Macrolide-lincosamide-streptogramin Research Articles

Feedstock-dependent antibiotic resistance gene patterns and expression profiles in industrial scale biogas plants revealed by meta-omics technology

This study investigated antimicrobial resistance in the anaerobic digesters of two industrial-scale biogas plants processing agricultural biomass and municipal wastewater sludge. A combination of deep sequencing and genome-centric workflow was implemented for metagenomic and metatranscriptomics data analysis to comprehensively examine potential antimicrobial resistance in microbial communities. Anaerobic microbes were found to harbour numerous antibiotic resistance genes (ARGs), with 58.85% of the metagenome-assembled genomes (MAGs) harbouring antibiotic resistance. A moderately positive correlation was observed between the abundance and expression of ARGs. ARGs were located primarily on bacterial chromosomes. A higher expression of resistance genes was observed on plasmids than on chromosomes. Risk index assessment suggests that most ARGs identified posed a significant risk to human health. However, potentially pathogenic bacteria showed lower ARG expression than non-pathogenic ones, indicating that anaerobic treatment is effective against pathogenic microbes. Resistomes at the gene category level were associated with various antibiotic resistance categories, including multidrug resistance, beta-lactams, glycopeptides, peptides, and macrolide-lincosamide-streptogramin (MLS). Differential expression analysis revealed specific genes associated with potential pathogenicity, emphasizing the importance of active gene expression in assessing the risks associated with ARGs.

Spatiotemporal profiles and underlying mechanisms of the antibiotic resistome in two water-diversion lakes

Human-induced interventions have altered the local characteristics of the lake ecosystems through changes in hydraulic exchange, which in turn impacts the ecological processes of antibiotic resistance genes (ARGs) in the lakes. However, the current understanding of the spatiotemporal patterns and driving factors of ARGs in water-diversion lakes is still seriously insufficient. In the present study, we investigated antibiotic resistome in the main regulation and storage hubs, namely Nansi Lake and Dongping Lake, of the eastern part of the South-to-North Water Diversion project in Shandong Province (China) using a metagenomic-based approach. A total of 653 ARG subtypes belonging to 25 ARG types were detected with a total abundance of 0.125–0.390 copies/cell, with the dominance of bacitracin, multidrug, and macrolide-lincosamide streptogramin resistance genes. The ARG compositions were sensitive to seasonal variation and also interfered by artificial regulation structures along the way. Human pathogenic bacteria such as Acinetobacter calcoaceticus, Acinetobacter lwoffii, Klebsiella pneumoniae, along with the multidrug resistance genes they carried, were the focus of risk control in the two studied lakes, especially in summer. Plasmids were the key mobile genetic elements (MGEs) driving the horizontal gene transfer of ARGs, especially multidrug and sulfonamide resistance genes. The null model revealed that stochastic process was the main driver of ecological drift for ARGs in the lakes. The partial least squares structural equation model further determined that seasonal changes of pH and temperature drove a shift in the bacterial community, which in turn shaped the profile of ARGs by altering the composition of MGEs, antibacterial biocide- and metal-resistance genes (BMGs), and virulence factor genes (VFGs). Our results highlighted the importance of seasonal factors in determining the water transfer period. These findings can aid in a deeper understanding of the spatiotemporal variations of ARGs in lakes and their driving factors, offering a scientific basis for antibiotic resistance management.

Inducible clindamycin-resistant and biofilm formation in the Staphylococcus aureus isolated from healthcare worker’s anterior nasal carriage

ObjectiveThe purpose of this study is a new update on the resistance profile, Macrolide–Lincosamide–Streptogramin B resistance mechanisms and biofilm formation in the Staphylococcus aureus isolated from health care workers (HCWs) nasal carriage at a children’s teaching hospital in Babol (Northern Iran).ResultsA total of 143 non-repetitive nasal swab samples were collected from volunteers, where 53.8% (n; 77/143) were HCWs, 33.6% (n; 48/143) medical students, and 12.6% (n; 18/143) resident students. The prevalence of nasal carriers of S. aureus was 22.4% (n; 32/143), among them, 40.6% (n; 13/32) were identified as methicillin-resistant Staphylococcus aureus (MRSA( carriers. Antimicrobial susceptibility testing showed that erythromycin (68.8%, n; 22/32) and ciprofloxacin (15.6%, n; 5/32) had the highest and lowest resistance rate, respectively. The frequency of resistance genes in the strains was as follows; ermC (n; 17/32, 53.1%), ermA (n; 11/32, 34.4%), ermB (n; 6/32, 18.7%), ereA (n; 3/32, 9.4%). Moreover, 50.0% (n; 16/32), 28.1% (n; 9/32) and 21.8% (n; 7/32) of isolates were strongly, weakly and moderately biofilm producer, respectively. Macrolides-lincosamides-streptogramins B (MLSB) antibiotic resistance among S. aureus isolates from HCWs nasal carriage have found significant prevalence rates throughout the globe. It is crucial to remember that the development of biofilms and MLS B antibiotic resistance are both dynamic processes.

A comparison of antibiotic resistance genes and mobile genetic elements in wild and captive Himalayan vultures.

As the most widely distributed scavenger birds on the Qinghai-Tibetan Plateau, Himalayan vultures (Gyps himalayensis) feed on the carcasses of various wild and domestic animals, facing the dual selection pressure of pathogens and antibiotics and are suitable biological sentinel species for monitoring antibiotic resistance genes (ARGs). This study used metagenomic sequencing to comparatively investigate the ARGs and mobile genetic elements (MGEs) of wild and captive Himalayan vultures. Overall, the resistome of Himalayan vultures contained 414 ARG subtypes resistant to 20 ARG types, with abundances ranging from 0.01 to 1,493.60 ppm. The most abundant resistance type was beta-lactam (175 subtypes), followed by multidrug resistance genes with 68 subtypes. Decreases in the abundance of macrolide-lincosamide-streptogramin (MLS) resistance genes were observed in the wild group compared with the zoo group. A total of 75 genera (five phyla) of bacteria were predicted to be the hosts of ARGs in Himalayan vultures, and the clinical (102 ARGs) and high-risk ARGs (35 Rank I and 56 Rank II ARGs) were also analyzed. Among these ARGs, twenty-two clinical ARGs, nine Rank I ARG subtypes, sixteen Rank II ARG subtypes were found to differ significantly between the two groups. Five types of MGEs (128 subtypes) were found in Himalayan vultures. Plasmids (62 subtypes) and transposases (44 subtypes) were found to be the main MGE types. Efflux pump and antibiotic deactivation were the main resistance mechanisms of ARGs in Himalayan vultures. Decreases in the abundance of cellular protection were identified in wild Himalayan vultures compared with the captive Himalayan vultures. Procrustes analysis and the co-occurrence networks analysis revealed different patterns of correlations among gut microbes, ARGs, and MGEs in wild and captive Himalayan vultures. This study is the first step in describing the characterization of the ARGs in the gut of Himalayan vultures and highlights the need to pay more attention to scavenging birds.

Molecular Detection of Macrolide-Induced Clindamycin Resistance Among Clinical Isolates of Staphylococcus aureus from Selected Hospitals in Katsina Metropolis

Study’s Novelty/Excerpt This study investigates the prevalence and characteristics of inducible clindamycin resistance in Staphylococcus aureus isolates from clinical specimens in Katsina Metropolis, Nigeria, highlighting its significant clinical challenge. Antibiogram profiling revealed high efficacy rates for chloramphenicol (87.8%), clindamycin (79.6%), tetracycline (69.4%), and azithromycin (67.3%), while cefoxitin, ciprofloxacin, and trimethoprim-sulfamethoxazole showed the highest resistance levels. The D-test identified the Macrolide Lincosamide Streptogramin B (MLSB) phenotypes, with the ermC gene predominant among D-test-positive isolates expressing the inducible MLSB (iMLSB) phenotype, underscoring the need for targeted treatment strategies and continuous surveillance to manage antimicrobial resistance in this region. Full Abstract The emergence of inducible clindamycin resistance presents a significant challenge in treating Staphylococcus aureus (S. aureus) infections. This phenotype, evading routine susceptibility testing, compromises treatment efficacy and prolongs patient illness. Despite its clinical importance, limited data exist on its prevalence in Katsina Metropolis, Nigeria. This study aims to assess its prevalence and evaluate the phenotypic and genotypic characteristics among clinical isolates collected from selected hospitals in Katsina Metropolis. S. aureus isolates from various clinical specimens were obtained from three hospitals and identified using standard bacteriological methods. Antibiogram profiles were determined following CLSI guidelines, revealing varying efficacy among commonly prescribed antibiotics. Notably, chloramphenicol (87.8%), clindamycin (79.6%), tetracycline (69.4%), and azithromycin (67.3%) demonstrated high efficacy rates, while cefoxitin, ciprofloxacin, and trimethoprim-sulfamethoxazole exhibited the highest resistance level of (44.9%), (42.9%), and (40.8%) respectively. Prevalence of Macrolide Lincosamide Streptogramin B (MLSB) phenotypes was assessed using the D-test, unveiling specific resistance phenotypes among the isolates. Polymerase chain reaction detected the ermC gene as predominant among D-test-positive isolates, all expressing the iMLSB phenotype. These findings shed light on the prevalence and mechanisms of inducible clindamycin resistance in S. aureus clinical isolates in Katsina Metropolis, emphasizing the importance of tailored treatment strategies and ongoing surveillance in combating antimicrobial resistance effectively

Tetracycline susceptibility in multidrug resistant Staphylococcus aureus isolated from clinical samples in tertiary care hospitals of Kathmandu, Nepal.

Staphylococcus aureus, being an opportunistic pathogen, is frequently associated with various infections in human. The clinical sector feels challenge regarding the management of multidrug resistant S. aureus. Besides the B-lactam antibiotics, Glycopeptides, Tetracycline, Quinolones, Macrolide-lincosamide streptogramin B family of antibiotics are also commonly prescribed to deal with such infections as an alternative drug. Therefore, this study was conducted to assess tetracycline susceptibility in multidrug resistant S. aureus in clinical samples. This study was conducted over the period of 15 months from March 2020–May 2021. The clinical samples were collected from the three different tertiary care hospitals of Kathmandu, Dirghayu Guru Hospital, Chabahil, Bhaktapur Cancer Hospital, Bhaktapur, and Shankarapur Hospital, Jorpati. The sample processing and laboratory work was carried out in the Microbiology Laboratory of Dirghyau Guru Hospital to determine the proportion of different phenotypes of MDR among S. aureus and their association with methicillin resistance. Two hundred sixty six isolates of S. aureus were included in the study. Methicillin resistance was detected by cefoxitin disc diffusion method. Among 2004 clinical samples processed, 266 (13.27%) isolates were S. aureus. The multidrug resistant strain isolated from OPD was 56.84% (54/95) and from inpatient was 43.15% (41/95). Among the 266 S. aureus, 28.94% MRSA and 71.05% MSSA isolates were detected. Tetracycline resistance was found in 9.8% of total S. aureus isolates whereas 27.36% (26/95) among MDR S. aureus isolates. Resistance to Tetracycline was higher in MRSA as compared to MSSA. Detection rate of MRSA in this study shows the necessity to improve health care practices to control MRSA infections. Tetracycline can be used as an alternative antibiotic against the S. aureus infection.

Genome-centric analyses of 165 metagenomes show that mobile genetic elements are crucial for the transmission of antimicrobial resistance genes to pathogens in activated sludge and wastewater.

Antimicrobial resistance (AMR) threatens the health of humans, animals, and natural ecosystems. In our study, an analysis of 165 metagenomes from wastewater revealed antibiotic-targeted alteration, efflux, and inactivation as the most prevalent AMR mechanisms. We identified several genera correlated with multiple ARGs, including Klebsiella, Escherichia, Acinetobacter, Nitrospira, Ottowia, Pseudomonas, and Thauera, which could have significant implications for AMR transmission. The abundance of bacA, mexL, and aph(3")-I in the genomes calls for their urgent management in wastewater. Our approach could be applied to different ecosystems to assess the risk of potential pathogens containing ARGs. Our findings highlight the importance of managing AMR in wastewater and can help design measures to reduce the transmission and evolution of AMR in these systems.

Antimicrobial Resistance in Enterococcus spp. Isolates from Red Foxes (Vulpes vulpes) in Latvia.

Antimicrobial resistance (AMR) is an emerging public health threat and is one of the One Health priorities for humans, animals, and environmental health. Red foxes (Vulpes vulpes) are a widespread predator species with great ecological significance, and they may serve as a sentinel of antimicrobial resistance in the general environment. The present study was carried out to detect antimicrobial resistance, antimicrobial resistance genes, and genetic diversity in faecal isolates of red foxes (Vulpes vulpes). In total, 34 Enterococcus isolates, including E. faecium (n = 17), E. faecalis (n = 12), E. durans (n = 3), and E. hirae (n = 2), were isolated. Antimicrobial resistance to 12 antimicrobial agents was detected with EUVENC panels using the minimum inhibitory concentration (MIC). The presence of antimicrobial resistance genes (ARGs) was determined using whole-genome sequencing (WGS). Resistance to tetracycline (6/34), erythromycin (3/34), ciprofloxacin (2/34), tigecycline (2/34), and daptomycin (2/34) was identified in 44% (15/34) of Enterococcus isolates, while all the isolates were found to be susceptible to ampicillin, chloramphenicol, gentamicin, linezolid, teicoplanin, and vancomycin. No multi-resistant Enterococcus spp. were detected. A total of 12 ARGs were identified in Enterococcus spp., with the presence of at least 1 ARG in every isolate. The identified ARGs encoded resistance to aminoglycosides (aac(6')-I, ant(6)-Ia, aac(6')-Iih and spw), tetracyclines (tet(M), tet(L) and tet(S)), and macrolide-lincosamide-streptogramin AB (lnu(B,G), lsa(A,E), and msr(C)), and their presence was associated with phenotypical resistance. Core genome multilocus sequence typing (cgMLST) revealed the high diversity of E. faecalis and E. faecium isolates, even within the same geographical area. The distribution of resistant Enterococcus spp. in wild foxes in Latvia highlights the importance of a One Health approach in tackling AMR.

Inducible Clindamycin Resistance in Staphylococcus aureus Isolates in Kermanshah, Iran

Background: Staphylococcus aureus is the most common agent of nosocomial infections. Macrolide Lincosamide-Streptogramin B (MLSB) antibiotics are the therapeutic choices for treatment of infections due to methicillin resistant S. aureus (MRSA) isolates. The most frequent mechanism for inducible resistance in S. aureus is modification in target site by erm (erythromycin ribosome methylase) genes. Objectives: The aim of this research was to determine inducible MLSB (iMLSB) and detection the erm genes in clinical samples of S. aureus isolated from hospitalized patients in the Imam Reza hospital of Kermanshah, west of Iran. Methods: This study performed on 126 samples of S. aureus. Identification of isolates were performed using microbiological and biochemical procedures. Inducible resistance to clindamycin was tested by D-test. The prevalence of genes, such as femB, mecA, ermA and ermB was assessed by polymerase chain reaction (PCR). Results: Eighty-three cases (65.9%) of isolates were methicillin resistant S. aureus (MRSA). The resistance rate against erythromycin and clindamycin was 67.4% and 52.2%, respectively. Totally, 49 cases (38.9%) of isolates were resistant to both erythromycin and clindamycin indicating constitutive MLSB phenotype (cMLSB); 20 cases (15.9%) isolates showed positive D test indicating inducible MLSB phenotype (iMLSB), while 16 cases (12.7%) were negative for D test indicating MS phenotype. Among 20 cases with iMLSB phenotype, ermC and ermA genes were showed in 7 cases (35%) and 4 cases (20%) isolates, respectively. The ermB gene is not detected in any cases and 9 cases (45%) isolates did not have any erm genes. Conclusions: In general, findings of this study showed high frequency of resistance to clindamycin and erythromycin among S. aureus isolates and cMLSB to be the most pattern phenotype and ermC gene is the most common gene in iMLSB phenotype. Because variation of antimicrobial resistance pattern in geographic regions obtaining local results is useful for detecting and more appropriate control of nosocomial infection due to S. aureus isolates.

First WGS Characterization of Streptococcus suis Isolated From a Case of Human Meningitis in Southern Italy

This study is the first report in Italy on the molecular characterization by whole‐genome sequencing (WGS) analysis of a Streptococcus suis strain isolated from a human case of meningitis in Italy. The characterized S. suis strain was classified as a serotype 2 (SS2), multilocus sequence typing (MLST) sequence type ST1. The strain exhibited the presence of several virulence genes and resistance to penicillin, tetracycline and macrolide–lincosamide–streptogramin. Finally, we found a frameshift mutation in the gene mrp determining the translation of two truncated forms of the corresponding muramidase‐release protein. These results highlight the importance of complete genomic data to understand the pathogenesis and epidemiology of this bacterium, capable to pose serious risks to human health.

Metagenomic perspectives on antibiotic resistance genes in tap water: The environmental characteristic, potential mobility and health threat

As an emerging environmental contaminant, antibiotic resistance genes (ARGs) in tap water have attracted great attention. Although studies have provided ARG profiles in tap water, research on their abundance levels, composition characteristics, and potential threat is still insufficient. Here, 9 household tap water samples were collected from the Guangdong-Hong Kong-Macao Greater Bay Area (GBA) in China. Additionally, 75 sets of environmental sample data (9 types) were downloaded from the public database. Metagenomics was then performed to explore the differences in the abundance and composition of ARGs. 221 ARG subtypes consisting of 17 types were detected in tap water. Although the ARG abundance in tap water was not significantly different from that found in drinking water plants and reservoirs, their composition varied. In tap water samples, the three most abundant classes of resistance genes were multidrug, fosfomycin and MLS (macrolide-lincosamide-streptogramin) ARGs, and their corresponding subtypes ompR, fosX and macB were also the most abundant ARG subtypes. Regarding the potential mobility, vanS had the highest abundance on plasmids and viruses, but the absence of key genes rendered resistance to vancomycin ineffective. Generally, the majority of ARGs present in tap water were those that have not been assessed and are currently not listed as high-threat level ARG families based on the World Health Organization Guideline. Although the current potential threat to human health posed by ARGs in tap water is limited, with persistent transfer and accumulation, especially in pathogens, the potential danger to human health posed by ARGs should not be ignored.

A Comparative Assessment of High-Throughput Quantitative Polymerase Chain Reaction versus Shotgun Metagenomic Sequencing in Sediment Resistome Profiling

Prolonged and excessive use of antibiotics has resulted in the development of antimicrobial resistance (AMR), which is considered an emerging global challenge that warrants a deeper understanding of the antibiotic-resistant gene elements (ARGEs/resistomes) involved in its rapid dissemination. Currently, advanced molecular methods such as high-throughput quantitative polymerase chain reaction (HT-qPCR) and shotgun metagenomic sequencing (SMS) are commonly applied for the surveillance and monitoring of AMR in the environment. Although both methods are considered complementary to each other, there are some appreciable differences that we wish to highlight in this communication. We compared both these approaches to map the ARGEs in the coastal sediments of Kuwait. The study area represents an excellent model as it receives recurrent emergency waste and other anthropogenic contaminants. The HT-qPCR identified about 100 ARGs, 5 integrons, and 18 MGEs (total—122). These ARGs coded for resistance against the drug classes of beta-lactams > aminoglycoside > tetracycline, macrolide lincosamide streptogramin B (MLSB) > phenicol > trimethoprim, quinolone, and sulfonamide. The SMS picked a greater number of ARGs (402), plasmid sequences (1567), and integrons (168). Based on the evidence, we feel the SMS is a better method to undertake ARG assessment to fulfil the WHO mandate of “One Health Approach.” This manuscript is a useful resource for environmental scientists involved in AMR monitoring.

Microbial community and antibiotic resistance gene distribution in food waste, anaerobic digestate, and paddy soil

The study assessed the occurrence and distribution of microbial community and antibiotic resistance genes (ARGs) in food waste, anaerobic digestate, and paddy soil samples, and revealed the potential hosts of ARGs and factors influencing their distribution. A total of 24 bacterial phyla were identified, of which 16 were shared by all samples, with Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria accounting for 65.9–92.3 % of the total bacterial community. Firmicutes was the most abundant bacteria in food waste and digestate samples, accounting for 33–83 % of the total microbial community. However, in paddy soil samples with digestate, Proteobacteria had the highest relative abundance of 38–60 %. Further, 22 ARGs were detected in food waste and digestate samples, with multidrug, macrolide-lincosamide-streptogramin (MLS), bacitracin, aminoglycoside, tetracycline, vancomycin, sulfonamide, and rifamycin resistance genes being the most abundant and shared by all samples. The highest total relative abundance of ARGs in food waste, digestate, and soil without and with digestate was detected in samples from January 2020, May 2020, October 2019, and May 2020, respectively. The MLS, vancomycin, tetracycline, aminoglycoside, and sulfonamide resistance genes had higher relative abundance in food waste and anaerobic digestate samples, whereas multidrug, bacteriocin, quinolone, and rifampin resistance genes were more abundant in paddy soil samples. Redundancy analysis demonstrated that aminoglycoside, tetracycline, sulfonamide, and rifamycin resistance genes were positively correlated with total ammonia nitrogen and pH of food waste and digestate samples. Vancomycin, multidrug, bacitracin, and fosmidomycin resistance genes had positive correlations with potassium, moisture, and organic matter in soil samples. The co-occurrence of ARG subtypes with bacterial genera was investigated using network analysis. Actinobacteria, Proteobacteria, Bacteroidetes, and Acidobacteria were identified as potential hosts of multidrug resistance genes.

Metaviromic analyses of DNA virus community from sediments of the N-Choe stream, North India

Virome exploration from the freshwater stream ecosystem is less explored. We deciphered the DNA virome from sediments of the N-Choe stream in Chandigarh, India. This study utilized the long-read nanopore sequencing data analyzed by assembly-free and assembly-based approaches to study the viral community structure and its genetic potential. In the classified fraction of the virome, we observed the dominance of the ssDNA viruses. The prominent ssDNA virus families were Microviridae, Circoviridae, and Genomoviridae. The majority of dsDNA viruses were bacteriophages belonging to class Caudoviricetes. We also recovered metagenome-assembled viruses of Microviridae, CRESS DNA viruses, and viral-like circular molecules. We identified the structural and functional gene repertoire of the viromes and their gene ontology. Furthermore, we detected auxiliary metabolic genes (AMGs) involved in pathways such as pyrimidine synthesis, organosulfur metabolism indicating the functional importance of viruses in the ecosystem. The antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and mobile genetic elements (MGEs) present in the viromes and their co-occurrence were studied. ARGs of the glycopeptide, macrolide, lincosamide, streptogramin (MLS), and mupirocin categories were well represented. Among the reads containing ARGs, a few reads were also classified as viruses, indicating that environmental viruses act as reservoirs of ARGs.

A First Insight into the Microbial and Viral Communities of Comau Fjord-A Unique Human-Impacted Ecosystem in Patagonia (42∘ S).

While progress has been made in surveying the oceans to understand microbial and viral communities, the coastal ocean and, specifically, estuarine waters, where the effects of anthropogenic activity are greatest, remain partially understudied. The coastal waters of Northern Patagonia are of interest since this region experiences high-density salmon farming as well as other disturbances such as maritime transport of humans and cargo. Here, we hypothesized that viral and microbial communities from the Comau Fjord would be distinct from those collected in global surveys yet would have the distinctive features of microbes from coastal and temperate regions. We further hypothesized that microbial communities will be functionally enriched in antibiotic resistance genes (ARGs) in general and in those related to salmon farming in particular. Here, the analysis of metagenomes and viromes obtained for three surface water sites showed that the structure of the microbial communities was distinct in comparison to global surveys such as the Tara Ocean, though their composition converges with that of cosmopolitan marine microbes belonging to Proteobacteria, Bacteroidetes, and Actinobacteria. Similarly, viral communities were also divergent in structure and composition but matched known viral members from North America and the southern oceans. Microbial communities were functionally enriched in ARGs dominated by beta-lactams and tetracyclines, bacitracin, and the group macrolide-lincosamide-streptogramin (MLS) but were not different from other communities from the South Atlantic, South Pacific, and Southern Oceans. Similarly, viral communities were characterized by exhibiting protein clusters similar to those described globally (Tara Oceans Virome); however, Comau Fjord viromes displayed up to 50% uniqueness in their protein content. Altogether, our results indicate that microbial and viral communities from the Comau Fjord are a reservoir of untapped diversity and that, given the increasing anthropogenic impacts in the region, they warrant further study, specifically regarding resilience and resistance against antimicrobials and hydrocarbons.

The ecological and molecular mechanism underlying effective reduction of antibiotic resistance genes pollution in soil by fermentation broth from fruit and vegetable waste

The strategies to relieve antibiotic resistance genes (ARGs) pollution are urgently needed. Fermentation broth from fruit and vegetable waste (FFVW), an agricultural amendment, exhibits a remarkable capacity to reduce ARG pollution; however, the underlying mechanism of this effect remains unclear. We performed microcosm experiments to reappear the phenomenon of FFVW-driven reduction in ARGs. Moderate-level FFVW reduced gene resistance to sulfonamide (41.2 %), macrolide–lincosamide–streptogramin (MLS) (47.2 %), chloramphenicol (63.2 %), and tetracycline (61.4 %). Binning and network analyses revealed that Actinobacteria comprise the primary hosts of ARGs in arable soil, and FFVW substantially inhibited the growth and metabolic activity of these organisms. Moreover, tetracycline and MLS production was partially/completely inhibited by FFVW, further reducing the transfer frequency by 52.9–86.1 % and 46.6–66.6 % in the intragenic and intergenic mating systems, respectively. Furthermore, the expression of genes related to conjugation pairing and plasmid transfer was downregulated. Thus, FFVW effectively reduces ARG pollution by inhibiting Actinobacteria proliferation, thereby reducing selective pressure and restricting horizontal gene transfer. Our findings highlight the important underlying mechanisms of FFVW involved in ARG reduction, supporting its use in arable soil.

Phenotypic and Genotypic Characterization of Macrolide-Lincosamide-Streptogramin Resistance in Staphylococcus aureus Isolates from Bovine and Human

Abstract In this study, penicillin, oxacillin, and macrolide-lincosamide-streptogramin (MLS) resistance in S. aureus strains that were isolated from bovine mastitis cases, and human patients were investigated. Inducible clindamycin resistance (iML) was not found in 30 bovine isolates, while it was detected in 3 (10%) of 30 human isolates. MIC90 values of penicillin, oxacillin and macrolide-lincosamides (ML) were 2, 0.19, >256 µg/ml in bovine isolates and were 3, 3 and 0.19-1.5 µg/ml in human isolates, respectively. Streptogramin resistance was not found in both bovine and human isolates. Although the mecA gene was detected in all of the oxacillin resistant isolates, blaZ gene could not be detected in penicillin resistant isolates. The erm(B) gene was detected in 5 (38.6%) of 13 ML-resistant bovine isolates, and the mph(C) gene was detected in 2 (66.66%) of 3 human isolates. As a result, resistance to penicillin and oxacillin was found to be higher in human S. aureus isolates, while ML resistance was found to be higher in bovine isolates in this investigation. It was concluded that the presence of genes in extra-chromosomal elements associated to penicillin and macrolide resistance should be investigated. The data obtained from this study will contribute to the studies on antimicrobial susceptibility in the field of human and veterinary medicine.

Occurrence of Staphylococcus spp. in the wastewaters from Iran: Diversity, antimicrobial resistance, and virulence potential

Abstract The prevalence, antibiotic resistance, and virulence characteristics of Staphylococci from hospitals, livestock, municipals, and poultry wastewaters were investigated in Ardabil, Iran. From 155 staphylococcal isolates, 44.5% were coagulase-positive Staphylococcus (CoPS) and 55.5% were coagulase-negative Staphylococcus (CoNS) spp. Both CoPS and CoNS species were mainly found in hospital and poultry wastewater samples. The most prominent CoPS and CoNS species were Staphylococcus aureus at 80% and Staphylococcus xylosus at 37%. Methicillin resistance was found in 2% of S. aureus isolates. Overall, 49.2% of CoPS and 47.6% of CoNS isolates exhibited multidrug resistance phenotypes. CoPS isolates were the most resistant to penicillin (89%) and erythromycin (62%) and CoNS isolates exhibited the highest resistance to erythromycin (55%) and tetracycline (49%). Inducible clindamycin resistance was detected in 11% of S. aureus isolates. The ermC and aac genes were detected as the most common macrolide–lincosamide–streptogramin B and aminoglycoside-resistance encoding genes in 82.5 and 22.5% of S. aureus isolates, respectively. Most of the S. aureus isolates were positive for multiple virulence factors. The methicillin-resistant S. aureus isolates belonged to SCCmec type V. A new spa type t19215 was also identified. The occurrence of multidrug-resistant S. aureus with diverse genetic resistance and virulence background in wastewater is of great health concern.

Optimization of loop-mediated isothermal amplification-based method for detection of macrolide-lincosamide-streptogramin B resistance in Staphylococcus aureus.

Optimization of loop-mediated isothermal amplification-based method for detection of macrolide-lincosamide-streptogramin B resistance in Staphylococcus aureus.

Metagenomic binning analyses of pig manure composting reveal potential antibiotic-degrading bacteria and their risk of antibiotic resistance genes

Antibiotic-degrading bacteria are commonly used to treat antibiotic contamination, but the antibiotic resistance genes (ARGs) they carry are often overlooked. This study used metagenomic assembly and binning analyses to explore potential antibiotic-degrading bacteria and their ARGs during pig manure composting. The result showed that 35 metagenome-assembled genomes (MAGs) mainly containing alkyl-aryl transferase and decarboxylase genes involved in the removal of antibiotics. Multidrug (124), β-lactam (67), macrolide-lincosamide-streptogramin (MLS) (64), and tetracycline (43) were the central ARG types detected in the 35 MAGs. Furthermore, the risk of ARGs was evaluated using the arg_ranker framework, and 19 MAGs were found to contain intermediate-high-risk ARGs with human-associated-enrichment, gene transferability, and host pathogenicity. Bin 34 of the genus of Geofilum had the highest ARG risk. Bin 6, Bin 11 and Bin 14 of the genus of Limnochorda, Chelatococcus and Niabella, had a lower ARG risk and were considered as potential antibiotic-degrading bacteria.