Resistance to macrolide, lincosamide, streptogramin, ketolide, and oxazolidinone antibiotics

Recent development and fighting strategies for lincosamide antibiotic resistance

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

Decoding antimicrobial resistance: unraveling molecular mechanisms and targeted strategies

Antimicrobial resistance poses a significant global health threat, necessitating innovative approaches for combatting it. This review explores various mechanisms of antimicrobial resistance observed in various strains of bacteria. We examine various strategies, including antimicrobial peptides (AMPs), novel antimicrobial materials, drug delivery systems, vaccines, antibody therapies, and non-traditional antibiotic treatments. Through a comprehensive literature review, the efficacy and challenges of these strategies are evaluated. Findings reveal the potential of AMPs in combating resistance due to their unique mechanisms and lower propensity for resistance development. Additionally, novel drug delivery systems, such as nanoparticles, show promise in enhancing antibiotic efficacy and overcoming resistance mechanisms. Vaccines and antibody therapies offer preventive measures, although challenges exist in their development. Non-traditional antibiotic treatments, including CRISPR-Cas systems, present alternative approaches to combat resistance. Overall, this review underscores the importance of multifaceted strategies and coordinated global efforts to address antimicrobial resistance effectively.

Strategies to Overcome Antimicrobial Resistance in Nosocomial Infections, A Review and Update

Nosocomial infections, also known as healthcare-associated infections, are a significant global concern due to their strong association with high mortality and morbidity in both developed and developing countries. These infections are caused by a variety of pathogens, particularly the ESKAPE group of bacteria, which includes the six pathogens Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. These bacteria have demonstrated noteworthy resistance to different antibiotics. Antimicrobial resistance mechanisms can manifest in various forms, including restricting drug uptake, modifying drug targets, inactivating drugs, active drug efflux, and biofilm formation. Accordingly, various strategies have been developed to combat antibiotic-resistant bacteria. These strategies encompass the development of new antibiotics, the utilization of bacteriophages that specifically target these bacteria, antimicrobial combination therapy and the use of peptides or enzymes that target the genomes or essential proteins of resistant bacteria. Among promising approaches to overcome antibiotic resistance, the CRISPR/Cas system stands out and offers many advantages. This system enables precise and efficient editing of genetic material at specific locations in the genome. Functioning as a bacterial "adaptive immune system," the CRISPR/Cas system recognizes, degrades, and remembers foreign DNA sequences through the use of spacer DNA segments that are transcribed into CRISPR RNAs (crRNA). This paper has focused on nosocomial infections, specifically the pathogens involved in hospital infections, the mechanisms underlying bacterial resistance, and the strategies currently employed to address this issue. Special emphasis has been placed on the application of CRISPR/Cas technology for overcoming antimicrobial resistance.

Emergence and spread of antibiotic-resistant foodborne pathogens from farm to table

Antibiotics have been overused and misused for preventive and therapeutic purposes. Specifically, antibiotics are frequently used as growth promoters for improving productivity and performance of food-producing animals such as pigs, cattle, and poultry. The increasing use of antibiotics has been of great concern worldwide due to the emergence of antibiotic resistant bacteria. Food-producing animals are considered reservoirs for antibiotic resistance genes (ARGs) and residual antibiotics that transfer from the farm through the table. The accumulation of residual antibiotics can lead to additional antibiotic resistance in bacteria. Therefore, this review evaluates the risk of carriage and spread of antibiotic resistance through food chain and the potential impact of antibiotic use in food-producing animals on food safety. This review also includes in-depth discussion of promising antibiotic alternatives such as vaccines, immune modulators, phytochemicals, antimicrobial peptides, probiotics, and bacteriophages.

Antibiotic Resistance and Mechanisms of Pathogenic Bacteria in Tubo-Ovarian Abscess

A tubo-ovarian abscess (TOA) is a common type of inflammatory lump in clinical practice. TOA is an important, life-threatening disease, and it has become more common in recent years, posing a major health risk to women. Broad-spectrum antimicrobial agents are necessary to cover the most likely pathogens because the pathogens that cause TOA are polymicrobial. However, the response rate of antibiotic treatment is about 70%, whereas one-third of patients have poor clinical consequences and they require drainage or surgery. Rising antimicrobial resistance serves as a significant reason for the unsatisfactory medical outcomes. It is important to study the antibiotic resistance mechanism of TOA pathogens in solving the problems of multi-drug resistant strains. This paper focuses on the most common pathogenic bacteria isolated from TOA specimens and discusses the emerging trends and epidemiology of resistant Escherichia coli, Bacteroides fragilis, and gram-positive anaerobic cocci. Besides that, new methods that aim to solve the antibiotic resistance of related pathogens are discussed, such as CRISPR, nanoparticles, bacteriophages, antimicrobial peptides, and pathogen-specific monoclonal antibodies. Through this review, we hope to reveal the current situation of antibiotic resistance of common TOA pathogens, relevant mechanisms, and possible antibacterial strategies, providing references for the clinical treatment of drug-resistant pathogens.

Migration of antibiotic resistance genes and evolution of flora structure in the Xenopus tropicalis intestinal tract with combined exposure to roxithromycin and oxytetracycline

The intestinal flora is one of the most important environments for antibiotic resistance development, owing to its diverse mix of bacteria. An excellent medicine model organism, Xenopus tropicalis, was selected to investigate the spread of antibiotic resistance genes (ARGs) in the intestinal bacterial community with single or combined exposure to roxithromycin (ROX) and oxytetracycline (OTC). Seventeen resistance genes (tetA, tetB, tetE, tetM, tetO, tetS, tetX, ermF, msrA, mefA, ereA, ereB, mphA, mphB, intI1, intI2, intI3) were detected in the intestines of Xenopus tropicalis living in three testing tanks (ROX tanks, OTC tanks, ROX + OTC tanks) and a blank tank for 20 days. The results showed that the relative abundance of total ARGs increased obviously in the tank with single stress but decreased in the tank with combined stress, and the genes encoding the macrolide antibiotic efflux pump (msrA), phosphatase (mphB) and integron (intI2, intI3) were the most sensitive. With the aid of AFM scanning, DNA was found to be scattered short chain in the blank, became extended or curled and then compacted with the stress from a single antibiotic, and was compacted and then fragmented with combined stress, which might be the reason for the variation of the abundance of ARGs with stress. The ratio of Firmicutes/Bacteroides related to diseases was increased by ROX and OTC. The very significant correlation between intI2 and intI3 with tetS (p ≤ 0.001) hinted at a high risk of ARG transmission in the intestines. Collectively, our results suggested that the relative abundance of intestinal ARGs could be changed depending on the intestinal microbiome and DNA structures upon exposure to antibiotics at environmental concentrations.

Metagenomic Insights Into the Changes of Antibiotic Resistance and Pathogenicity Factor Pools Upon Thermophilic Composting of Human Excreta

In times of climate change, practicing a form of sustainable, climate-resilient and productive agriculture is of primordial importance. Compost could be one form of sustainable fertilizer, which is increasing humus, water holding capacity, and nutrient contents of soils. It could thereby strengthen agriculture toward the adverse effects of climate change, especially when additionally combined with biochar. To get access to sufficient amounts of suitable materials for composting, resources, which are currently treated as waste, such as human excreta, could be a promising option. However, the safety of the produced compost regarding human pathogens, pharmaceuticals (like antibiotics) and related resistance genes must be considered. In this context, we have investigated the effect of 140- and 154-days of thermophilic composting on the hygienization of human excreta and saw dust from dry toilets together with straw and green cuttings with and without addition of biochar. Compost samples were taken at the beginning and end of the composting process and metagenomic analysis was conducted to assess the fate of antibiotic resistance genes (ARGs) and pathogenicity factors of the microbial community over composting. Potential ARGs conferring resistance to major classes of antibiotics, such as beta-lactam antibiotics, vancomycin, the MLS_B group, aminoglycosides, tetracyclines and quinolones were detected in all samples. However, relative abundance of ARGs decreased from the beginning to the end of composting. This trend was also found for genes encoding type III, type IV, and type VI secretion systems, that are involved in pathogenicity, protein effector transport into eukaryotic cells and horizontal gene transfer between bacteria, respectively. The results suggest that the occurrence of potentially pathogenic microorganisms harboring ARGs declines during thermophilic composting. Nevertheless, ARG levels did not decline below the detection limit of quantitative PCR (qPCR). Thresholds for the usage of compost regarding acceptable resistance gene levels are yet to be evaluated and defined.

Recent advances in porous organic frameworks for sample pretreatment of pesticide and veterinary drug residues: a review

Rapid and accurate detection of pesticide and veterinary drug residues is a continuing challenge because of the complex matrix effects. Thus, appropriate sample pretreatment is a crucial step for the effective extraction of the analytes and removal of the interferences. Recently, the development of nanomaterial adsorbents has greatly promoted the innovation of food sample pretreatment approaches. Porous organic frameworks (POFs), including polymers of intrinsic microporosity, covalent organic frameworks, hyper crosslinked polymers, conjugated microporous polymers, and porous aromatic frameworks, have been widely utilized due to their tailorable skeletons and pores as well as fascinating features. This review summarizes the recent advances for POFs to be utilized in adsorption and sample preparation of pesticide and veterinary drug residues. In addition, future prospects and challenges are discussed, hoping to offer a reference for further study on POFs in sample pretreatment.

EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Ru G, Simmons M, Skandamis P, Suffredini E, Andersson DI, Bampidis V, Bengtsson‐Palme J, Bouchard D, Ferran A, Kouba M, López Puente S, López‐Alonso M, Nielsen SS, Pechová A, Petkova M, Girault S, Broglia A, Guerra B, Innocenti ML, Liébana E, López‐Gálvez G, Manini P, Stella P, Peixe L. Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 5: Lincosamides: lincomycin

The specific concentrations of lincomycin in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels of lincomycin in feed that showed to have an effect on growth promotion/increased yield were reported. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for lincomycin.

EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Ru G, Simmons M, Skandamis P, Suffredini E, Andersson DI, Bampidis V, Bengtsson‐Palme J, Bouchard D, Ferran A, Kouba M, López Puente S, López‐Alonso M, Nielsen SS, Pechová A, Petkova M, Girault S, Broglia A, Guerra B, Innocenti ML, Liébana E, López‐Gálvez G, Manini P, Stella P, Peixe L. Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 6: Macrolides: tilmicosin, tylosin and tylvalosin

The specific concentrations of tilmicosin, tylosin and tylvalosin in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield, were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for tilmicosin and tylosin, whilst for tylvalosin no suitable data for the assessment were available. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these three antimicrobials.

Incorporation of Antibiotics into Solid Lipid Nanoparticles: A Promising Approach to Reduce Antibiotic Resistance Emergence

Antimicrobial resistance is one of the biggest threats to global health as current antibiotics are becoming useless against resistant infectious pathogens. Consequently, new antimicrobial strategies are urgently required. Drug delivery systems represent a potential solution to improve current antibiotic properties and reverse resistance mechanisms. Among different drug delivery systems, solid lipid nanoparticles represent a highly interesting option as they offer many advantages for nontoxic targeted drug delivery. Several publications have demonstrated the capacity of SLNs to significantly improve antibiotic characteristics increasing treatment efficiency. In this review article, antibiotic-loaded solid lipid nanoparticle-related works are analyzed to summarize all information associated with applying these new formulations to tackle the antibiotic resistance problem. The main antimicrobial resistance mechanisms and relevant solid lipid nanoparticle characteristics are presented to later discuss the potential of these nanoparticles to improve current antibiotic treatment characteristics and overcome antimicrobial resistance mechanisms. Moreover, solid lipid nanoparticles also offer new possibilities for other antimicrobial agents that cannot be administrated as free drugs. The advantages and disadvantages of these new formulations are also discussed in this review. Finally, given the progress of the studies carried out to date, future directions are discussed.

Investigation of the Prevalence of Antibiotic Resistance Genes According to the Wastewater Treatment Scale Using Metagenomic Analysis

Although extensive efforts have been made to investigate the dynamics of the occurrence and abundance of antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs), understanding the acquisition of antibiotic resistance based on the WWTP scale and the potential effects on WWTPs is of relatively less interest. In this study, metagenomic analysis was carried out to investigate whether the WWTP scale could be affected by the prevalence and persistence of ARGs and mobile genetic elements (MGEs). As a result, 152 ARG subtypes were identified in small-scale WWTP samples, while 234 ARG subtypes were identified in large-scale WWTP samples. Among the detectable ARGs, multidrug, MLS (macrolide–lincosamide–streptogramin), sulfonamide, and tetracycline resistance genes had the highest abundance, and large and small WWTPs had similar composition characteristics of ARGs. In MGE analysis, plasmids and integrons were 1.5–2.0-fold more abundant in large-scale WWTPs than in small-scale WWTPs. The profile of bacteria at the phylum level showed that Proteobacteria and Actinobacteria were the most dominant bacteria, representing approximately 70% across large- and small-scale WWTPs. Overall, the results of this study elucidate the different abundances and dissemination of ARGs between large- and small-scale WWTPs, which facilitates the development of next-generation engineered wastewater treatment systems.

Quantitative proteomics analysis of Mycoplasma pneumoniae identifies potential macrolide resistance determinants

Mycoplasma pneumoniae is one of the leading causes of community-acquired pneumonia in children and adolescents. Because of the wide application of macrolides in clinical treatment, macrolide-resistant M. pneumoniae strains have become increasingly common worldwide. However, the molecular mechanisms underlying drug resistance in M. pneumoniae are poorly understood. In the present work, we analyzed the whole proteomes of macrolide-sensitive and macrolide-resistant strains of M. pneumoniae using a tandem mass tag-labeling quantitative proteomic technique, Data are available via ProteomeXchange with identifier PXD022220. In total, 165 differentially expressed proteins were identified, of which 80 were upregulated and 85 were downregulated in the drug-resistant strain compared with the sensitive strain. Functional analysis revealed that these proteins were predominantly involved in protein and peptide biosynthesis processes, the ribosome, and transmembrane transporter activity, which implicates them in the mechanism(s) of resistance of M. pneumoniae to macrolides. Our results provide new insights into drug resistance in M. pneumoniae and identify potential targets for further studies on resistance mechanisms in this bacterium.

Potentials of nanotechnology in treatment of methicillin-resistant Staphylococcus aureus

Abuse of antibiotics has led to the emergence of drug-resistant pathogens. Methicillin-resistant Staphylococcus aureus (MRSA) was reported just two years after the clinical use of methicillin, which can cause severe infections with high morbidity and mortality in both community and hospital. The treatment of MRSA infection is greatly challenging since it has developed the resistance to almost all types of antibiotics. As such, it is of great significance and importance to develop novel therapeutic approaches. The fast development of nanotechnology provides a promising solution to this dilemma. Functional nanomaterials and nanoparticles can act either as drug carriers or as antibacterial agents for antibacterial therapy. Herein, we aim to provide a comprehensive understanding of the drug resistance mechanisms of MRSA and discuss the potential applications of some functionalized nanomaterials in anti-MRSA therapy. Also, the concerns and possible solutions for the nanomaterials-based anti-MRSA therapy are discussed.

Emergence of macrolide-resistant Streptococcus pyogenes emm12 in southern Taiwan from 2000 to 2019

BACKGROUND

Group A Streptococcus (GAS) is an important pathogen causing morbidity and mortality worldwide. Surveillance of resistance and emm type has important implication to provide helpful information on the changing GAS epidemiology and empirical treatment.

METHODS

To study the emergence of resistant GAS in children with upper respiratory tract infection (URTI), a retrospective study was conducted from 2000 to 2019 in southern Taiwan. Microbiological studies, including antibiotic susceptibility, were performed. GAS emm types and sequences were determined by molecular methods. The population was divided into two separate decades to analyze potential changes over time. The 1st decade was 2000-2009; the 2nd decade was 2010-2019. Multivariate analyses were performed to identify independent risk factors associated with macrolide resistance between these periods.

RESULTS

A total of 320 GAS from 339 children were enrolled. Most of the children (75%) were under 9 years of age. The most common diagnosis was scarlet fever (225, 66.4%), and the frequency increased from 54.8% in the 1st to 77.9% in the 2nd decade (p < 0.0001). There was a significant increase in resistance to erythromycin and azithromycin from 18.1%, 19.3% in the 1st to 58.4%, 61.0% in the 2nd decade (p < 0.0001). This was associated with clonal expansion of the GAS emm12-ST36 which carrying erm(B) and tet(M) from 3.0% in the 1st to 53.2% in the 2nd decade (p < 0.0001).

CONCLUSIONS

Significant emergence of macrolide-resistant GAS emm12-ST36 in children supports the need for continuing surveillance and investigation for the clonal virulence.

Non-Tuberculous Mycobacteria: Molecular and Physiological Bases of Virulence and Adaptation to Ecological Niches

Non-tuberculous mycobacteria (NTM) are paradigmatic colonizers of the total environment, circulating at the interfaces of the atmosphere, lithosphere, hydrosphere, biosphere, and anthroposphere. Their striking adaptive ecology on the interconnection of multiple spheres results from the combination of several biological features related to their exclusive hydrophobic and lipid-rich impermeable cell wall, transcriptional regulation signatures, biofilm phenotype, and symbiosis with protozoa. This unique blend of traits is reviewed in this work, with highlights to the prodigious plasticity and persistence hallmarks of NTM in a wide diversity of environments, from extreme natural milieus to microniches in the human body. Knowledge on the taxonomy, evolution, and functional diversity of NTM is updated, as well as the molecular and physiological bases for environmental adaptation, tolerance to xenobiotics, and infection biology in the human and non-human host. The complex interplay between individual, species-specific and ecological niche traits contributing to NTM resilience across ecosystems are also explored. This work hinges current understandings of NTM, approaching their biology and heterogeneity from several angles and reinforcing the complexity of these microorganisms often associated with a multiplicity of diseases, including pulmonary, soft-tissue, or milliary. In addition to emphasizing the cornerstones of knowledge involving these bacteria, we identify research gaps that need to be addressed, stressing out the need for decision-makers to recognize NTM infection as a public health issue that has to be tackled, especially when considering an increasingly susceptible elderly and immunocompromised population in developed countries, as well as in low- or middle-income countries, where NTM infections are still highly misdiagnosed and neglected.

Actinomycete-Derived Polyketides as a Source of Antibiotics and Lead Structures for the Development of New Antimicrobial Drugs

Actinomycetes are remarkable producers of compounds essential for human and veterinary medicine as well as for agriculture. The genomes of those microorganisms possess several sets of genes (biosynthetic gene cluster (BGC)) encoding pathways for the production of the valuable secondary metabolites. A significant proportion of the identified BGCs in actinomycetes encode pathways for the biosynthesis of polyketide compounds, nonribosomal peptides, or hybrid products resulting from the combination of both polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). The potency of these molecules, in terms of bioactivity, was recognized in the 1940s, and started the "Golden Age" of antimicrobial drug discovery. Since then, several valuable polyketide drugs, such as erythromycin A, tylosin, monensin A, rifamycin, tetracyclines, amphotericin B, and many others were isolated from actinomycetes. This review covers the most relevant actinomycetes-derived polyketide drugs with antimicrobial activity, including anti-fungal agents. We provide an overview of the source of the compounds, structure of the molecules, the biosynthetic principle, bioactivity and mechanisms of action, and the current stage of development. This review emphasizes the importance of actinomycetes-derived antimicrobial polyketides and should serve as a "lexicon", not only to scientists from the Natural Products field, but also to clinicians and others interested in this topic.

Comparative diversity of microbiomes and Resistomes in beef feedlots, downstream environments and urban sewage influent

Background

Comparative knowledge of microbiomes and resistomes across environmental interfaces between animal production systems and urban settings is lacking. In this study, we executed a comparative analysis of the microbiota and resistomes of metagenomes from cattle feces, catch basin water, manured agricultural soil and urban sewage.

Results

Metagenomic DNA from composite fecal samples (FC; n = 12) collected from penned cattle at four feedlots in Alberta, Canada, along with water from adjacent catchment basins (CB; n = 13), soil (n = 4) from fields in the vicinity of one of the feedlots and urban sewage influent (SI; n = 6) from two municipalities were subjected to Illumina HiSeq2000 sequencing. Firmicutes exhibited the highest prevalence (40%) in FC, whereas Proteobacteria were most abundant in CB (64%), soil (60%) and SI (83%). Among sample types, SI had the highest diversity of antimicrobial resistance (AMR), and metal and biocide resistance (MBR) classes (13 & 15) followed by FC (10 & 8), CB (8 & 4), and soil (6 & 1). The highest antimicrobial resistant (AMR) gene (ARG) abundance was harboured by FC, whereas soil samples had a very small, but unique resistome which did not overlap with FC & CB resistomes. In the beef production system, tetracycline resistance predominated followed by macrolide resistance. The SI resistome harboured β-lactam, macrolide, tetracycline, aminoglycoside, fluoroquinolone and fosfomycin resistance determinants. Metal and biocide resistance accounted for 26% of the SI resistome with a predominance of mercury resistance.

Conclusions

This study demonstrates an increasing divergence in the nature of the microbiome and resistome as the distance from the feedlot increases. Consistent with antimicrobial use, tetracycline and macrolide resistance genes were predominant in the beef production system. One of the feedlots contributed both conventional (raised with antibiotics) and natural (raised without antibiotics) pens samples. Although natural pen samples exhibited a microbiota composition that was similar to samples from conventional pens, their resistome was less complex. Similarly, the SI resistome was indicative of drug classes used in humans and the greater abundance of mercury resistance may be associated with contamination of municipal water with household and industrial products.

Electronic supplementary material

The online version of this article (10.1186/s12866-019-1548-x) contains supplementary material, which is available to authorized users.

[Antibiotic prophylaxis in preterm premature rupture of membranes: CNGOF preterm premature rupture of membranes guidelines]

OBJECTIVE

To analyse benefits and risks of antibiotic prophylaxis in the management of preterm premature rupture of membranes.

METHODS

PubMed and Cochrane Central databases search.

RESULTS

Streptoccoccus agalactiae (group B streptococcus) and Escherichia coli are the two main bacteria identified in early neonatal sepsis (EL3). Antibiotic prophylaxis at admission is associated with significant prolongation of pregnancy (EL2), reduction in neonatal morbidity (EL1) without impact on neonatal mortality (EL2). Co-amoxiclav could be associated with an increased risk for neonatal necrotising enterocolitis (EL2). Antibiotic prophylaxis at admission in women with preterm premature rupture of the membranes is recommended (Grade A). Monotherapy with amoxicillin, third generation cephalosporin and erythromycin can be used as well as combination of erythromycin and amoxicillin (Professional consensus) for 7 days (GradeC). Shorter treatment is possible when initial vaginal culture is negative (Professional consensus). Co-amxiclav, aminoglycosides, glycopeptides, first and second generation cephalosporin, clindamycin and metronidazole are not recommended (Professional consensus).

CONCLUSIONS

Antibiotic prophylaxis against Streptoccoccus agalactiae (group B streptococcus) and E. coli is recommended in women with preterm premature of the membranes (Grade A). Monotherapy with amoxicillin, third generation cephalosporin or erythromycin, as well as combination of erythromycin and amoxicillin are recommended (Professional consensus).

An overview of the antimicrobial resistance mechanisms of bacteria

Resistance to antimicrobial agents has become a major source of morbidity and mortality worldwide. When antibiotics were first introduced in the 1900's, it was thought that we had won the war against microorganisms. It was soon discovered however, that the microorganisms were capable of developing resistance to any of the drugs that were used. Apparently most pathogenic microorganisms have the capability of developing resistance to at least some antimicrobial agents. The main mechanisms of resistance are: limiting uptake of a drug, modification of a drug target, inactivation of a drug, and active efflux of a drug. These mechanisms may be native to the microorganisms, or acquired from other microorganisms. Understanding more about these mechanisms should hopefully lead to better treatment options for infective diseases, and development of antimicrobial drugs that can withstand the microorganisms attempts to become resistant.

Impact of sequencing depth on the characterization of the microbiome and resistome

Developments in high-throughput next generation sequencing (NGS) technology have rapidly advanced the understanding of overall microbial ecology as well as occurrence and diversity of specific genes within diverse environments. In the present study, we compared the ability of varying sequencing depths to generate meaningful information about the taxonomic structure and prevalence of antimicrobial resistance genes (ARGs) in the bovine fecal microbial community. Metagenomic sequencing was conducted on eight composite fecal samples originating from four beef cattle feedlots. Metagenomic DNA was sequenced to various depths, D1, D0.5 and D0.25, with average sample read counts of 117, 59 and 26 million, respectively. A comparative analysis of the relative abundance of reads aligning to different phyla and antimicrobial classes indicated that the relative proportions of read assignments remained fairly constant regardless of depth. However, the number of reads being assigned to ARGs as well as to microbial taxa increased significantly with increasing depth. We found a depth of D0.5 was suitable to describe the microbiome and resistome of cattle fecal samples. This study helps define a balance between cost and required sequencing depth to acquire meaningful results.

Antimicrobial Resistance in Rhodococcus equi

Pneumonia caused by Rhodococcus equi remains an important cause of disease and death in foals. The combination of a macrolide (erythromycin, azithromycin, or clarithromycin) with rifampin has been the recommended treatment for foals with clinical signs of infection caused by R. equi since the early 1980s with, until recently, only rare reports of resistance. Resistance to macrolides and rifampin in isolates of R. equi cultured from horses is increasing, with isolates resistant to all macrolides and rifampin now being cultured from up to 40% of infected foals at some farms. This text reviews the available data regarding antimicrobial resistance in R. equi, with emphasis on the molecular mechanisms of the recent emergence of resistance to macrolides and rifampin in equine isolates of R. equi.

Detection of antibiotic resistance genes in the feces of young adult Japanese

Antibiotic resistance genes in the feces of healthy young adult Japanese were analyzed with polymerase chain reaction using specific primers. Antibiotic resistance genes against macrolides (ermB, ermF, ermX, and mefA/E), tetracyclines (tetW, tetQ, tetO, and tetX), β-lactam antibiotics (blaTEM ), and streptomycin (aadE) were detected in more than 50% of subjects. These antibiotic resistance genes are likely widespread in the large intestinal bacteria of young adult Japanese.

Characterization of antibiotic resistance genes in representative organic solid wastes: Food waste-recycling wastewater, manure, and sewage sludge

In this research, the distribution of antibiotic resistance genes (ARGs) was characterized in representative organic solid waste (OSW) in Korea: food waste-recycling wastewater (FRW), manure, and sewage sludge. The amounts of total ARG (gene copies/16S rRNA gene copies) was greatest in manure followed by sewage sludge and FRW. Interestingly, there were significantly different patterns in the diversity and mechanisms of ARGs. For example, a significant proportion of ARGs were tetracycline resistant genes in all the OSW (40.4-78.2%). β-lactam antibiotics resistant genes were higher in the FRW samples than in other types of OSW but sulfonamides resistant genes represented the greatest proportion in sludge. Regarding the characteristics of antibiotic resistance mechanisms, there was a relatively higher proportion of the ribosomal protection mechanism to tetracycline observed in the FRW and manure samples. However, tetracycline resistant genes with direct interaction were relatively higher in the sewage sludge samples. sul1 was the dominant subtype in all the OSW types and detection of ermB was observed although there was no ermC detected in sewage sludge. There were significant correlations between the occurrences of ARG subtypes: tetB and tetG in all OSW (P<0.01); tetE and tetQ only in sludge (P<0.01). The Class 1 integron-integrase gene (intI1) was significantly correlated with total ARGs only in manure and sludge (P<0.05), revealing potential horizontal gene transfer in these OSW.

Presence and distribution of Macrolides-Lincosamide-Streptogramin resistance genes and potential indicator ARGs in the university ponds in Guangzhou, China

This study aimed to determine the occurrence, abundance, and variation of seven Macrolides-Lincosamide-Streptogramin (MLS) resistance genes (ereB, ermA, ermB, ermF, mefA, vatB, mphA) and six potential indicator ARGs (tet (B), sul1, qnrS, fexA, IntI1, ermB) from three ponds at university by quantitative PCR and assess the impacts on the surroundings. Solid samples (fish feces, soil and sediment) and water samples were tested. All the genes were found at low levels in soil samples. For the MLS resistance genes, only two MLS genes (ermB, ermF) were detected in all samples and significant correlations between ermB and Σ MLS (R = 0.91 in solid samples; R = 0.86 in water samples, p < 0.01) were found. For the potential indicators, intl1 and sul1 were present at high levels in the three different ponds while the other genes showed varying levels. These findings show that the ermB gene can probably be served as an indicator to evaluate the overall level of MLS resistance genes. The fairly low abundance of all the tested resistance genes in soil samples and the moderate levels in other samples suggests that the university ponds kept a good state and did not have a significant impact on their surroundings.

Novel transferable erm(46) determinant responsible for emerging macrolide resistance in Rhodococcus equi

OBJECTIVES

The objective of this study was to identify the molecular mechanism of macrolide resistance in the actinomycete Rhodococcus equi, a major equine pathogen and zoonotic agent causing opportunistic infections in people.

METHODS

Macrolide-resistant (n = 62) and macrolide-susceptible (n = 62) clinical isolates of R. equi from foals in the USA were studied. WGS of 18 macrolide-resistant and 6 macrolide-susceptible R. equi was performed. Representative sequences of all known macrolide resistance genes identified to date were used to search the genome assemblies for putative homologues. PCR was used to screen for the presence of the identified resistance determinant in the rest of the isolates. Mating experiments were performed to verify mobility of the gene.

RESULTS

A novel erm gene, erm(46), was identified in all sequenced resistant isolates, but not in susceptible isolates. There was complete association between macrolide resistance and the presence of erm(46) as detected by PCR screening of all 124 clinical isolates of R. equi. Expression of erm(46) in a macrolide-susceptible strain of R. equi induced high-level resistance to macrolides, lincosamides and streptogramins B, but not to other classes of antimicrobial agents. Transfer of erm(46) to macrolide-susceptible R. equi was confirmed. The transfer frequency ranged from 3 × 10(-3) to 1 × 10(-2).

CONCLUSIONS

This is the first molecular characterization of resistance to macrolides, lincosamides and streptogramins B in R. equi. Resistance was due to the presence of a novel erm(46) gene mobilizable likely by conjugation, which has spread among equine isolates of R. equi in the USA.

Effects of in-feed copper and tylosin supplementations on copper and antimicrobial resistance in faecal enterococci of feedlot cattle

AIMS

The objective was to investigate whether in-feed supplementation of copper, at elevated level, co-selects for macrolide resistance in faecal enterococci.

METHODS AND RESULTS

The study was conducted in cattle (n = 80) with a 2 × 2 factorial design of copper (10 or 100 mg kg(-1) of feed) and tylosin (0 or 10 mg kg(-1) of feed). Thirty-seven isolates (4·6%; 37/800) of faecal enterococci were positive for the tcrB and all were Enterococcus faecium. The prevalence was higher among cattle fed diets with copper and tylosin (8·5%) compared to control (2·0%), copper (4·5%) and tylosin (3·5%) alone. All tcrB-positive isolates were positive for erm(B) and tet(M) genes. Median copper minimum inhibitory concentrations (MICs) for tcrB-positive and tcrB-negative enterococci were 20 and 4 mmol l(-1) , respectively.

CONCLUSIONS

Feeding of elevated dietary copper and tylosin alone or in combination resulted in an increased prevalence of tcrB and erm(B)-mediated copper and tylosin-resistant faecal enterococci in feedlot cattle.

SIGNIFICANCE AND IMPACT OF THE STUDY

In-feed supplementation of elevated dietary copper has the potential to co-select for macrolide resistance. Further studies are warranted to investigate the factors involved in maintenance and dissemination of the resistance determinants and their co-selection mechanism in relation to feed-grade antimicrobials' usage in feedlot cattle.

Decline in macrolide resistance rates among Streptococcus pyogenes causing pharyngitis in children isolated in Italy

Macrolides are often used to treat group A streptococcus (GAS) infections, but their resistance rates reached high proportions worldwide. The aim of the present study was to give an update on the characteristics and contemporary prevalence of macrolide-resistant pharyngeal GAS in Central Italy. A total of 592 isolates causing pharyngitis in children were collected in the period 2012–2013. Clonality was assessed by emm typing and pulsed-field gel electrophoresis (PFGE) for all macrolide-resistant strains and for selected susceptible isolates. Genetic determinants of resistance were screened by polymerase chain reaction (PCR). Forty-four GAS were erythromycin-resistant (7.4 %). Among them, 52.3 % and 50 % were clindamycin- and tetracycline-resistant, respectively. erm(B)-positive isolates (52.3 %) expressed the constitutive cMLS_B phenotype. mef(A) and its associated M phenotype were recorded in 40.9 % of the cases. The remaining erm(A)-positive isolates expressed the iMLS_B phenotype. Seventeen tetracycline-resistant isolates carried tet(M) and five isolates carried tet(O). Twenty-five emm types were found among all strains, with the predominance of emm types 12, 89, 1, and 4. Eleven emm types and 12 PFGE clusters characterized macrolide-resistant strains, with almost two-thirds belonging to emm12, emm4, and emm11. Macrolide-susceptible and -resistant emm types 12, 89, 11, and 4 shared related PFGE profiles. There was a dramatic decline in macrolide resistance in Central Italy among pharyngeal GAS isolates in 2012–2013 when compared to previous studies from the same region (p < 0.05), although macrolide consumption remained stable over the past 15 years. We observed a decrease in the proportion of macrolide-resistant strains within emm types commonly associated with macrolide resistance in the past, namely emm12, 1, and 89.

High-resolution structure of the Escherichia coli ribosome

Protein synthesis by the ribosome is highly dependent on the ionic conditions in the cellular environment, but the roles of ribosome solvation remain poorly understood. Moreover, the function of modifications to ribosomal RNA and ribosomal proteins are unclear. Here we present the structure of the Escherichia coli 70S ribosome to 2.4 Å resolution. The structure reveals details of the ribosomal subunit interface that are conserved in all domains of life, and suggest how solvation contributes to ribosome integrity and function. The structure also suggests how the conformation of ribosomal protein uS12 likely impacts its contribution to messenger RNA decoding. This structure helps to explain the phylogenetic conservation of key elements of the ribosome, including posttranscriptional and posttranslational modifications and should serve as a basis for future antibiotic development.

Abundance and distribution of Macrolide-Lincosamide-Streptogramin resistance genes in an anaerobic-aerobic system treating spiramycin production wastewater

The behaviors of the Macrolide-Lincosamide-Streptogramin (MLS) resistance genes were investigated in an anaerobic-aerobic pilot-scale system treating spiramycin (SPM) production wastewater. After screening fifteen typical MLS resistance genes with different mechanisms using conventional PCR, eight detected genes were determined by quantitative PCR, together with three mobile elements. Aerobic sludge in the pilot system exhibited a total relative abundance of MLS resistance genes (per 16S rRNA gene) 2.5 logs higher than those in control samples collected from sewage and inosine wastewater treatment systems (P < 0.05), implying the presence of SPM could induce the production of MLS resistance genes. However, the total relative gene abundance in anaerobic sludge (4.3 × 10(-1)) was lower than that in aerobic sludge (3.7 × 10(0)) despite of the higher SPM level in anaerobic reactor, showing the advantage of anaerobic treatment in reducing the production of MLS resistance genes. The rRNA methylase genes (erm(B), erm(F), erm(X)) were the most abundant in the aerobic sludge (5.3 × 10(-1)-1.7 × 10(0)), followed by esterase gene ere(A) (1.3 × 10(-1)) and phosphorylase gene mph(B) (5.7 × 10(-2)). In anaerobic sludge, erm(B), erm(F), ere(A), and msr(D) were the major ones (1.2 × 10(-2)-3.2 × 10(-1)). These MLS resistance genes (except for msr(D)) were positively correlated with Class 1 integron (r(2) = 0.74-0.93, P < 0.05), implying the significance of horizontal transfer in their proliferation.

Simultaneous determination of tylosin and josamycin residues in muscles, liver, eggs and milk by MLC with a monolithic column and time-programmed UV detection: application to baby food and formulae

Background

Tylosin and Josamycin are macrolide antibiotics. They are used in the treatment of pneumonia, arthritis and mastitis in cattle, and mycoplasma infections in poultry. The incorrect use of antibiotics has lead to the presence of antibiotic residues in foods. The residues cause toxic effects on consumers.

Results

A simple and sensitive method was optimized and validated for the analysis of tylosin and josamycin residues in food samples. Analytical separation was performed in less than 10 min using a RP C₁₈ monolithic column with time-programmed UV detection at 287 nm and 232 nm and a micellar solution of 0.17 M sodium dodecyl sulphate, 14% methanol and 0.3% triethylamine in 0.02 M phosphoric acid buffered at pH 4 as the mobile phase. The method was fully validated in accordance with ICH guidelines. The micellar method was successfully applied to quantitatively determine tylosin and josamycin residues in spiked chicken muscles, chicken liver, bovine muscles, liver, milk and eggs. It was also extended to the determination of tylosin and josamycin residues in chicken-based baby food and baby formulae. The compounds were separated by a monolithic column which, on account of its particular structure, could bear higher flow rates than usually found for this kind of analysis. High extraction efficiency for tylosin and josamycin was obtained without matrix interference in the extraction process and in the subsequent chromatographic determination. No organic solvent was used during the pretreatment step. Hence, it is considered an interesting technique for “green” chemistry.

Conclusion

The proposed method was validated and successfully applied for the determination of tylosin and josamycin residues in spiked chicken muscles, chicken liver, bovine muscles, liver, milk and eggs. It was also extended to the determination of tylosin and josamycin residues in chicken-based baby food and baby formulae.

[New therapeutic strategies against Helicobacter pylori]

The standard therapy for Helicobacter pylori infection in Korea is a triple-drug regimen consisting of a proton pump inhibitor with two antibiotics such as clarithromycin, amoxicillin, and metronidazole. However, as the eradication rate of this regimen has declined over the past decade, this prompted the formulation of new therapeutic regimens. New therapeutic strategies against H. pylori infection that had been tried all over the world include sequential therapy, concomitant therapy, and tailored therapy This article will review the basic concepts and the results of previous clinical trials on the aforementioned new therapeutic regiments.

Effects of Chlorophyll-Derived Efflux Pump Inhibitor Pheophorbide a and Pyropheophorbide a on Growth and Macrolide Antibiotic Resistance of Indicator and Anaerobic Swine Manure Bacteria

Natural plant compounds, such as the chlorophyll a catabolites pheophorbide a (php) and pyropheophorbide a (pyp), are potentially active in the gastrointestinal tracts and manure of livestock as antimicrobial resistance-modifying agents through inhibition of bacterial efflux pumps. To investigate whether php, a known efflux pump inhibitor, and pyp influence bacterial resistance, we determined their long-term effects on the MICs of erythromycin for reference strains of clinically relevant indicator bacteria with macrolide or multidrug resistance efflux pumps. Pyp reduced the final MIC endpoint for Staphylococcus (S.) aureus and Escherichia (E.) coli by up to 1536 and 1024 μg erythromycin mL−1 or 1.4- and 1.2-fold, respectively. Estimation of growth parameters of S. aureus revealed that pyp exerted an intrinsic inhibitory effect under anaerobic conditions and was synergistically active, thereby potentiating the effect of erythromycin and partially reversing high-level erythromycin resistance. Anaerobe colony counts of total and erythromycin-resistant bacteria from stored swine manure samples tended to be lower in the presence of pyp. Tylosin, php, and pyp were not detectable by HPLC in the manure or medium. This is the first study showing that pyp affects growth and the level of sensitivity to erythromycin of S. aureus, E. coli, and anaerobic manure bacteria.

Tylosin content in meat and honey samples over a two-year period in Croatia

A total of 646 meat and 96 honey samples were examined over a 2-year period for the presence of tylosin residues. ELISA method used was validated according to the criteria of Commission Decision 2002/657/EC established for qualitative screening methods. The CCβ values were 32.1 µg kg⁻¹ in muscle and 24.4 µg kg⁻¹ in honey. The recoveries from spiked samples ranged from 66.4-118.6%, with a coefficient of variation between 12.6% and 18.6%. All the investigated samples showed no presence of tylosin. Calculated estimated daily intakes show exposure levels lower than the acceptable daily intakes set by World Health Organization.

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.

Mutational and transcriptomic changes involved in the development of macrolide resistance in Campylobacter jejuni

Macrolide antibiotics are important for clinical treatment of infections caused by Campylobacter jejuni. Development of resistance to this class of antibiotics in Campylobacter is a complex process, and the dynamic molecular changes involved in this process remain poorly defined. Multiple lineages of macrolide-resistant mutants were selected by stepwise exposure of C. jejuni to escalating doses of erythromycin or tylosin. Mutations in target genes were determined by DNA sequencing, and the dynamic changes in the expression of antibiotic efflux transporters and the transcriptome of C. jejuni were examined by real-time reverse transcription-PCR, immunoblotting, and DNA microarray analysis. Multiple types of mutations in ribosomal proteins L4 and L22 occurred early during stepwise selection. On the contrary, the mutations in the 23S rRNA gene, mediating high resistance to macrolides, were observed only in the late-stage mutants. Upregulation of antibiotic efflux genes was observed in the intermediately resistant mutants, and the magnitude of upregulation declined with the occurrence of mutations in the 23S rRNA gene. DNA microarray analysis revealed the differential expression of 265 genes, most of which occurred in the intermediate mutant, including the upregulation of genes encoding ribosomal proteins and the downregulation of genes involved in energy metabolism and motility. These results indicate (i) that mutations in L4 and L22 along with temporal overexpression of antibiotic efflux genes precede and may facilitate the development of high-level macrolide resistance and (ii) that the development of macrolide resistance affects the pathways important for physiology and metabolism in C. jejuni, providing an explanation for the reduced fitness of macrolide-resistant Campylobacter.

Comparison of sequential and standard therapy for Helicobacter pylori eradication in children and investigation of clarithromycin resistance

AIMS

The aim of the present study was to compare the efficacy of sequential and standard triple-drug regimen for Helicobacter pylori (H pylori) eradication in children and to determine the primary resistance rate to clarithromycin.

METHODS

Children with H pylori infection randomized to receive either standard regimen (n = 28) consisting of lansoprazole for 30 days, amoxicillin and clarithromycin for 14 days or sequential regimen (n = 16) consisting of lansoprazole for 30 days, amoxicillin for 7 days, followed by clarithromycin and metronidazole for the next 7 days. Clarithromycin susceptibility of H pylori was assessed with fluorescence in-situ hybridization technique. Eradication was controlled by C urea breath test or monoclonal stool antigen test 4 weeks after the end of the therapy.

RESULTS

H pylori eradication rate was higher in the sequential therapy group (93.7%), compared with the standard therapy group (46.4%) (P = 0.002). There was no difference in adverse drug reactions and in compliance to the treatment between the groups. Primary clarithromycin resistance rate for H pylori was found as 25.7% (n = 9). All of the patients having clarithromycin resistance were coincidentally in the standard therapy group. After the exclusion of these 9 patients, sequential therapy was again found to be more effective than the standard therapy (P = 0.02).

CONCLUSIONS

Sequential therapy seems highly effective for eradicating H pylori in children; however, the difference between 2 groups in resistant strains was the limitation of the study. Our country needs to reassess the effectiveness of standard triple therapy regimen for H pylori eradication.

Helicobacter pylori Eradication Therapies in the Era of Increasing Antibiotic Resistance: A Paradigm Shift to Improved Efficacy

With the rising prevalence of antimicrobial resistance, the eradication rates of Helicobacter pylori (H. pylori) with standard treatments are decreasing to unacceptable levels (i.e., ≤80%) in most countries. After these disappointing results, several authorities have proposed that infection with H. pylori should be approached and treated as any other bacterial infectious disease. This implicates that clinicians should prescribe empirical treatments yielding a per protocol eradication of at least 90%. In recent years several treatments producing ≥90% cure rates have been proposed including sequential therapy, concomitant quadruple therapy, hybrid (dual-concomitant) therapy, and bismuth-containing quadruple therapy. These treatments are likely to represent the recommended first-line treatments in the near future. In the present paper, we are considering a series of critical issues regarding currently available means and approaches for the management of H. pylori infection. Clinical needs and realistic endpoints are taken into account. Furthermore, emerging strategies for the eradication of H. pylori and the existing evidence of their clinical validation and widespread applicability are discussed.

Helicobacter pylori Eradication Therapies in the Era of Increasing Antibiotic Resistance: A Paradigm Shift to Improved Efficacy

With the rising prevalence of antimicrobial resistance, the eradication rates of Helicobacter pylori (H. pylori) with standard treatments are decreasing to unacceptable levels (i.e., ≤80%) in most countries. After these disappointing results, several authorities have proposed that infection with H. pylori should be approached and treated as any other bacterial infectious disease. This implicates that clinicians should prescribe empirical treatments yielding a per protocol eradication of at least 90%. In recent years several treatments producing ≥90% cure rates have been proposed including sequential therapy, concomitant quadruple therapy, hybrid (dual-concomitant) therapy, and bismuth-containing quadruple therapy. These treatments are likely to represent the recommended first-line treatments in the near future. In the present paper, we are considering a series of critical issues regarding currently available means and approaches for the management of H. pylori infection. Clinical needs and realistic endpoints are taken into account. Furthermore, emerging strategies for the eradication of H. pylori and the existing evidence of their clinical validation and widespread applicability are discussed.

Update on non-bismuth quadruple (concomitant) therapy for eradication of Helicobacter pylori

BACKGROUND

Traditional standard triple therapy for Helicobacter pylori (H. pylori) infection (proton pump inhibitor-clarithromycin-amoxicillin) can easily be converted to non-bismuth quadruple (concomitant) therapy by the addition of a nitroimidazole twice daily.

AIM

To critically review evidence on the role of non-bismuth quadruple therapy (proton pump inhibitor-clarithromycin-amoxicillin-nitroimidazole) in the treatment of H. pylori infection.

METHODS

Bibliographical searches were performed in MEDLINE and relevant congresses up to December 2011. We performed a meta-analysis of the studies evaluating the concomitant therapy, and of the randomized controlled trials comparing the concomitant and the standard triple therapy.

RESULTS

A meta-analysis of 19 studies (2070 patients) revealed a mean H. pylori cure rate (intention-to-treat) of 88% (95% confidence interval from 85% to 91%) for non-bismuth quadruple therapy. We performed a meta-analysis of the randomized controlled studies comparing the concomitant (481 patients) and the standard triple therapy (503 patients). The former was more effective than the latter: 90% versus 78% (intention-to-treat analysis). Results were homogeneous (I(2) = 0%). The odds ratio for this comparison was 2.36 (95% confidence interval from 1.67 to 3.34). A tendency toward better results with longer treatments (7-10 days versus 3-5 days) has been observed, so it seems reasonable to recommend the length of treatment achieving the highest cure rates (10 days). Clarithromycin resistance may reduce the efficacy of non-bismuth quadruple therapy, although the decrease in eradication rates seems to be far lower than in standard triple therapy. Experience with the non-bismuth quadruple therapy in patients with metronidazole-resistant strains is still very limited.

CONCLUSION

Non-bismuth quadruple (concomitant) therapy appears to be an effective, safe, and well-tolerated alternative to triple therapy and is less complex than sequential therapy. Therefore, this regimen appears well suited for use in settings where the efficacy of triple therapy is unacceptably low.

Frequency of antibiotic resistance in a swine facility 2.5 years after a ban on antibiotics

The addition of antibiotics to livestock feed has contributed to the selection of antibiotic-resistant bacteria in concentrated animal feeding operations and agricultural ecosystems. The objective of this study was to assess the occurrence of resistance to chlortetracycline and tylosin among bacterial populations at the Swine Complex of McGill University (Province of Quebec, Canada) in the absence of antibiotic administration to pigs for 2.5 years prior to the beginning of this study. Feces from ten pigs born from the same sow and provided feed without antibiotic were sampled during suckling (n = 6 for enumerations, n = 10 for PCR), weanling (n = 10 both for PCR and enumerations), growing (n = 10 both for PCR and enumerations), and finishing (n = 10 both for PCR and enumerations). The percentage of chlortetracycline-resistant anaerobic bacterial populations (Tet(R)) was higher than that of tylosin-resistant anaerobic bacterial populations (Tyl(R)) at weanling, growing, and finishing. Prior to the transportation of animals to the slaughterhouse, resistant populations varied between 6.5 and 9.4 Log colony-forming units g humid feces(-1). In all pigs, tet(L), tet(O), and erm(B) were detected at suckling and weanling, whereas only tet(O) was detected at growing and finishing. The abundance of tet(O) was similar between males and females at weanling and growing and reached 5.1 × 10(5) and 5.6 × 10(5) copies of tet(O)/ng of total DNA in males and females, respectively, at finishing. Results showed high abundances and proportions of Tet(R) and Tyl(R) anaerobic bacterial populations, as well as the occurrence of tet and erm resistance genes within these populations despite the absence of antibiotic administration to pigs at this swine production facility since January 2007, i.e., 2.5 years prior to the beginning of this study. This work showed that the occurrence of bacterial resistance to chlortetracycline and tylosin is high at the Swine Complex of McGill University.