies.

Molecular and Anti-Microbial Resistance (AMR) Profiling of Methicillin-Resistant Staphylococcus aureus (MRSA) from Hospital and Long-Term Care Facilities (LTCF) Environment

To provide evidence of the cross-contamination of emerging pathogenic microbes in a local network between long-term care facilities (LTCFs) and hospitals, this study emphasizes the molecular typing, the prevalence of virulence genes, and the antibiotic resistance pattern of methicillin-resistant Staphylococcus aureus. MRSA isolates were characterized from 246 samples collected from LTCFs, medical tubes of LTCF residents, and hospital environments of two cities, Chiayi and Changhua. Species identification, molecular characterization, and drug resistance analysis were performed. Hospital environments had a higher MRSA detection rate than that of LTCF environments, where moist samples are a hotspot of MRSA habitats, including tube samples from LTCF residents. All MRSA isolates in this study carried the exfoliative toxin eta gene (100%). The majority of MRSA isolates were resistant to erythromycin (76.7%), gentamicin (60%), and ciprofloxacin (55%). The percentage of multidrug-resistant MRSA isolates was approximately 50%. The enterobacterial repetitive intergenic consensus polymerase chain reaction results showed that 18 MRSA isolates belonged to a specific cluster. This implied that genetically similar isolates were spread between hospitals and LTCFs in Changhua city. This study highlights the threat to the health of LTCFs’ residents posed by hospital contact with MRSA.

Prevalence, Genetic Diversity, Antimicrobial Resistance, and Toxigenic Profile of Vibrio vulnificus Isolated from Aquatic Environments in Taiwan

Vibrio vulnificus is a gram-negative, opportunistic human pathogen associated with life-threatening wound infections and is commonly found in warm coastal marine water environments, globally. In this study, two fishing harbors and three tributaries of the river basin were analyzed for the prevalence of V. vulnificus in the water bodies and shellfish that are under the pressure of external pollutions. The average detection rate of V. vulnificus in the river basins and fishing harbors was 8.3% and 4.2%, respectively, in all seasons. A total of nine strains of V. vulnificus were isolated in pure cultures from 160 samples belonging to river basins and fishing harbors to analyze the antibiotic susceptibility, virulence gene profiles, and enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) fingerprinting. All isolates were susceptible to 10 tested antibiotics. The genotypic characterization revealed that 11.1% (n = 1/9) strain was nonvirulent, whereas 88.9% (n = 8/9) isolates were virulent strains, which possessed the four most prevalent toxin genes such as vcgC (88.9%), 16S B (88.9%), vvhA (88.9%), and manIIA (88.9%), followed by nanA (77.8%), CPS1 (66.7), and PRXII (44.4%). Additionally, ERIC-PCR fingerprinting grouped these nine isolates into two main clusters, among which the river basin isolates showed genetically diverse profiles, suggesting multiple sources of V. vulnificus. Ultimately, this study highlighted the virulent strains of V. vulnificus in the coastal aquatic environments of Taiwan, harboring a potential risk of infection to human health through water-borne transmission.

Antimicrobial resistance and genotyping of Staphylococcus aureus obtained from food animals in Sichuan Province, China

Background

Staphylococcus aureus (S. aureus), especially methicillin-resistant Staphylococcus aureus (MRSA), is considered a common zoonotic pathogen, causing severe infections. The objective of this study was to investigate the antimicrobial susceptibility, resistance genes and molecular epidemiology among MRSA and methicillin-susceptible Staphylococcus aureus (MSSA) isolated from food animals in Sichuan Province, China.

Methods

This study was conducted on 236 S. aureus isolates. All isolates were subjected to antimicrobial susceptibility testing by using a standard microbroth dilution method. The Polymerase Chain Reaction (PCR) was performed to identify genes encoding the β-lactams resistance (blaZ, mecA), macrolides (ermA, ermB, ermC) and aminoglycosides (aacA-aphD). The molecular structures and genomic relatedness of MRSA isolates were determined by staphylococcal chromosome cassette mec (SCCmec) typing and pulsed-field gel electrophoresis (PFGE), respectively.

Results

Among 236 isolates, 24 (10.17 %) were recognized as MRSA. MRSA isolates showed different resistance rates to 11 antimicrobials ranging from 33.33 to 100 %, while for MSSA isolates the rates varied from 8.02 to 91.51 %. Multi-drug resistance phenotype was found in all MRSA isolates. The ermC gene encoding macrolides-lincosamides-streptogramin B was the most prevalent gene detected in 87.29 % of the S. aureus isolates, followed by ermB (83.05 %), blaZ (63.98 %), aacA-aphD (44.07 %), ermA (11.44 %) and mecA (11.02 %) genes. The prevalence of resistance genes in MRSA isolates was significantly higher than that of MSSA. Regarding the molecular morphology, SCCmec III (12/24, 50 %) was the most common SCCmec type. Furthermore, the PFGE typing showed that 24 MRSA were divided into 15 cluster groups (A to O), the major pulsotype J encompassed 25 % of MRSA isolates.

Conclusions

The S. aureus isolates from food animals in Sichuan province of China have severe antimicrobials resistance with various resistance genes, especially MRSA isolates. Additionally, the genetic pool of MRSA isolates is diverse and complex, and further investigation is necessary.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-021-02884-z.