Resistance to tetracycline, macrolide-lincosamide-streptogramin, trimethoprim, and sulfonamide drug classes

Mass spectrometry-based identification reveals the polymicrobial nature of canine urinary tract infections

Canine urinary tract infections (UTIs) are common in veterinary practice and often have a complex etiology. Typically, diagnoses rely on classical phenotypic tests or are limited to identifying the genus of the pathogen. Treatments are frequently administered without prior in vitro antimicrobial susceptibility testing. This study analyzed 389 urine samples from dogs with clinical signs of UTI, collected by cystocentesis, through microbiological culture. Species-level identification of bacteria and yeasts was performed using mass spectrometry, while bacterial isolates underwent antimicrobial susceptibility testing via the disk diffusion method. Of the 389 samples, 170 (43.7%) showed microbial growth, with 192 microorganisms identified. Among these, 98.4% (189/192) were bacteria, and 1.6% (3/192) were fungi/yeasts. The predominant pathogens included Enterobacteria (116/192 = 60%), enterococci (26/192 = 13.5%), and staphylococci (24/192 = 12.5%). Novel pathogens, such as Lactobacillus murinus and Stenotrophomonas maltophilia, were identified as primary agents of canine UTIs. Coinfections commonly involved E. coli with either E. faecalis (5/21 = 23.8%) or S. canis (4/21 = 19%). Amoxicillin/clavulanic acid was the most effective antimicrobial (≥ 70%), followed by amikacin and marbofloxacin (≥ 60%). Observed antimicrobial resistance rates included enterobacteria (18%), enterococci (> 40%), staphylococci (18%), streptococci (30%), Pseudomonas aeruginosa (60%), and other organisms (> 30%). Multidrug resistance affected 18% (34/189) of bacterial isolates. This study highlights the polymicrobial nature of canine UTIs and emphasizes concerns about multidrug-resistant bacteria. These findings contribute to improving molecular diagnostics and monitoring antimicrobial resistance in domestic animals, a critical global issue.

Antimicrobial-resistant genes in feces from otters (Lontra longicaudis) within the Peñas Blancas river basin, Costa Rica

Antimicrobial resistance poses a growing threat to human health, yet its implications for wildlife remain a subject of ongoing research. River otters inhabiting the Peñas Blancas River face exposure to various anthropogenic activities in their habitat, potentially leading to the accumulation of antibiotic-resistant genes (ARGs) with unknown consequences for their health. This study aimed to identify specific ARGs in otter feces from this river basin, employing quantitative polymerase chain reaction (qPCR), DNA sequencing of ARGs, and phylogenetic analysis techniques. Over the period from 2019 to 2022, we collected 102 fecal samples from otters through the Peñas Blancas River watershed, spanning its upper and middle basins. We assessed the bacterial presence via the 16S rRNA gene through qPCR analysis and screened for 12 ARGs. Sequences of 16 ARG-positive samples were subsequently analyzed using Maximum-likelihood-base taxonomic placement. In total, 56 samples tested positive for the 16S rRNA gene, with 24 exhibiting at least one ARG. Notably, three samples showcased a "multi-resistance microbiome". qPCR analyses identified seven distinct ARGs: tetB (in 26.8 % of the samples), sulI (21.4 %), sulII (21.4 %), qnrS (10.7 %), tetQ (8.9 %), tetW (7.1 %), and tetA (3.6 %). Phylogenetic analysis confirmed the taxonomic association of all detected ARGs, which were compared with The Comprehensive Antibiotic Resistance Database. Our findings underscore the importance of comprehending the spread of ARGs in wildlife populations, with river otters serving as potential sentinels for ARG dissemination. Moreover, they highlight the potential impact of anthropogenic activities on the health of aquatic ecosystems, emphasizing the need for proactive measures to mitigate antimicrobial resistance in natural environments.

gcPathogen: a comprehensive genomic resource of human pathogens for public health

Here, we present the manually curated Global Catalogue of Pathogens (gcPathogen), an extensive genomic resource designed to facilitate rapid and accurate pathogen analysis, epidemiological exploration and monitoring of antibiotic resistance features and virulence factors. The catalogue seamlessly integrates and analyzes genomic data and associated metadata for human pathogens isolated from infected patients, animal hosts, food and the environment. The pathogen list is supported by evidence from medical or government pathogenic lists and publications. The current version of gcPathogen boasts an impressive collection of 1 164 974 assemblies comprising 986 044 strains from 497 bacterial taxa, 4794 assemblies encompassing 4319 strains from 265 fungal taxa, 89 965 assemblies featuring 13 687 strains from 222 viral taxa, and 646 assemblies including 387 strains from 159 parasitic taxa. Through this database, researchers gain access to a comprehensive 'one-stop shop' that facilitates global, long-term public health surveillance while enabling in-depth analysis of genomes, sequence types, antibiotic resistance genes, virulence factors and mobile genetic elements across different countries, diseases and hosts. To access and explore the data and statistics, an interactive web interface has been developed, which can be accessed at https://nmdc.cn/gcpathogen/. This user-friendly platform allows seamless querying and exploration of the extensive information housed within the gcPathogen database.

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

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.

A review of the emergence of antibiotic resistance in bioaerosols and its monitoring methods

Despite significant public health concerns regarding infectious diseases in air environments, potentially harmful microbiological indicators, such as antibiotic resistance genes (ARGs) in bioaerosols, have not received significant attention. Traditionally, bioaerosol studies have focused on the characterization of microbial communities; however, a more serious problem has recently arisen due to the presence of ARGs in bioaerosols, leading to an increased prevalence of horizontal gene transfer (HGT). This constitutes a process by which bacteria transfer genes to other environmental media and consequently cause infectious disease. Antibiotic resistance in water and soil environments has been extensively investigated in the past few years by applying advanced molecular and biotechnological methods. However, ARGs in bioaerosols have not received much attention. In addition, ARG and HGT profiling in air environments is greatly limited in field studies due to the absence of suitable methodological approaches. Therefore, this study comprehensively describes recent findings from published studies and some of the appropriate molecular and biotechnological methods for monitoring antibiotic resistance in bioaerosols. In addition, this review discusses the main knowledge gaps regarding current methodological issues and future research directions.

Prevalence of Antibiotic Resistance Genes in Pharmaceutical Wastewaters

Pharmaceutical wastewaters are recognized as reservoirs of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB), and also as hotspots for their horizontal gene transfer (HGT) using mobile genetic elements. Our study employed the use of PCR analysis of metagenomic DNA samples obtained from four pharmaceutical wastewaters using known primers to study the prevalence of thirty-six ARGs and four MGEs active against the commonly used antibiotics in Nigeria. The ARGs most frequently detected from the metagenomic DNA samples in each of the antibiotic classes under study include tetracycline [tet(G)], aminoglycoside [aadA, strA and strB], chloramphenicol [catA1], sulphonamides [sulI and sulII], and β-lactams and penicillins [blaOXA]. The ARGs showed a 100% prevalence in their various environmental sources. The pharmaceutical facility PFIV showed the highest concentration of ARGs in this study. The highest concentration for MGEs was shown by pharmaceutical facility PFIII, positive for intl1, intl2, and IFS genes. This study highlights the wide distribution of ARGs to the antibiotics tested in the wastewater, making pharmaceutical wastewater reservoirs of ARGs which could potentially be transferred from commensal microorganisms to human pathogens.

Exploring Antibiotic Resistance Diversity in Leuconostoc spp. by a Genome-Based Approach: Focus on the lsaA Gene

Leuconostoc spp. are environmental microorganisms commonly associated with fermented foods. Absence of antibiotic resistance (AR) in bacteria is a critical issue for global food safety. Herein, we updated the occurrence of AR genes in the Leuconostoc genus through in silico analyses of the genomes of 17 type strains. A total of 131 putative AR traits associated with the main clinically relevant antibiotics were detected. We found, for the first time, the lsaA gene in L. fallax ATCC 700006^T and L. pseudomesenteroides NCDO 768^T. Their amino acid sequences displayed high similarities (59.07% and 52.21%) with LsaA of Enterococcusfaecalis V583, involved in clindamycin (CLI) and quinupristin-dalfopristin (QUD) resistance. This trait has different distribution patterns in Leuconostoc nontype strains-i.e., L. pseudomesenteroides, L. lactis and L. falkenbergense isolates from fermented vegetables, cheeses, and starters. To better explore the role of lsaA, MIC for CLI and QUD were assessed in ATCC 700006^T and NCDO 768^T; both strains were resistant towards CLI, potentially linking lsaA to their resistant phenotype. Contrarily, NCDO 768^T was sensitive towards QUD; however, expression of lsaA increased in presence of this antibiotic, indicating an active involvement of this trait and thus suggesting a revision of the QUD thresholds for this species.

Inside environmental Clostridium perfringens genomes: antibiotic resistance genes, virulence factors and genomic features

Until recently, research has focused on Clostridium perfringens in clinical settings without considering environmental isolates. In this study, environmental genomes were used to investigate possible antibiotic resistance and the presence of virulence traits in C. perfringens strains from raw surface water. In silico assembly of three C. perfringens strains, DNA generated almost complete genomes setting their length ranging from 3.4 to 3.6 Mbp with GC content of 28.18%. An average of 3,175 open reading frames was identified, with the majority associated with carbohydrate and protein metabolisms. The genomes harboured several antibiotic resistance genes for glycopeptides, macrolide-lincosamide-streptogramin B, β-lactam, trimethoprim, tetracycline and aminoglycosides and also the presence of several genes encoding for polypeptides and multidrug resistance efflux pumps and 35 virulence genes. Some of these encode for haemolysins, sialidase, hyaluronidase, collagenase, perfringolysin O and phospholipase C. All three genomes contained sequences indicating phage, antibiotic resistance and pathogenic islands integration sites. A genomic comparison of these three strains confirmed high similarity and shared core genes with clinical C. perfringens strains, highlighting their health security risks. This study provides a genomic insight into the potential pathogenicity of C. perfringens present in the environment and emphasises the importance of monitoring this niche in the future.

Antibiotic Resistance Genes Occurrence in Wastewaters from Selected Pharmaceutical Facilities in Nigeria

The proliferation of antibiotic-resistant bacteria (ARB) and the prevalence of antibiotic resistance genes (ARGs) in wastewaters are well-established factors that contribute to the reduced potency of antibiotics used in healthcare worldwide. The human health risk associated with the proliferation of ARB and ARGs need to be understood in order to design mitigation measures to combat their dissemination. Using the PCR analysis of genomic DNA, the prevalence of 41 ARGs active against the commonly used six classes of antibiotics was evaluated in 60 bacterial isolates obtained from pharmaceutical wastewaters in Nigeria. The ARGs most frequently detected from the bacterial isolates in each of the antibiotic classes under study include catA1 (58.3%); sulI (31.7%); tet(E) (30%); aac(3)-IV (28.3%); ermC (20%); blaTEM, blaCTX-M, blaNDM-1 at 18.3% each; which encode for resistance to chloramphenicol, sulfonamides, tetracycline, aminoglycoside, macrolide-lincosamide-streptogramin and β-lactams and penicillins, respectively. Acinetobacter spp., accession number MH396735 expressed the highest number of ARGs of all the bacterial isolates, having at least one gene that encodes for resistance to all the classes of antibiotics in the study. This study highlights wide distribution of ARB and ARGs to the antibiotics tested in the wastewater, making pharmaceutical wastewater reservoirs of ARGs which could potentially be transferred from commensal microorganisms to human pathogens.

Shigella flexneri: an emerging pathogen

Shigella flexneri is a leading etiologic agent of diarrhea in low socioeconomic countries. Notably, various serotypes in S. flexneri are reported from different regions of the world. The precise approximations of illness and death owing to shigellosis are missing in low socioeconomic countries, although it is widespread in different regions. The inadequate statistics available reveal S. flexneri to be a significant food and waterborne pathogen. All over the world, different antibiotic-resistant strains of S. flexneri serotypes have been emerged especially multidrug-resistant strains. Recently, increased resistance was observed in cephalosporins (3rd generation), azithromycin, and fluoroquinolones. There is a need for a continuous surveillance study on antibiotic resistance that will be helpful in the update of the antibiogram. The shigellosis burden can be reduced by adopting preventive measures like delivery of safe drinking water, suitable sanitation, and development of an effective and inexpensive multivalent vaccine. This review attempts to provide the recent findings of S. flexneri related to epidemiology and the emergence of multidrug resistance.

Comparative genomics of multidrug-resistant Enterococcus spp. isolated from wastewater treatment plants

BACKGROUND

Wastewater treatment plants (WWTPs) are considered hotspots for the environmental dissemination of antimicrobial resistance (AMR) determinants. Vancomycin-Resistant Enterococcus (VRE) are candidates for gauging the degree of AMR bacteria in wastewater. Enterococcus faecalis and Enterococcus faecium are recognized indicators of fecal contamination in water. Comparative genomics of enterococci isolated from conventional activated sludge (CAS) and biological aerated filter (BAF) WWTPs was conducted.

RESULTS

VRE isolates, including E. faecalis (n = 24), E. faecium (n = 11), E. casseliflavus (n = 2) and E. gallinarum (n = 2) were selected for sequencing based on WWTP source, species and AMR phenotype. The pangenomes of E. faecium and E. faecalis were both open. The genomic fraction related to the mobilome was positively correlated with genome size in E. faecium (p < 0.001) and E. faecalis (p < 0.001) and with the number of AMR genes in E. faecium (p = 0.005). Genes conferring vancomycin resistance, including vanA and vanM (E. faecium), vanG (E. faecalis), and vanC (E. casseliflavus/E. gallinarum), were detected in 20 genomes. The most prominent functional AMR genes were efflux pumps and transporters. A minimum of 16, 6, 5 and 3 virulence genes were detected in E. faecium, E. faecalis, E. casseliflavus and E. gallinarum, respectively. Virulence genes were more common in E. faecalis and E. faecium, than E. casseliflavus and E. gallinarum. A number of mobile genetic elements were shared among species. Functional CRISPR/Cas arrays were detected in 13 E. faecalis genomes, with all but one also containing a prophage. The lack of a functional CRISPR/Cas arrays was associated with multi-drug resistance in E. faecium. Phylogenetic analysis demonstrated differential clustering of isolates based on original source but not WWTP. Genes related to phage and CRISPR/Cas arrays could potentially serve as environmental biomarkers.

CONCLUSIONS

There was no discernible difference between enterococcal genomes from the CAS and BAF WWTPs. E. faecalis and E. faecium have smaller genomes and harbor more virulence, AMR, and mobile genetic elements than other Enterococcus spp.

Climatic and regional antibiotic resistance patterns of Staphylococcus aureus in South African dairy herds

South Africa is a large country of approximately 1.22 million km2, made up of nine provinces with three climatic zones. Farming in the country is mostly defined by regional differences. Of the different organisms isolated from milk samples of dairy cows, Staphylococcus aureus poses a challenge to maintain udder health and wholesome dairy products for human consumption. Antibiotic resistant bacteria are therefore a potential health hazard. The objective of this study was to investigate the seasonal and regional relationships of antibiotic resistance of S. aureus, of which little is known. This study was undertaken to evaluate a data set of 3410 S. aureus isolates, taken from milk samples with a somatic cell count of > 400 000 cells/mL from commercial dairy herds. These isolates were tested for antimicrobial susceptibility using the Kirby Bauer method for ampicillin, cloxacillin, penicillin G, clindamycin, oxy-tetracycline, cephalexin, cefuroxime and tylosin. The samples were from 830 dairy herds, out of the estimated 2000 commercial dairy herds in South Africa. All the antibiotics tested, except for cephalosporins, showed a predicted prevalence of resistance of above 50% in most provinces, which is a concern. The lowest prevalence of resistance to the majority of the categories of antibiotics tested was present in KwaZulu-Natal during spring. The cephalosporins had the lowest levels of prevalence of bacterial resistance in Gauteng during winter. Resistance patterns of S. aureus to the eight antibiotics varied in the different seasons and provinces, possibly because of different weather conditions, and the action and spectrum of antibiotics.

Analysis of Resistance to Macrolide-Lincosamide-Streptogramin B Among mecA-Positive Staphylococcus Aureus Isolates

Objectives

Genetic determinants conferring resistance to macrolide, lincosamide, and streptogramin B (MLS_B) via ribosomal modification such as, erm, msrA/B and ereA/B genes are distributed in bacteria. The main goals of this work were to evaluate the dissemination of MLS_B resistance phenotypes and genotypes in methicillin-resistant Staphylococcus aureus (MRSA) isolates collected from clinical samples.

Methods

A total of 106 MRSA isolates were studied. Isolates were recovered from 3 hospitals in Tehran between May 2016 to July 2017. The prevalence of MLS_B-resistant strains were determined by D-test, and then M-PCR was performed to identify genes encoding resistance to macrolides, lincosamides, and streptogramins in the tested isolates.

Results

The frequency of constitutive resistance MLS_B, inducible resistance MLS_B and MS_B resistance were 56.2%, 22.9%, and 16.6%, respectively. Of 11 isolates with the inducible resistance MLS_B phenotype, ermC, ermB, ermA and ereA were positive in 81.8%, 63.6%, 54.5% and 18.2% of these isolates, respectively. In isolates with the constitutive resistance MLS_B phenotype, the prevalence of ermA, ermB, ermC, msrA, msrB, ereA and ereB were 25.9%, 18.5%, 44.4%, 0.0%, 0.0%, 11.1% and 0.0%, respectively.

Conclusion

Clindamycin is commonly administered in severe MRSA infections depending upon the antimicrobial susceptibility findings. This study showed that the D-test should be used as an obligatory method in routine disk diffusion assay to detect inducible clindamycin resistance in MRSA so that effective antibiotic treatment can be provided.

Azithromycin and erythromycin susceptibility and macrolide resistance genes in Prevotella from patients with periodontal disease

OBJECTIVES

To study oral Prevotella spp. isolated from patients with chronic periodontitis, to determine their susceptibility to azithromycin and erythromycin and to screen the presence of macrolide resistance genes therein.

MATERIAL AND METHODS

Isolates with a Prevotella-like morphology were obtained from subgingival samples of 52 patients with chronic periodontitis. Each isolate was identified to the species level by sequencing of the 16S rRNA gene. In 100 Prevotella spp. isolates, azithromycin and erythromycin susceptibility was determined using the E test method, and the screening of erm(A), erm(B), erm(C), erm(F), erm(G), erm(Q) and mef(A) genes was done by PCR.

RESULTS

Prevotella intermedia and Prevotella nigrescens were the most identified species (33% each). Minimum inhibitory concentrations (MICs) ranges for both antibiotics were 0.016/0.032 to >256 μg/ml. MIC₅₀ values for azithromycin and erythromycin were 1.5 and 1 μg/ml, respectively, and MIC₉₀ values were >256 μg/ml for both antibiotics. Nineteen per cent of the isolates carried erm(B), and 51% carried erm(F).

CONCLUSIONS

The MIC values found were high compared to previous studies. erm(F) was greatly prevalent, and we describe for the first time the erm(B) gene in Prevotella spp. The presence of either of the genes seems to be associated with a higher degree of resistance to azithromycin and erythromycin.

Distribution of acquired antibiotic resistance genes among Enterococcus spp. isolated from a hospital in Baotou, China

OBJECTIVE

This study investigated the distribution of acquired antibiotic resistance genes in Enterococcus species isolated from clinical patients in Baotou, China.

RESULT

A total of 73 enterococca lisolates from clinical samples were collected from December 2016 to September 2017. Of the 73 enterococcal isolates, 36 (49.3%), 35 (47.9%), 1 (1.4%), and 1 (1.4%) were identified as E. faecium, E. faecalis, E. gallinarum, and E. raffinosus, respectively. The resistance rates of the enterococci to nitrofurantoin, tetracycline, gentamicin (high-level), ampicillin, ciprofloxacin and erythromycin were 24.7%, 49.3%, 50.7%, 54.8%, 74.0% and 89.0%, respectively. The most prevalent aminoglycoside resistance genes were aac(6')-Ie-aph(2″)-Ia (64.9%) and aph(3')IIIa (64.9%). The most common erythromycin ribosome methylation gene was erm(B) (67.7%), followed by erm(A) (4.6%) and erm(C) (1.5%). The tetracycline resistance gene tetM was found to be present in 100.0% of the tetracycline-resistant strains of enterococci. Thus, E. faecium and E. faecalis were identified as the species of greatest clinical importance associated with hospital-acquired enterococcal infections in Baotou, China. The antimicrobial resistance genes aac(6')-Ie-aph(2″)-Ia, aph(3')IIIa, tetM, and erm(B) were significantly more prevalent among the enterococcal isolates. Therefore, action should be taken to monitor drug resistance and antimicrobial resistance genes to manage multi-drug-resistant enterococcal infections.

Fate of antibiotic resistance genes and antibiotic-resistant bacteria in water resource recovery facilities

Many important diseases are showing resistance to commonly used antibiotics, and the resistance is potentially caused by widespread use of antibiotics for maintaining human health and improving food production. Antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) are associated with this increase, and their fate in water resource recovery facilities is an important, emerging area of research. This literature review summarizes current findings of worldwide research on the fate of ARB and ARGs in various types of treatment plants. Twenty-five published studies were reviewed which contained 215 observations in activated sludge, membrane bioreactors, anaerobic digestion, constructed wetlands, coagulation-filtration, and three types of disinfection. We found 70% decreased observations, 18% increased observations, and 12% unchanged observations of all observations in all treatment processes. Resistance genes to tetracycline were most often observed, but more studies are needed in other antibiotic resistance genes. The causes for increased abundance of ARGs and ARB are not well understood, and further studies are warranted. PRACTITIONER POINTS: Antibiotic resistance is increasing with concern that treatment plants may acclimate bacteria to antibiotics. A literature survey found 215 resistance observations with 70% decreased, 18% increased, 12% unchanged after treatment. The type of treatment process is important with activated sludge showing the greatest reductions.

Antibiotics, Resistome and Resistance Mechanisms: A Bacterial Perspective

History of mankind is regarded as struggle against infectious diseases. Rather than observing the withering away of bacterial diseases, antibiotic resistance has emerged as a serious global health concern. Medium of antibiotic resistance in bacteria varies greatly and comprises of target protection, target substitution, antibiotic detoxification and block of intracellular antibiotic accumulation. Further aggravation to prevailing situation arose on observing bacteria gradually becoming resistant to different classes of antibiotics through acquisition of resistance genes from same and different genera of bacteria. Attributing bacteria with feature of better adaptability, dispersal of antibiotic resistance genes to minimize effects of antibiotics by various means including horizontal gene transfer (conjugation, transformation, and transduction), Mobile genetic elements (plasmids, transposons, insertion sequences, integrons, and integrative-conjugative elements) and bacterial toxin-antitoxin system led to speedy bloom of antibiotic resistance amongst bacteria. Proficiency of bacteria to obtain resistance genes generated an unpleasant situation; a grave, but a lot unacknowledged, feature of resistance gene transfer.

Dissipation of antimicrobial resistance genes in compost originating from cattle manure after direct oral administration or post-excretion fortification of antimicrobials

Dissipation of antimicrobial resistance genes (ARG) during composting of cattle manure generated through fortification versus administration of antimicrobials in feed was compared. Manure was collected from cattle fed diets containing (kg^-1) dry matter (DM): (1) 44 mg chlortetracycline (CTC), (2) a mixture of 44 mg each of chlortetracycline and sulfamethazine (CTCSMZ), (3) 11 mg tylosin (TYL) or (4) Control, no antimicrobials. Manures were composted for 30 d with a single mixing after 16 d to generate the second heating cycle. Quantitative PCR (qPCR) was used to measure 16S rDNA and tetracycline (tet), erythromycin (erm) and sulfamethazine (sul) genes. Temperature peaks ranged from 48 to 68°C across treatments in the first composting cycle, but except for the control, did not exceed 55°C in the second cycle. Copy numbers of 16S rDNA decreased (P < 0.05) during composting, but were not altered by antimcrobials. Except tet(L), all ARG decreased by 0.1-1.6 log₁₀ g DM^-1 in the first cycle, but some genes (tet[B], tet[L], erm[F], erm[X]) increased (P < 0.05) by 1.0-3.1 log₁₀ g DM^-1 in the second. During composting, levels of tet(M) and tet(W) in CTC, erm(A), erm(B) and erm(X) in TYL, and sul(1) in CTCSMZ remained higher (P < 0.05) in fed than fortified treatments. The dissipation of ARG during composting of manure fortified with antimicrobials differs from manure generated by cattle that are administered antimicrobials in feed, and does not always align with the dissipation of antimicrobial residues.

First Description in Greece of mphC-Positive Staphylococci Causing Subclinical Mastitis in Ewes

The aim of the present study was to describe the first mphC-positive staphylococci, including two Staphylococcus lentus (Sle-087lar and Sle-091lar) and one Staphylococcus xylosus (Sxy-228lar), isolated from samples of animal origin, in Greece. Isolates Sle-087lar and Sxy-228lar were resistant to erythromycin, whereas Sle-091lar was resistant to erythromycin and lincomycin. All three isolates were susceptible to the remaining antibiotics. PCR screening showed that isolate Sle-091lar carried also ermB. For Sxy-228lar, whole-genome sequencing (WGS) and de novo assembly obtained an mphC-positive contig of 57.3-kb exhibiting high similarity with the genome of mphC-negative S. xylosus S170. However, mphC of Sxy-228lar was 91% similar to that found in plasmid pJW2311 from S. xylosus JW2311. Additionally, WGS data showed that Sle-087lar and Sle-091lar harbored mphC-carrying sequences being highly similar to the recently announced genome of the mphC-carrying S. lentus isolate 050AP from Tanzania. However, differences were observed in the mphC environment, suggesting the independent acquisition of the gene by each isolate. Sle-091lar also harbored transposon Tn917, which carries ermB resistance gene, integrated into S. lentus chromosome. These findings indicated that acquisition of resistance genes can lead to the emergence of multiresistant staphylococci, causing animal infections with economic burden.

Comparative genomics of Enterococcus spp. isolated from bovine feces

Background

Enterococcus is ubiquitous in nature and is a commensal of both the bovine and human gastrointestinal (GI) tract. It is also associated with clinical infections in humans. Subtherapeutic administration of antibiotics to cattle selects for antibiotic resistant enterococci in the bovine GI tract. Antibiotic resistance genes (ARGs) may be present in enterococci following antibiotic use in cattle. If located on mobile genetic elements (MGEs) their dissemination between Enterococcus species and to pathogenic bacteria may be promoted, reducing the efficacy of antibiotics.

Results

We present a comparative genomic analysis of twenty-one Enterococcus spp. isolated from bovine feces including Enterococcus hirae (n = 10), Enterococcus faecium (n = 3), Enterococcus villorum (n = 2), Enterococcus casseliflavus (n = 2), Enterococcus faecalis (n = 1), Enterococcus durans (n = 1), Enterococcus gallinarum (n = 1) and Enterococcus thailandicus (n = 1). The analysis revealed E. faecium and E. faecalis from bovine feces share features with human clinical isolates, including virulence factors. The Tn917 transposon conferring macrolide-lincosamide-streptogramin B resistance was identified in both E. faecium and E. hirae, suggesting dissemination of ARGs on MGEs may occur in the bovine GI tract. An E. faecium isolate was also identified with two integrative conjugative elements (ICEs) belonging to the Tn916 family of ICE, Tn916 and Tn5801, both conferring tetracycline resistance.

Conclusions

This study confirms the presence of enterococci in the bovine GI tract possessing ARGs on MGEs, but the predominant species in cattle, E. hirae is not commonly associated with infections in humans. Analysis using additional complete genomes of E. faecium from the NCBI database demonstrated differential clustering of commensal and clinical isolates, suggesting that these strains may be specifically adapted to their respective environments.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-017-0962-1) contains supplementary material, which is available to authorized users.

The antibacterial activities of aditoprim and its efficacy in the treatment of swine streptococcosis

Aditoprim (ADP) has potential use as an antimicrobial agent in animals. However, its pharmacodynamic properties have not been systematically studied yet. In this study, the in vitro antibacterial activities of ADP and its main metabolites were assayed, and the in vivo antibacterial efficacy of ADP for the treatment of swine streptococcosis was evaluated. It was shown that Salmonella and Streptococcus from swine, Escherichia coli and Salmonella from chickens, E. coli, Streptococcus, Mannheimia, Pasteurella from calves, Streptococcus and Mannheimia from sheep, and E. coli, Flavobacterium columnare, Acinetobacter baumannii and Yersinia ruckeri from fishes were highly susceptible to ADP. Haemophilus parasuis from swine, Staphylococcus aureus, Aeromonas punctate, Mycobacterium tuberculosis, Streptococcus agalactiae from fishes, and Klebsiella from calves and sheep showed moderate susceptibility to ADP, whereas E. coli, Actinobacillus pleuropneumonia, Pasteurella, S. aureus, Clostridium perfringens from swine, S. aureus, C. perfringens from chickens, and S. aureus from calves were resistant to ADP. The main metabolites of ADP showed equal activity to that of their parent compound, and the prevention and therapeutic dosages of ADP recommended for swine streptococcosis were 10 and 20~40 mg/kg b.w., respectively. This study firstly showed that ADP had strong antibacterial activity and had potential to be used as a single drug in the treatment of bacterial infectious diseases.

Simultaneous determination of aditoprim and its three major metabolites in pigs, broilers and carp tissues, and its application in tissue distribution and depletion studies

Aditoprim (ADP) is a recently developed dihydrofolate reductase inhibitor that has shown promise for therapeutic use in veterinary medicine because of its excellent pharmacokinetic properties. In this study, a sensitive and reliable multi-residue chromatography-ultraviolet (HPLC-UV) method for the quantitative analysis of ADP and its three major metabolites was developed, and the tissue distribution and depletion profiles of ADP and its major metabolites in pigs, broilers and carp were investigated. Edible and additional tissues (heart, lung, stomach, intestine and swim bladder) were collected for analysis at six different withdrawal periods after ADP administration for 7 days. ADP, N-monomethyl-ADP and N-didesmethyl-ADP were detected in almost all tissues in the three species. The liver, kidney and lung showed higher residue concentrations, and the liver showed a longer residue half-life (t1/2) than other tissues. In the liver, ADP was the most abundant component with the longest persistence. The results suggest that the liver was the residual target tissue and ADP was the marker residue, and the conclusive withdrawal time (WDT) of 20 days in pigs, 16 days in broilers and 25 days in carp was estimated using the assessment methodologies approved by the Joint FAO/WHO Expert Committee on Food Additives (JECFA).

Staphylococcus aureus Nasal Carriage among Beefpacking Workers in a Midwestern United States Slaughterhouse

Occupational contact with livestock is an established risk factor for exposure to livestock-associated methicillin-resistant Staphylococcus aureus (MRSA), particularly among industrial swine workers. While S. aureus is known to infect cattle, livestock-associated S. aureus carriage among workers in the beef production chain has received limited attention. Beefpacking workers, who slaughter, butcher and process cattle, have intensified exposure to potentially infectious animal materials and may be at risk of livestock-associated S. aureus exposure. We conducted a cross-sectional study of beefpacking workers (n = 137) at an industrial slaughterhouse in the Midwestern United States to evaluate prevalence and characteristics of S. aureus nasal colonization, specifically the absence of the scn gene to identify putative association with livestock, antibiotic susceptibility, presence of Panton-Valentin leukocidin (PVL) genes lukS-PV and lukF-PV, and spa type. Overall prevalence of S. aureus nasal carriage was 27.0%. No workers carried livestock-associated MRSA. Methicillin-sensitive S. aureus isolates (MSSA) recovered from five workers (3.6%) lacked the scn gene and were considered putative livestock-associated S. aureus (pLA-SA). Among pLA-SA isolates, spa types t338, t748, t1476 and t2379 were identified. To our knowledge, these spa types have not previously been identified as associated with livestock. Prevalence of human-adapted MRSA carriage in workers was 3.6%. MRSA isolates were identified as spa types t002, t008 and t024, and four of five MRSA isolates were PVL-positive. To date, this is the first study to indicate that industrial beefpacking workers in the United States may be exposed to livestock-associated S. aureus, notably MSSA, and to spa types not previously identified in livestock and livestock workers. Occupational exposure to livestock-associated S. aureus in the beef production chain requires further epidemiologic investigation.

Macrolide-lincosamide-streptogramin resistance phenotypes and genotypes of coagulase-positive Staphylococcus aureus and coagulase-negative staphylococcal isolates from bovine mastitis

Background

There are limited data available on macrolide-lincosamide-streptogramin (MLS) resistance of Staphylococcus aureus (S. aureus) and coagulase-negative staphylococci (CoNS) from bovine milk in China. To address this knowledge gap, MLS resistance was determined in 121 S. aureus and 97 CoNS isolates. Minimum inhibitory concentrations (MICs) of MLS antibiotics were determined by an agar dilution method, while differentiation of MLS phenotypes was performed by a double-disc diffusion test. MLS resistance genotypes were determined by PCR for corresponding resistance genes.

Results

Forty (33.1 %) S. aureus and 65 (67.0 %) CoNS were resistant to erythromycin, whereas all 218 isolates were susceptible to quinupristin/dalfopristin. Among 40 erythromycin-resistant (ER-R) S. aureus and 65 ER-R CoNS isolates, 38 S. aureus and 40 CoNS isolates exhibited the inducible MLS (iMLS) resistance phenotype and 2 S. aureus and 20 CoNS isolates expressed the constitutive MLS resistance (cMLS) phenotype. At the same time, 5 CoNS isolates exhibited resistance to erythromycin but susceptibility to clindamycin (the MS phenotype). An inactivating enzyme gene lnu(A), methylase genes erm(C) and erm(B), efflux genes msr(A)/msr(B), a phosphotransferase gene mph(C), an esterase gene ere(A) and the streptogramin resistance determinant vga(A) were detected individually or in combinations. Among them, genes lnu(A), erm(C) and mph(C) predominated. The ereA gene was detected for the first time in staphylococci of bovine milk origin. Resistance genes also existed in erythromycin-susceptible isolates.

Conclusions

Our study demonstrated a high level of resistance to MLS antibiotics in staphylococci from bovine mastitic milk, especially with a high rate of the iMLS phenotype in S. aureus isolates. These data suggest that MLS antibiotics should be used judiciously to treat or prevent bovine mastitis caused by staphylococci.

Diversity of Plasmids and Antimicrobial Resistance Genes in Multidrug-Resistant Escherichia coli Isolated from Healthy Companion Animals

The presence and transfer of antimicrobial resistance genes from commensal bacteria in companion animals to more pathogenic bacteria may contribute to dissemination of antimicrobial resistance. The purpose of this study was to determine antimicrobial resistance gene content and the presence of genetic elements in antimicrobial resistant Escherichia coli from healthy companion animals. In our previous study, from May to August, 2007, healthy companion animals (155 dogs and 121 cats) from three veterinary clinics in the Athens, GA, USA area were sampled and multidrug-resistant E. coli (n = 36; MDR, resistance to ≥ 2 antimicrobial classes) were obtained. Of the 25 different plasmid replicon types tested by PCR, at least one plasmid replicon type was detected in 94% (34/36) of the MDR E. coli; four isolates contained as many as five different plasmid replicons. Nine replicon types (FIA, FIB, FII, I2, A/C, U, P, I1 and HI2) were identified with FIB, FII, I2 as the most common pattern. The presence of class I integrons (intI) was detected in 61% (22/36) of the isolates with eight isolates containing aminoglycoside- and/or trimethoprim-resistance genes in the variable cassette region of intI. Microarray analysis of a subset of the MDR E. coli (n = 9) identified the presence of genes conferring resistance to aminoglycosides (aac, aad, aph and strA/B), β-lactams (ampC, cmy, tem and vim), chloramphenicol (cat), sulfonamides (sulI and sulII), tetracycline [tet(A), tet(B), tet(C), tet(D) and regulator, tetR] and trimethoprim (dfrA). Antimicrobial resistance to eight antimicrobials (ampicillin, cefoxitin, ceftiofur, amoxicillin/clavulanic acid, streptomycin, gentamicin, sulfisoxazole and trimethoprim-sulfamethoxazole) and five plasmid replicons (FIA, FIB, FII, I1 and I2) were transferred via conjugation. The presence of antimicrobial resistance genes, intI and transferable plasmid replicons indicate that E. coli from companion animals may play an important role in the dissemination of antimicrobial resistance, particularly to human hosts during contact.

The role of class I integrons in the dissemination of sulfonamide resistance genes in the Pearl River and Pearl River Estuary, South China

Antibiotic resistance genes (ARGs), as a newly emerging contaminant, are unique because they are disseminated through horizontal gene transfer in the environment. In the present study, a class 1 integron gene (int1) and various ARGs (sul1, sul2, sul3, qnrS, and ermB) were measured in water and sediment samples from the Pearl River (PR) to the Pearl River Estuary (PRE), where there is a distinct gradient in anthropogenic impact. The int1, sul1, and sul2 genes were detected in all samples, and their concentrations exhibited a clear trend of decline consistent with anthropogenic impact. Both the int1 and sul genes had dynamically migrated between water and sediments. The relative abundance of the int1 gene normalized to the 16S rRNA gene correlated significantly with the total concentrations of antibiotics in water and sediments. Good correlations were also observed between the abundance of int1 and each type of sul gene in the samples. However, the sul1 gene showed a much stronger relationship with int1 in different seasons, probably due to the presence of sul1 in the conserved region of class 1 integron. Our results strongly support that integrons play an important role in the dissemination of ARGs in human-impacted aquatic environments.

Potential for reduction of streptogramin A resistance revealed by structural analysis of acetyltransferase VatA

Combinations of group A and B streptogramins (i.e., dalfopristin and quinupristin) are "last-resort" antibiotics for the treatment of infections caused by Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecium. Resistance to streptogramins has arisen via multiple mechanisms, including the deactivation of the group A component by the large family of virginiamycin O-acetyltransferase (Vat) enzymes. Despite the structural elucidation performed for the VatD acetyltransferase, which provided a general molecular framework for activity, a detailed characterization of the essential catalytic and antibiotic substrate-binding determinants in Vat enzymes is still lacking. We have determined the crystal structure of S. aureus VatA in apo, virginiamycin M1- and acetyl-coenzyme A (CoA)-bound forms and provide an extensive mutagenesis and functional analysis of the structural determinants required for catalysis and streptogramin A recognition. Based on an updated genomic survey across the Vat enzyme family, we identified key conserved residues critical for VatA activity that are not part of the O-acetylation catalytic apparatus. Exploiting such constraints of the Vat active site may lead to the development of streptogramin A compounds that evade inactivation by Vat enzymes while retaining binding to their ribosomal target.

The novel macrolide-Lincosamide-Streptogramin B resistance gene erm(44) is associated with a prophage in Staphylococcus xylosus

A novel erythromycin ribosome methylase gene, erm(44), that confers resistance to macrolide, lincosamide, and streptogramin B (MLSB) antibiotics was identified by whole-genome sequencing of the chromosome of Staphylococcus xylosus isolated from bovine mastitis milk. The erm(44) gene is preceded by a regulatory sequence that encodes two leader peptides responsible for the inducible expression of the methylase gene, as demonstrated by cloning in Staphylococcus aureus. The erm(44) gene is located on a 53-kb putative prophage designated ΦJW4341-pro. The 56 predicted open reading frames of ΦJW4341-pro are structurally organized into the five functional modules found in members of the family Siphoviridae. ΦJW4341-pro is site-specifically integrated into the S. xylosus chromosome, where it is flanked by two perfect 19-bp direct repeats, and exhibits the ability to circularize. The presence of erm(44) in three additional S. xylosus strains suggests that this putative prophage has the potential to disseminate MLSB resistance.

Intracellular and extracellular antimicrobial resistance genes in the sludge of livestock waste management structures

The sludge compartment in livestock waste management structures is a potential hotbed for the emergence and proliferation of antimicrobial resistance among bacteria. Little is known about the distribution of antimicrobial resistance genes (ARGs) between the intracellular and extracellular DNA pools in the sludge. The overall objective of this study was to assess the significance of extracellular ARGs to the total ARGs in the sludge of livestock waste management structures. In this study, sludge samples were collected from four cattle manure storage ponds and three swine waste treatment lagoons and analyzed for genetic indicators of resistance. Intracellular DNA (iDNA) and extracellular DNA (eDNA) in the sludge were separately extracted using an optimized protocol. ARGs [sul(I), sul(II), tet(O), tet(Q), and tet(X)] in both the iDNA and eDNA extracts were quantified using quantitative polymerase chain reaction (qPCR), and antimicrobials, including sulfonamides and tetracyclines, were measured using liquid chromatography tandem mass spectrometry. Results showed that eDNA constituted less than 1.5% of the total DNA in sludge. All ARGs tested were detected in nearly all eDNA and iDNA samples. Furthermore, every gram of dry sludge contained from 1.7 × 10(3) to 4.2 × 10(8) copies of extracellular ARG and from 3.2 × 10(7) to 3.2 × 10(10) copies of intracellular ARG. Chlortetracycline concentrations ranged between 187 and 2674 μg/g of sludge wet weight (ww), while sulfonamide concentrations were lower than 6.3 μg/g of sludge ww. The detection of ARGs in eDNA extracts suggests that transformation is a potential mechanism in ARG proliferation in the sludge of livestock waste management structures.

Genetic mechanisms of antimicrobial resistance identified in Salmonella enterica, Escherichia coli, and Enteroccocus spp. isolated from U.S. food animals

The prevalence of antimicrobial resistance (AR) in bacteria isolated from U.S. food animals has increased over the last several decades as have concerns of AR foodborne zoonotic human infections. Resistance mechanisms identified in U.S. animal isolates of Salmonella enterica included resistance to aminoglycosides (e.g., alleles of aacC, aadA, aadB, ant, aphA, and StrAB), β-lactams (e.g., bla_{CMY−2, TEM−1, PSE−1}), chloramphenicol (e.g., floR, cmlA, cat1, cat2), folate pathway inhibitors (e.g., alleles of sul and dfr), and tetracycline [e.g., alleles of tet(A), (B), (C), (D), (G), and tetR]. In the U.S., multi-drug resistance (MDR) mechanisms in Salmonella animal isolates were associated with integrons, or mobile genetic elements (MGEs) such as IncA/C plasmids which can be transferred among bacteria. It is thought that AR Salmonella originates in food animals and is transmitted through food to humans. However, some AR Salmonella isolated from humans in the U.S. have different AR elements than those isolated from food animals, suggesting a different etiology for some AR human infections. The AR mechanisms identified in isolates from outside the U.S. are also predominantly different. For example the extended spectrum β-lactamases (ESBLs) are found in human and animal isolates globally; however, in the U.S., ESBLs thus far have only been found in human and not food animal isolates. Commensal bacteria in animals including Escherichia coli and Enterococcus spp. may be reservoirs for AR mechanisms. Many of the AR genes and MGEs found in E. coli isolated from U.S. animals are similar to those found in Salmonella. Enterococcus spp. isolated from animals frequently carry MGEs with AR genes, including resistances to aminoglycosides (e.g., alleles of aac, ant, and aph), macrolides [e.g., erm(A), erm(B), and msrC], and tetracyclines [e.g., tet(K), (L), (M), (O), (S)]. Continuing investigations are required to help understand and mitigate the impact of AR bacteria on human and animal health.

Acquired antibiotic resistance genes: an overview

In this review an overview is given on antibiotic resistance (AR) mechanisms with special attentions to the AR genes described so far preceded by a short introduction on the discovery and mode of action of the different classes of antibiotics. As this review is only dealing with acquired resistance, attention is also paid to mobile genetic elements such as plasmids, transposons, and integrons, which are associated with AR genes, and involved in the dispersal of antimicrobial determinants between different bacteria.

Effect of various sludge digestion conditions on sulfonamide, macrolide, and tetracycline resistance genes and class I integrons

Wastewater treatment processes are of growing interest as a potential means to limit the dissemination of antibiotic resistance. This study examines the response of nine representative antibiotic resistance genes (ARGs) encoding resistance to sulfonamide (sulI, sulII), erythromycin (erm(B), erm(F)), and tetracycline (tet(O), tet(W), tet(C), tet(G), tet(X)) to various laboratory-scale sludge digestion processes. The class I integron gene (intI1) was also monitored as an indicator of horizontal gene transfer potential and multiple antibiotic resistance. Mesophilic anaerobic digestion at both 10 and 20 day solids retention times (SRTs) significantly reduced sulI, suII, tet(C), tet(G), and tet(X) with longer SRT exhibiting a greater extent of removal; however, tet(W), erm(B) and erm(F) genes increased relative to the feed. Thermophilic anaerobic digesters operating at 47 °C, 52 °C, and 59 °C performed similarly to each other and provided more effective reduction of erm(B), erm(F), tet(O), and tet(W) compared to mesophilic digestion. However, thermophilic digestion resulted in similar or poorer removal of all other ARGs and intI1. Thermal hydrolysis pretreatment drastically reduced all ARGs, but they generally rebounded during subsequent anaerobic and aerobic digestion treatments. To gain insight into potential mechanisms driving ARG behavior in the digesters, the dominant bacterial communities were compared by denaturing gradient gel electrophoresis. The overall results suggest that bacterial community composition of the sludge digestion process, as controlled by the physical operating characteristics, drives the distribution of ARGs present in the produced biosolids, more so than the influent ARG composition.

Insects in confined swine operations carry a large antibiotic resistant and potentially virulent enterococcal community

BACKGROUND

Extensive use of antibiotics as growth promoters in the livestock industry constitutes strong selection pressure for evolution and selection of antibiotic resistant bacterial strains. Unfortunately, the microbial ecology and spread of these bacteria in the agricultural, urban, and suburban environments are poorly understood. Insects such as house flies (Musca domestica) and German cockroaches (Blattella germanica) can move freely between animal waste and food and may play a significant role in the dissemination of antibiotic resistant bacteria within and between animal production farms and from farms to residential settings.

RESULTS

Enterococci from the digestive tract of house flies (n = 162), and feces of German cockroaches (n = 83) and pigs (n = 119), collected from two commercial swine farms were isolated, quantified, identified, and screened for antibiotic resistance and virulence. The majority of samples (93.7%) were positive for enterococci with concentrations 4.2 ± 0.7 × 10⁴ CFU/house fly, 5.5 ± 1.1 × 10⁶ CFU/g of cockroach feces, and 3.2 ± 0.8 × 10⁵ CFU/g of pig feces. Among all the identified isolates (n = 639) Enterococcus faecalis was the most common (55.5%), followed by E. hirae (24.9%), E. faecium (12.8%), and E. casseliflavus (6.7%). E. faecalis was most prevalent in house flies and cockroaches, and E. hirae was most common in pig feces. Our data showed that multi-drug (mainly tetracycline and erythromycin) resistant enterococci were common from all three sources and frequently carried antibiotic resistance genes including tet(M) and erm(B) and Tn916/1545 transposon family. E. faecalis frequently harbored virulence factors gelE, esp, and asa1. PFGE analysis of selected E. faecalis and E. faecium isolates demonstrated that cockroaches and house flies shared some of the same enterococcal clones that were detected in the swine manure indicating that insects acquired enterococci from swine manure.

CONCLUSIONS

This study shows that house flies and German cockroaches in the confined swine production environment likely serve as vectors and/or reservoirs of antibiotic resistant and potentially virulent enterococci and consequently may play an important role in animal and public health.

Sewage sludge and liquid pig manure as possible sources of antibiotic resistant bacteria

Within the last decades, the environmental spread of antibiotic resistant bacteria has become a topic of concern. In this study, liquid pig manure (n=305) and sewage sludge (n=111) - used as agricultural fertilizers between 2002 and 2005 - were investigated for the presence of Escherichia coli, Enterococcus faecalis and Enterococcus faecium. Bacteria were tested for their resistance against 40 chemotherapeutics including several "reserve drugs". E. coli (n=613) from pig manure were at a significantly higher degree resistant to streptomycin, doxycycline, spectinomycin, cotrimoxazole, and chloramphenicol than E. coli (n=116) from sewage sludge. Enterococci (Ent. faecalis, n=387, and Ent. faecium, n=183) from pig manure were significantly more often resistant to high levels of doxycycline, rifampicin, erythromycin, and streptomycin than Ent. faecalis (n=44) and Ent. faecium (n=125) from sewage sludge. Significant differences in enterococcal resistance were also seen for tylosin, chloramphenicol, gentamicin high level, fosfomycin, clindamicin, enrofloxacin, moxifloxacin, nitrofurantoin, and quinupristin/dalfopristin. By contrast, aminopenicillins were more effective in enterococci from pig manure, and mean MIC-values of piperacillin+tazobactam and third generation cefalosporines were significantly lower in E. coli from pig manure than in E. coli from sewage sludge. 13.4% (E. coli) to 25.3% (Ent. faecium) of pig manure isolates were high-level multiresistant to substances from more than three different classes of antimicrobial agents. In sewage sludge, high-level-multiresistance reached from 0% (Ent. faecalis) to 16% (Ent. faecium). High rates of (multi-) resistant bacteria in pig manure emphasize the need for a prudent - cautious - use of antibiotics in farm animals.

Molecular ecology of macrolide-lincosamide-streptogramin B methylases in waste lagoons and subsurface waters associated with swine production

RNA methylase genes are common antibiotic resistance determinants for multiple drugs of the macrolide, lincosamide, and streptogramin B (MLS(B)) families. We used molecular methods to investigate the diversity, distribution, and abundance of MLS(B) methylases in waste lagoons and groundwater wells at two swine farms with a history of tylosin (a macrolide antibiotic structurally related to erythromycin) and tetracycline usage. Phylogenetic analysis guided primer design for quantification of MLS(B) resistance genes found in tylosin-producing Streptomyces (tlr(B), tlr(D)) and commensal/pathogenic bacteria (erm(A), erm(B), erm(C), erm(F), erm(G), erm(Q)). The near absence of tlr genes at these sites suggested a lack of native antibiotic-producing organisms. The gene combination erm(ABCF) was found in all lagoon samples analyzed. These four genes were also detected with high frequency in wells previously found to be contaminated by lagoon leakage. A weak correlation was found between the distribution of erm genes and previously reported patterns of tetracycline resistance determinants, suggesting that dissemination of these genes into the environment is not necessarily linked. Considerations of gene origins in history (i.e., phylogeny) and gene distributions in the landscape provide a useful "molecular ecology" framework for studying environmental spread of antibiotic resistance.

Class 1 integronase gene and tetracycline resistance genes tetA and tetC in different water environments of Jiangsu Province, China

Class 1 integronase gene (intI1) and tetracycline resistance genes (tetA and tetC) from various environmental sites in Jiangsu Province (China) were detected using qualitative PCR (polymerase chain reaction) and quantified with SYBR Green-based qRT-PCR (quantitative real-time PCR) in this study. Qualitative PCR assays demonstrated that intI1, tetA and tetC occurred in the water environments of Taihu Lake, the Nanjing section of the Yangtze River, a sewage treatment plant (STP) in Nanjing City, and two drinking water treating bioreactors. qRT-PCR results showed that abundance of intI1 in lake water and sediments was lower than the tet genes, for a given sample site and date (P < 0.05). On a volumetric basis, lake sediments contained higher concentrations of the three genes by four to five orders of magnitude than water samples, and lake water and sediments sampled in April contained fewer copies of all the genes than the samples collected in June and August (P < 0.05). The levels of intI1, tetA and tetC in the Yangtze River water increased significantly after the river flowed through Nanjing City (P < 0.05). 94.1% integron, 97.2% tetA and 98.3% tetC were removed by the activated sludge process in the STP, and more than 80% of each gene was removed in both of the two biofilters in terms of relative concentration based on sample volume. However, on the basis of DNA mass, lower removals were obtained for both the activated sludge and biofiltration processes.

Antibiotic resistance genes in water environment

The use of antibiotics may accelerate the development of antibiotic resistance genes (ARGs) and bacteria which shade health risks to humans and animals. The emerging of ARGs in the water environment is becoming an increasing worldwide concern. Hundreds of various ARGs encoding resistance to a broad range of antibiotics have been found in microorganisms distributed not only in hospital wastewaters and animal production wastewaters, but also in sewage, wastewater treatment plants, surface water, groundwater, and even in drinking water. This review summarizes recently published information on the types, distributions, and horizontal transfer of ARGs in various aquatic environments, as well as the molecular methods used to detect environmental ARGs, including specific and multiplex PCR (polymerase chain reaction), real-time PCR, DNA sequencing, and hybridization based techniques.

The weird and wonderful world of bacterial ribosome regulation

In every organism, translation of the genetic information into functional proteins is performed on the ribosome. In Escherichia coli up to 40% of the cell's total energy turnover is channelled toward the ribosome and protein synthesis. Thus, elaborate networks of translation regulation pathways have evolved to modulate gene expression in response to growth rate and external factors, ranging from nutrient deprivation, to chemical (pH, ionic strength) and physical (temperature) fluctuations. Since the fundamental players involved in regulation of the different phases of translation have already been extensively reviewed elsewhere, this review focuses on lesser known and characterized factors that regulate the ribosome, ranging from processing, modification and assembly factors, unusual initiation and elongation factors, to a variety of stress response proteins.

Antibiotic susceptibility of Bifidobacterium thermophilum and Bifidobacterium pseudolongum isolates from animal sources

The widespread use of antimicrobial substances has led to resistant populations of microorganisms in several ecosystems. In animal husbandry, the application of antibiotics has contributed to resistance development in pathogenic and commensal bacteria. These strains or their resistance genes can be spread along several ecological routes, including the food chain. Antibiotic resistance is important in terms of the safety of industrial strains, such as probiotics for food and feed. Bifidobacterium thermophilum and Bifidobacterium pseudolongum are known to comprise the major part of the bifidobacterial microbiota in the gut and feces of cattle and pigs. In this study, the antimicrobial susceptibility in bifidobacterial isolates of these species was investigated. Isolates from the beef and pork production chain were identified and typed to strain level, and the antimicrobial susceptibility level was tested to a set of antibiotics. Isolates with low susceptibility levels were screened by PCR for already described resistance genes. Strains atypically resistant to clindamycin, erythromycin, and tetracycline were determined. The resistance genes tet(O), tet(W), and erm(X) were detected in the bifidobacterial species that were examined.

Ecology of antibiotic resistance genes: characterization of enterococci from houseflies collected in food settings

In this project, enterococci from the digestive tracts of 260 houseflies (Musca domestica L.) collected from five restaurants were characterized. Houseflies frequently (97% of the flies were positive) carried enterococci (mean, 3.1 x 10(3) CFU/fly). Using multiplex PCR, 205 of 355 randomly selected enterococcal isolates were identified and characterized. The majority of these isolates were Enterococcus faecalis (88.2%); in addition, 6.8% were E. faecium, and 4.9% were E. casseliflavus. E. faecalis isolates were phenotypically resistant to tetracycline (66.3%), erythromycin (23.8%), streptomycin (11.6%), ciprofloxacin (9.9%), and kanamycin (8.3%). Tetracycline resistance in E. faecalis was encoded by tet(M) (65.8%), tet(O) (1.7%), and tet(W) (0.8%). The majority (78.3%) of the erythromycin-resistant E. faecalis isolates carried erm(B). The conjugative transposon Tn916 and members of the Tn916/Tn1545 family were detected in 30.2% and 34.6% of the identified isolates, respectively. E. faecalis carried virulence genes, including a gelatinase gene (gelE; 70.7%), an aggregation substance gene (asa1; 33.2%), an enterococcus surface protein gene (esp; 8.8%), and a cytolysin gene (cylA; 8.8%). Phenotypic assays showed that 91.4% of the isolates with the gelE gene were gelatinolytic and that 46.7% of the isolates with the asa1 gene aggregated. All isolates with the cylA gene were hemolytic on human blood. This study showed that houseflies in food-handling and -serving facilities carry antibiotic-resistant and potentially virulent enterococci that have the capacity for horizontal transfer of antibiotic resistance genes to other bacteria.

Antimicrobial resistance of coagulase-negative staphylococci from bovine subclinical mastitis with particular reference to macrolide–lincosamide resistance phenotypes and genotypes

OBJECTIVES

The aim of this study was to analyse coagulase-negative staphylococci (CoNS) for their resistance to antimicrobial agents approved for the control of pathogens involved in bovine mastitis, with particular reference to macrolide and/or lincosamide (ML) resistance and the resistance genes involved.

METHODS

A total of 298 CoNS collected between 2003 and 2005 in Germany from cases of subclinical mastitis in dairy cows were identified to the species level and investigated for their MICs by broth microdilution. ML-resistant isolates were subjected to plasmid profiling and electrotransformation experiments. The ML resistance genes were detected using PCR and hybridization. Selected PCR products were cloned and sequenced.

RESULTS

The CoNS isolates used in this study showed a low level of resistance to all antimicrobial agents tested (0-7.4%) except ampicillin (18.1%). In the erythromycin-resistant and/or pirlimycin-resistant isolates, the ML resistance genes erm(B), erm(C), msr(A), mph(C) and lnu(A) were present, either alone or in different combinations. Isolates carrying erm methylase genes or the exporter gene msr(A) showed higher MICs than those harbouring only the genes mph(C) or lnu(A) coding for inactivating enzymes. Most of the ML resistance genes were found on plasmids.

CONCLUSIONS

This is the first report of pirlimycin MICs for CoNS collected from cases of bovine subclinical mastitis in Germany. After 3-5 years of veterinary therapeutic use, pirlimycin resistance was rarely detected among CoNS. The finding that five different resistance genes--present in various combinations--were responsible for ML resistance underlines the heterogeneous character of this resistance trait.

DNA microarray detection of antimicrobial resistance genes in diverse bacteria

High throughput genotyping is essential for studying the spread of multiple antimicrobial resistance. A test oligonucleotide microarray designed to detect 94 antimicrobial resistance genes was constructed and successfully used to identify antimicrobial resistance genes in control strains. The microarray was then used to assay 51 distantly related bacteria, including Gram-negative and Gram-positive isolates, resulting in the identification of 61 different antimicrobial resistance genes in these bacteria. These results were consistent with their known gene content and resistance phenotypes. Microarray results were confirmed by polymerase chain reaction and Southern blot analysis. These results demonstrate that this approach could be used to construct a microarray to detect all sequenced antimicrobial resistance genes in nearly all bacteria.

Distribution of the ermG gene among bacterial isolates from porcine intestinal contents

The ermG gene was first found in the soil bacterium Bacillus sphaericus. More recently, it was found in several human intestinal Bacteroides species. We report here the first finding of ermG genes in gram-positive bacteria isolated from porcine feces and from under-barn manure pits used to store porcine wastes. The porcine ermG sequences were identical to the sequence of the B. sphaericus ermG gene except that six of the seven ermG-containing strains contained an insertion sequence element insertion in the C-terminal end of the gene. The porcine ermG genes were found in three different gram-positive genera, an indication that it is possible that the gene is being spread by horizontal gene transfer. A segment of a Bacteroides conjugative transposon that carries an ermG gene cross-hybridized with DNA from six of the seven porcine isolates, but the restriction patterns in the porcine strains were different from that of the Bacteroides conjugative transposon.

dfrA20, A novel trimethoprim resistance gene from Pasteurella multocida

A novel trimethoprim resistance gene, designated dfrA20, was detected on the 11-kb plasmid pCCK154 from Pasteurella multocida. The dfrA20 gene codes for a dihydrofolate reductase of 169 amino acids. Sequence comparisons revealed that the DfrA20 protein differed distinctly from all dihydrofolate reductases known so far.

The use of ribotyping and antibiotic resistance patterns for identification of host sources of Escherichia coli strains

AIMS

To compare antibiotic resistance and ribotyping patterns ability to identify triplicate isolates sent from a group of 40 Escherichia coli taken from seven host sources.

METHODS AND RESULTS

Of the 120 isolates, 22 isolates were resistant to ampicillin, streptomycin, tetracycline and trimethoprim and 98 isolates were susceptible. Antibiotic patterns identified 33 of the triplicates and three of the six groups had isolates from multiple hosts. Ribotyping divided the isolates into 27 ribotype groups with all triplicates grouped into the same ribotype group with one host per group.

CONCLUSIONS

Antibiotic susceptibility pattern placed 98 of the isolates in a single group with 50% of the antibiotic susceptibility pattern groups containing multiple host species. Ribotyping groups were host specific with each host having one to seven ribotype groups.

SIGNIFICANCE AND IMPACT OF THE STUDY

Antibiotic susceptibility pattern groups have been used for environmental source identification and faecal pollution tracking, however these groups do not always distinguish between host species. Stability of the markers is a potential concern and this system can only be used if antibiotic resistance levels are high in the isolates studied. All isolates have a ribotype group which was stable and like other molecular methods has advantages over antibiotic susceptibility pattern groups which uses a phenotypic method.