Macrolide-lincosamide-streptogramin B Research Articles

Anthropogenic activities significantly interfered distribution and co-occurrence patterns of antibiotic resistance genes in a small rural watershed in Southwest China

The prevalence and spread of antibiotic resistance genes (ARGs) have been a significant concern for global public health in recent years. Small rural watersheds are the smallest units of factor mobility for agricultural production in China, and their ARG profiles are the best scale of the contamination status, but the mapping and the distribution and diffusion of ARGs in the water and soil of small rural watersheds are inadequate. In this study, based on microbial metagenomics, we invested prevalence maps of 209 ARGs corresponding to typical commonly used antibiotics (including multidrug, aminoglycoside, macrolide-lincosamide-streptogramin B (MLSB), and β-Lactamase) in water and soil in different agricultural types, as well as within water-soil interfaces in small rural watersheds in Southwest China. The results revealed that the most abundant ARGs in water and soil were consistent, but different in subtypes, and anthropogenic activities affect the transport of ARGs between water and soils. Livestock wastewater discharges influenced the diversity and abundance of ARGs in water, while in soil it is planting type and fertilizer management, and thus interfered with the co-occurrence patterns between bacteria and ARGs. Co-occurrence analysis revealed that Proteobacteria, Actinobacteria, and Bacteroidetes were the predominant ARG hosts in water and soil, but soil exhibited a more intricate ARG-bacterial association. Overall, this study provides integrated profiles of ARGs in water and soil influenced by anthropogenic activities at the small watershed scale in a typical rural area and provides a baseline for comparisons of ARGs.

Phenotypic and genotypic characterization of commensal staphylococci isolated from young volunteers in Alexandria, Egypt

Nasally colonized staphylococci carry antibiotic resistance genes and may lead to serious opportunistic infections. We are investigating nasal carriage of Staphylococcus aureus and Staphylococci other than S. aureus (SOSA) among young volunteers in Egypt to determine their risk potential. Nasal swabs collected over 1 week in June 2019 from 196 volunteers were cultured for staphylococcus isolation. The participants were interviewed to assess sex, age, general health, hospitalization and personal hygiene habits. Identification was carried out using biochemical tests and VITEK 2 automated system. Disc diffusion and minimum inhibitory concentration tests were performed to determine antibiotic susceptibility. Screening for macrolide resistance genes (ermA, ermB, ermC, ermT and msrA) was performed using polymerase chain reaction. Thirty four S. aureus and 69 SOSA were obtained. Multi-drug resistance (MDR) was detected among most staphylococcal species, ranging from 30.77% among S. hominis to 50% among S. epidermidis. Phenotypic resistance to all tested antibiotics, except for linezolid, was observed. Susceptibility to rifampicin, vancomycin and teicoplanin was highest. ermB showed the highest prevalence among all species (79.41% and 94.2% among S. aureus and SOSA, respectively), and constitutive macrolide-lincosamide-streptogramin B (MLSB) resistance was equally observed in S. aureus and SOSA (11.11% and 16.22%, respectively), whereas inducible MLSB resistance was more often found in S. aureus (77.78% and 43.24%, respectively). The species or resistance level of the carried isolates were not significantly associated with previous hospitalization or underlying diseases. Although over all colonization and carriage of resistance genes are within normal ranges, the increased carriage of MDR S. aureus is alarming. Also, the fact that many macrolide resitance genes were detected should be a warning sign, particularly in case of MLSB inducible phenotype. More in depth analysis using whole genome sequencing would give a better insight into the MDR staphylococci in the community in Egypt.

Comparison of qPCR and metagenomic sequencing methods for quantifying antibiotic resistance genes in wastewater.

Surveillance methods of circulating antibiotic resistance genes (ARGs) are of utmost importance in order to tackle what has been described as one of the greatest threats to humanity in the 21st century. In order to be effective, these methods have to be accurate, quickly deployable, and scalable. In this study, we compare metagenomic shotgun sequencing (TruSeq DNA sequencing) of wastewater samples with a state-of-the-art PCR-based method (Resistomap HT-qPCR) on four wastewater samples that were taken from hospital, industrial, urban and rural areas. ARGs that confer resistance to 11 antibiotic classes have been identified in these wastewater samples using both methods, with the most abundant observed classes of ARGs conferring resistance to aminoglycoside, multidrug-resistance (MDR), macrolide-lincosamide-streptogramin B (MLSB), tetracycline and beta-lactams. In comparing the methods, we observed a strong correlation of relative abundance of ARGs obtained by the two tested methods for the majority of antibiotic classes. Finally, we investigated the source of discrepancies in the results obtained by the two methods. This analysis revealed that false negatives were more likely to occur in qPCR due to mutated primer target sites, whereas ARGs with incomplete or low coverage were not detected by the sequencing method due to the parameters set in the bioinformatics pipeline. Indeed, despite the good correlation between the methods, each has its advantages and disadvantages which are also discussed here. By using both methods together, a more robust ARG surveillance program can be established. Overall, the work described here can aid wastewater treatment plants that plan on implementing an ARG surveillance program.

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

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.

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.

Novel macrolide-lincosamide-streptogramin B resistance gene erm(56) in Trueperella pyogenes.

Whole-genome sequence analysis of a macrolide, lincosamide, streptogramin B (MLSB)-resistant Trueperella pyogenes from a dog revealed a new 23S ribosomal RNA methylase gene erm(56). Expression of the cloned erm(56) confers resistance to MLSB in T. pyogenes and Escherichia coli. The erm(56) gene was flanked by two IS6100 integrated on the chromosome next to a sul1-containing class 1 integron. GenBank query revealed additional erm(56)-containing elements in another T. pyogenes and in Rothia nasimurium from livestock. IMPORTANCE A novel 23S ribosomal RNA methylase gene erm(56) flanked by insertion sequence IS6100 was identified in a Trueperella pyogenes isolated from the abscess of a dog and was also present in another T. pyogenes and in Rothia nasimurium from livestock. It was shown to confer resistance to macrolide, lincosamide, streptogramin B antibiotics in T. pyogenes and E. coli, indicating functionality in both Gram-positive and Gram-negative bacteria. The detection of erm(56) on different elements in unrelated bacteria from different animal sources and geographical origins suggests that it has been independently acquired and likely selected by the use of antibiotics in animals.

Population genetics of group B Streptococcus from maternal carriage in an ethnically diverse community in London.

Maternal immunization against Group B Streptococcus (GBS) has the potential to significantly reduce the burden of neonatal GBS infections. Population genetics of GBS from maternal carriage can offer key insights into vaccine target distribution. In this study we characterized the population structure of GBS isolates from maternal carriage (n = 535) in an ethnically diverse community in London, using whole genome sequencing. The isolates clustered into nine clonal complexes (CCs) but the majority (95%) belonged to five lineages: CC1 (26%), CC19 (26%), CC23 (20%), CC17 (13%) and CC8/10 (10%). Nine serotypes were identified, the most common were serotypes III (26%), V (21%), II (19%) and Ia (19%). Other serotypes (Ib, IV, VI, VII, IX) represented less than 10% of all isolates each. Intra-lineage serotype diversity was observed in all major CCs but was highest in CC1, which revealed nine serotypes. Nearly all isolates (99%) carried at least one of the four alpha family protein genes (alpha, alp1, alp23, and rib). All isolates were susceptible to penicillin. We found 21% and 13% of isolates to be resistant to clarithromycin and clindamycin, respectively. Prevalence of macrolide-lincosamide-streptogramin B (MLSB) resistance genes was 22% and they were most common in CC19 (37%) and CC1 (28%), and isolates with serotypes V (38%) and IV (32%). We identified some associations between maternal ethnicity and GBS population structure. Serotype Ib was significantly less common among the South Asian compared to Black women (S. Asian: 3/142, Black: 15/135, p = 0.03). There was also a significantly lower proportion of CC1 isolates among the White other (24/142) in comparison to Black (43/135) and S. Asian (44/142) women (p = 0.04). We found a significantly higher proportion of CC17 isolates among the White other compared to S. Asian women (White other: 32/142, S. Asian: 10/142, p = 0.004). Our study showed high prevalence of GBS vaccine targets among isolates from pregnant women in London. However, the observed serotype diversity in CC1 and high prevalence of MLSB resistance genes in CC19 demonstrates presence of high risk lineages, which might act as a reservoir of non-vaccine strains and antimicrobial resistance determinants.

The antimicrobial activity of cethromycin against Staphylococcus aureus and compared with erythromycin and telithromycin

BackgroundThis study aims to explore the antibacterial activity of cethromycin against Staphylococcus aureus (S. aureus), and its relationship with multilocus sequence typing (MLST), erythromycin ribosomal methylase (erm) genes and macrolide-lincosamide-streptogramin B (MLSB) phenotypes of S. aureus.ResultsThe minimum inhibitory concentrations (MICs) of cethromycin against 245 S. aureus clinical isolates ranged from 0.03125 to ≥ 8 mg/L, with the resistance of 38.8% in 121 methicillin-resistant S. aureus (MRSA). This study also found that cethromycin had strong antibacterial activity against S. aureus, with the MIC ≤ 0.5 mg/L in 55.4% of MRSA and 60.5% of methicillin-sensitive S. aureus (MSSA), respectively. The main MLSTs of 121 MRSA were ST239 and ST59, and the resistance of ST239 isolates to cethromycin was higher than that in ST59 isolates (P = 0.034). The top five MLSTs of 124 MSSA were ST7, ST59, ST398, ST88 and ST120, but there was no difference in the resistance of MSSA to cethromycin between these STs. The resistance of ermA isolates to cethromycin was higher than that of ermB or ermC isolates in MRSA (P = 0.016 and 0.041, respectively), but the resistance of ermB or ermC isolates to cethromycin was higher than that of ermA isolates in MSSA (P = 0.019 and 0.026, respectively). The resistance of constitutive MLSB (cMLSB) phenotype isolates to cethromycin was higher than that of inducible MLSB (iMLSB) phenotype isolates in MRSA (P < 0.001) or MSSA (P = 0.036). The ermA, ermB and ermC genes was mainly found in ST239, ST59 and ST1 isolates in MRSA, respectively. Among the MSSA, the ermC gene was more detected in ST7, ST88 and ST120 isolates, but more ermB genes were detected in ST59 and ST398 isolates. The cMLSB phenotype was more common in ST239 and ST59 isolates of MRSA, and was more frequently detected in ST59, ST398, and ST120 isolates of MSSA.ConclusionCethromycin had strong antibacterial activity against S. aureus. The resistance of MRSA to cethromycin may had some clonal aggregation in ST239. The resistance of S. aureus carrying various erm genes or MLSB phenotypes to cethromycin was different.

Antibiotic Resistance Genes in Aerosols: Baseline from Kuwait.

Antimicrobial resistance (AMR) is one of the biggest threats to human health worldwide. The World Health Organization (WHO, Geneva, Switzerland) has launched the "One-Health" approach, which encourages assessment of antibiotic-resistant genes (ARGs) within environments shared by human-animals-plants-microbes to constrain and alleviate the development of AMR. Aerosols as a medium to disseminate ARGs, have received minimal attention. In the present study, we investigated the distribution and abundance of ARGs in indoor and outdoor aerosols collected from an urban location in Kuwait and the interior of three hospitals. The high throughput quantitative polymerase chain reaction (HT-qPCR) approach was used for this purpose. The results demonstrate the presence of aminoglycoside, beta-lactam, fluoroquinolone, tetracycline, macrolide-lincosamide-streptogramin B (MLSB), multidrug-resistant (MDR) and vancomycin-resistant genes in the aerosols. The most dominant drug class was beta-lactam and the genes were IMP-2-group (0.85), Per-2 group (0.65), OXA-54 (0.57), QnrS (0.50) and OXA-55 (0.55) in the urban non-clinical settings. The indoor aerosols possessed a richer diversity (Observed, Chao1, Shannon's and Pielou's evenness) of ARGs compared to the outdoors. Seasonal variations (autumn vs. winter) in relative abundances and types of ARGs were also recorded (R2 of 0.132 at p < 0.08). The presence of ARGs was found in both the inhalable (2.1 µm, 1.1 µm, 0.7 µm and < 0.3 µm) and respirable (>9.0 µm, 5.8 µm, 4.7 µm and 3.3 µm) size fractions within hospital aerosols. All the ARGs are of pathogenic bacterial origin and are hosted by pathogenic forms. The findings present baseline data and underpin the need for detailed investigations looking at aerosol as a vehicle for ARG dissemination among human and non-human terrestrial biota.

Inhibition of Erythromycin and Erythromycin-Induced Resistance among Staphylococcus aureus Clinical Isolates.

The increasing incidence of erythromycin and erythromycin-induced resistance to clindamycin among Staphylococcus aureus (S. aureus) is a serious problem. Patients infected with inducible resistance phenotypes may fail to respond to clindamycin. This study aimed to identify the prevalence of erythromycin and erythromycin-induced resistance and assess for potential inhibitors. A total of 99 isolates were purified from various clinical sources. Phenotypic detection of macrolide-lincosamide-streptogramin B (MLSB)-resistance phenotypes was performed by D-test. MLSB-resistance genes were identified using PCR. Different compounds were tested for their effects on erythromycin and inducible clindamycin resistance by broth microdilution and checkerboard microdilution methods. The obtained data were evaluated using docking analysis. Ninety-one isolates were S. aureus. The prevalence of constitutive MLSB, inducible MLSB, and macrolide-streptogramin (MS) phenotypes was 39.6%, 14.3%, and 2.2%, respectively. Genes including ermC, ermA, ermB, msrA, msrB, lnuA, and mphC were found in 82.6%, 5.8%, 7.7%, 3.8%, 3.8%, 13.5%, and 3.8% of isolates, respectively. Erythromycin resistance was significantly reduced by doxorubicin, neomycin, and omeprazole. Quinine, ketoprofen, and fosfomycin combated and reversed erythromycin/clindamycin-induced resistance. This study highlighted the significance of managing antibiotic resistance and overcoming clindamycin treatment failure. Doxorubicin, neomycin, omeprazole, quinine, ketoprofen, and fosfomycin could be potential inhibitors of erythromycin and inducible clindamycin resistance.

Enrichment of antibiotic resistant genes and pathogens in face masks from coastal environments

Face masks (FMs) are essential to limit the spread of the coronavirus during pandemic, a considerable of which are accumulated on the coast. However, limited is known about the microbial profile in the biofilm of the face masks (so-called plastisphere) and the impacts of face masks on the surrounding environments. We herein performed face mask exposures to coastal sediments and characterized the microbial community and the antibiotic resistome. We detected 64 antibiotic-resistance genes (ARGs) and 12 mobile gene elements (MGEs) in the plastisphere. Significant enrichments were found in the relative abundance of total ARGs in the plastisphere compared to the sediments. In detail, the relative abundance of tetracycline, multidrug, macrolide-lincosamide-streptogramin B (MLSB), and phenicol-resistant genes had increased by 5–10 times. Moreover, the relative abundance of specific hydrocarbonoclastic bacteria (e.g., Polycyclovorans sp.), pathogens (e.g., Pseudomonas oleovorans), and total MGEs significantly increased in the sediments after face mask exposure, which was congruent with the alteration of pH value and metal concentrations in the microcosms. Our study demonstrated the negative impacts of FMs on coastal environments regardless of the profiles of ARGs or pathogens. These findings improved the understanding of the ecological risks of face masks and underlined the importance of beach cleaning.

Design, Synthesis and Biological Evaluation of Conjugates of 3-O-Descladinose-azithromycin and Nucleobases against rRNA A2058G- or A2059G-Mutated Strains.

Structurally unrelated antibiotics MLSB (macrolide-lincosamide-streptogramin B) compromised with clinically resistant pathogens because of the cross-resistance resulting from the structural modification of rRNA A2058. The structure-activity relationships of a novel 3-O-descladinose azithromycin chemotype conjugating with nucleobases were fully explored with the aid of engineered E. coli SQ110DTC and SQ110LPTD. The conjugates of macrolides with nucleobases, especially adenine, displayed antibacterial superiority over telithromycin, azithromycin and clindamycin against rRNA A2058/2059-mutated engineered E. coli strains at the cost of lowering permeability and increasing vulnerability to efflux proteins against clinical isolates.

Exposure to cadmium induced gut antibiotic resistance genes (ARGs) and microbiota alternations of Babylonia areolata

Cadmium (Cd) is widely distributed in aquatic environments and has multiple adverse effects on aquatic organisms such as the ivory shell (Babylonia areolata). However, its effects on antibiotic resistance genes (ARGs) and gut microbiota of B. areolata remain unclear. In this study, we explored the effects of different concentrations (0, 0.03, 0.18 and 1.08 mg/L) of Cd on intestinal microbial communities and ARGs in B. areolata through 16S rRNA gene sequencing and high-throughput quantitative PCR. The results showed that the structure and diversity of ARGs and microbiota in B. areolata gut were altered upon Cd exposure. Tetracycline, Vancomycin and Macrolide-Lincosamide-Streptogramin B (MLSB) resistance genes were identified as the major ARGs in B. areolata gut. The absolute abundance and alpha diversity of ARGs in B. areolata gut increased with the rise of cadmium concentration. The microbial communities at genus level were enriched in the low and medium Cd concentration groups, while decreased in the high Cd concentration group compared to the control groups. In addition, the influence of microbiota on the ARG profile was more significant than that of Cd concentration and MGEs in B. areolata gut. Null model analysis demonstrated that stochastic processes dominated ARG assembly in the Cd-exposed groups and were enhanced with the increasing Cd concentrations. Four opportunistic bacterial pathogens (Bacteroides, Legionella, Acinetobacter and Escherichia) detected in B. areolata gut maybe the potential hosts of ARGs. Our findings provide references for the hazards assessment of environmental Cd exposure of gut microbiome in aquatic animals.

Comparative virulence and antimicrobial resistance distribution of Streptococcus suis isolates obtained from the United States.

Streptococcus suis is a zoonotic bacterial swine pathogen causing substantial economic and health burdens to the pork industry worldwide. Most S. suis genome sequences available in public databases are from isolates obtained outside the United States. We sequenced the genomes of 106 S. suis isolates from the U.S. and analyzed them to identify their potential to function as zoonotic agents and/or reservoirs for antimicrobial resistance (AMR) dissemination. The objective of this study was to evaluate the genetic diversity of S. suis isolates obtained within the U.S., for the purpose of screening for genomic elements encoding AMR and any factors that could increase or contribute to the capacity of S. suis to transmit, colonize, and/or cause disease in humans. Forty-six sequence types (STs) were identified with ST28 observed as the most prevalent, followed by ST87. Of the 23 different serotypes identified, serotype 2 was the most prevalent, followed by serotype 8 and 3. Of the virulence genes analyzed, the highest nucleotide diversity was observed in sadP, mrp, and ofs. Tetracycline resistance was the most prevalent phenotypic antimicrobial resistance observed followed by macrolide-lincosamide-streptogramin B (MLSB) resistance. Numerous AMR elements were identified, many located within MGE sequences, with the highest frequency observed for ble, tetO and ermB. No genes encoding factors known to contribute to the transmission, colonization, and/or causation of disease in humans were identified in any of the S. suis genomes in this study. This includes the 89 K pathogenicity island carried by the virulent S. suis isolates responsible for human infections. Collectively, the data reported here provide a comprehensive evaluation of the genetic diversity among U.S. S. suis isolates. This study also serves as a baseline for determining any potential risks associated with occupational exposure to these bacteria, while also providing data needed to address public health concerns.

Prevalence and antimicrobial susceptibility pattern of methicillin-resistant Staphylococcus aureus isolates from retail raw meats in Turkey

The transmission of Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) through food products of animal origin may pose a public health concern. Therefore, the objectives of the present work were to determine the prevalence of S. aureus and MRSA in raw meat samples (beef, chicken, turkey, and duck) at retail level, and to determine the antimicrobial resistance profile of the MRSA isolates. Between September 2018 and January 2019, a total of 325 raw meat samples were collected from retail stores, and analysed for the presence of S. aureus and MRSA using primary enrichment method as well as using secondary selective enrichment methods for MRSA detection. All the suspected S. aureus and MRSA colonies obtained from the samples were confirmed by both phenotypic and genotypic methods. The MRSA isolates were tested against various antimicrobials, and the minimal inhibitory concentration (MIC) of vancomycin was determined. Macrolide-lincosamide-streptogramin B (MLSB) resistance phenotypes were also screened using the double-disk diffusion test. The overall prevalence of S. aureus was 57.2%, whereas the food-specific prevalence in beef, turkey, duck, and chicken samples was 75, 53, 48, and 46%, respectively. The overall prevalence of MRSA was 1.2%, whereas it was 3, 1, 0, and 0% in beef, turkey, chicken, and duck samples, respectively. All MRSA isolates were detected by the secondary selective enrichment method. These MRSA isolates had a variety of MLSB resistance phenotypes (i.e., iMLSB, cMLSB, and MS-MLSB) with vancomycin MIC values ranging between 1 - 2 µg/mL. These findings are important for developing interventions to reduce raw meat contamination with S. aureus and MRSA, and to improve public health.

Diversity and abundance of antibiotic resistance genes and their relationship with nutrients and land use of the inflow rivers of Taihu Lake.

Taihu Lake is the third largest freshwater lake in China and an important source for drinking water, flood protection, aquaculture, agriculture, and other activities. This lake is connected to many principal and small rivers with inflow from west and outflow on the eastern side of the lake and these inflow rivers are believed to significantly contribute to the water pollution of the lake. This study was aimed at assessing the diversity and abundance of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and their relationship with water quality parameters and land use patterns. Water samples were collected from 10 major inflow rivers and the source water protection area of the Taihu Lake in spring and summer 2019. High-throughput profiling was used to detect and quantify 384 ARGs and MGEs and in addition, 11 water quality parameters were analyzed. The results showed that the number of ARGs/MGEs detected in each inflow river ranged from 105 to 185 in spring and 107 to 180 in summer. The aminoglycoside resistance genes were the most dominant types ARGs detected followed by beta-lactam resistance, multidrug resistance, macrolide-lincosamide-streptogramin B (MLSB) resistance genes, which contributed to 65% of the ARGs. The water quality parameters showed significant correlation with absolute abundance of ARGs. Furthermore, significant correlation between ARGs and MGEs were also observed which demonstrates potential gene transfer among organisms through horizontal gene transfer via MGEs. ARGs showed strong positive correlation with cultivated and industrial lands whereas, negative correlation was observed with river, lake, forest, land for green buffer, and land for port and harbor. The overall results indicate that the inflow rivers of Taihu Lake are polluted by various sources including multiple nutrients and high abundance of ARGs, which needs attention for better management of the inflow rivers of this lake.

Phenotypic and genotypic characterization of macrolide resistance in Staphylococcus aureus isolates from wound infection

Microbiologists are increasingly concerned about the rise in S. aureus MLSB (macrolide, lincosamide, streptogramin B) drug resistance. Clindamycin has been effective in treating infections by S. aureus, and the variations in clindamycin sensitivity patterns cause treatment to fail. Inducible clindamycin resistance in S. aureus is expressed via erythromycin ribosome methylase genes. In the current study, 25 S. aureus isolates were identified by conventional chemical tests and the Vitek®2 system. Specific primers were used for the amplification of Macrolide genes by PCR. Among 25 S. aureus isolates, 23(92%) isolates were methicillin resistant and 2(8%) isolates were methicilin sensitive. The 5(20%) isolates showed resistance to Erythromycin and sensitivity to Clindamycin with a positive D test which was identified as inducible MLSB, while 2(8%) isolates showed resistance criteria for both Erythromycin and Clindamycin which identity as a constitutive MLSB and 18(92%) isolates were given the sensitivity for both Erythromycin and Clindamycin. The erm resistance genes (ermA, ermB, ermC, ermF, and ermG) were detected in 5(20%), 17(68%), 25(100%), 24(96%),11(44%) respectively. The D-test, and Vitek ®2 system should be routinely done to avoid treatment failure due to clindamycin resistance.

Corpse decomposition of freshwater economic fish leads to similar resistomes and the enrichment of high-risk antibiotic resistance genes in different water types

Animal carcass decay produces many poisonous metabolites and chemical pollutants, which pose potential ecological risks to the aquatic environment and human health. However, the effects of animal cadaver decomposition on high-risk antibiotic resistance genes (ARGs) and potential pathogens in different water types are still unknown. In this study, fifteen freshwater economic fish (Carassius auratus) corpses were put into three types of water (i.e., pond water, tap water, and domestic sewage) for a 100-day decomposition. Next generation sequencing and HT-qPCR were used to illustrate how corpse decomposition affected microbial communities and ARG profiles. Our results revealed that fish corpse degradation caused similar resistomes and microbiome in different water types. MLSB (Macrolide-Lincosamide-Streptogramin B), β-lactamase, sulfonamide, tetracycline resistance genes and transposase genes in the experimental groups were increased. Among them, tetracycline resistance genes were enriched by 224 to 136,218-fold during the process of corpse degradation. Furthermore, high-risk ARGs (ermB, floR and dfrA1), which resist to MLSB, multidrug and sulfonamide respectively, were significantly enriched in the cadaver groups and had co-occurrence patterns with opportunistic pathogens, such as Bacteroidetes, which was more than 37 times in carcass groups than that in control groups. The study is able to draw a general conclusion that cadaver decomposition of freshwater economic fish deteriorates the aquatic environment by affecting high-risk ARGs and pathogenic microorganisms regardless of water types, which poses potential threats to human health. Therefore, timely management and treatment of animal carcasses is of great significance to the protection of water environment.

Distribution Characteristics of Antibiotics and Antibiotic Resistance Genes in Manure and Surrounding Soil of Poultry Farm in Ningxia

Antibiotics and antibiotic resistance genes (ARGs) in livestock and poultry manure pose potential ecological risks. In order to understand the distribution characteristic of antibiotics and ARGs in manure and surrounding soils of poultry farms in Ningxia, the poultry manure and relative soil samples were collected from 12 layers of different poultry breeding farms. The compositions of antibiotics and ARGs in the samples were analyzed using UPLC-MS/MS and HT-qPCR. The results showed that:① tetracycline, aminoglycoside, and sulfonamide were the dominant antibiotics in poultry manure. The types and contents of antibiotics in poultry manure were different in different breeding periods. There were more types of antibiotics in the brooding period, the average content was high, and the initial stage showed the opposite trend. ② A small amount of antibiotics was detected in the surrounding soil only 20 m away from the poultry farm, and the poultry farm had little effect on the distribution of antibiotics in the surrounding soil. The content of quinolone in the soils with poultry manure application was significantly higher than that in the control and surrounding soil. ③ We detected 132-168 ARGs in poultry manure, and the number of aminoglycosides and tetracycline was higher. The relative abundance of ARGs in the rearing period was highest, and the initial stage showed the opposite trend. The total relative abundance of ARGs in the brooding period was highest, but the terminal period showed the opposite. There were 110 ARGs in poultry manure during all breeding periods. ④ There were 23-105 ARGs in the soils, and the number of aminoglycoside was highest, followed by multidrug ARGs. The poultry farm had a great effect on the number and relative abundance of ARGs in the surrounding soil. For example, the number and relative abundance of ARGs in the surrounding soil of poultry farms gradually decreased with the increase in the distance from the poultry farms. The number and relative abundance of ARGs in the soil with applied poultry manure were significantly increased; however, these values were lower than those in the soil 20 m away from the poultry farm. ⑤ β-lactamases, aminoglycosides, and macrolide lincosamide-streptogramin B (MLSB) ARGs were all at risk of horizontal movement in manure, and chloramphenicol ARGs were at risk of horizontal movement in soil. Correlation analysis showed that the relative abundance of aminoglycoside, tetracycline, sulfonamide, β-lactamase, and MLSB were not significantly correlated with their contents. ⑥ Different types of ARGs had related co-occurrence phenomena, such as the positive correlation between the relative abundance of ARGs in poultry manure, and aminoglycoside and β-lactamases, MGEs, multidrugs and vancomycins. The relative abundances of ARGs in soil, aminoglycoside and tetracyclines, vancomycins, sulfonamides, and MLSBs; tetracyclines and MLSBs; etc., all showed a significant positive correlation. In short, the co-occurrence among the relative abundance of ARGs in soil was significantly stronger than that in poultry manure. These results could provide the theoretical basis for the site selection of poultry farms, the selection of antibiotic types and dosages for large-scale breeding of laying hens, and the application of poultry manure.