High prevalence of the ermB gene among erythromycin-resistant streptococcus pneumoniae isolates in Germany during the winter of 2000-2001 and in vitro activity of telithromycin

Rapid Detection of Antimicrobial Resistance Genes in Critically Ill Children Using a Custom TaqMan Array Card

Bacteria are identified in only 22% of critically ill children with respiratory infections treated with antimicrobial therapy. Once an organism is isolated, antimicrobial susceptibility results (phenotypic testing) can take another day. A rapid diagnostic test identifying antimicrobial resistance (AMR) genes could help clinicians make earlier, informed antimicrobial decisions. Here we aimed to validate a custom AMR gene TaqMan Array Card (AMR-TAC) for the first time and assess its feasibility as a screening tool in critically ill children. An AMR-TAC was developed using a combination of commercial and bespoke targets capable of detecting 23 AMR genes. This was validated using isolates with known phenotypic resistance. The card was then tested on lower respiratory tract and faecal samples obtained from mechanically ventilated children in a single-centre observational study of respiratory infection. There were 82 children with samples available, with a median age of 1.2 years. Major comorbidity was present in 29 (35%) children. A bacterial respiratory pathogen was identified in 13/82 (16%) of children, of which 4/13 (31%) had phenotypic AMR. One AMR gene was detected in 49/82 (60%), and multiple AMR genes were detected in 14/82 (17%) children. Most AMR gene detections were not associated with the identification of phenotypic AMR. AMR genes are commonly detected in samples collected from mechanically ventilated children with suspected respiratory infections. AMR-TAC may have a role as an adjunct test in selected children in whom there is a high suspicion of antimicrobial treatment failure.

Analysis of virulence factors and antibiotic resistance genes in group B streptococcus from clinical samples

BACKGROUND

Streptococcus agalacticae (Group B Streptococcus, GBS) is one of the most important causative agents of serious infections among neonates. This study was carried out to identify antibiotic resistance and virulence genes associated with GBS isolated from pregnant women.

METHODS

A total of 43 GBS isolates were obtained from 420 vaginal samples collected from HIV positive and negative women who were 13-35 weeks pregnant attending Antenatal Care at Chitungwiza and Harare Central Hospitals in Zimbabwe. Identification tests of GBS isolates was done using standard bacteriological methods and molecular identification testing. Antibiotic susceptibility testing was done using the modified Kirby-Bauer method and E-test strips. The boiling method was used to extract DNA and Polymerase Chain Reaction (PCR) was used to screen for 13 genes. Data was fed into SPSS 24.0.

RESULTS

Nine distinct virulence gene profiles were identified and hly-scpB-bca-rib 37.2% (16/43) was common. The virulence genes identified were namely hly 97.8% (42/43), scpB 90.1% (39/43), bca 86.0% (37/43), rib 69.8% (30/43) and bac 11.6% (5/43). High resistance to tetracycline 97.7% (42/43) was reported followed by 72.1% (31/43) cefazolin, 69.8% (30/43) penicillin G, 58.1% (25/43) ampicillin, 55.8% (24/43) clindamycin, 46.5% (20/43) ceftriaxone, 34.9% (15/43) chloramphenicol, and 30.2% (13/43) for both erythromycin and vancomycin using disk diffusion. Antibiotic resistance genes among the resistant and intermediate-resistant isolates showed high frequencies for tetM 97.6% (41/42) and low frequencies for ermB 34.5% (10/29), ermTR 10.3% (3/29), mefA 3.4% (1/29), tetO 2.4% (1/42) and linB 0% (0/35). The atr housekeeping gene yielded 100% (43/43) positive results, whilst the mobile genetic element IS1548 yielded 9.3% (4/43).

CONCLUSION

The study showed high prevalence of hly, scpB, bca and rib virulence genes in S. agalactiae strains isolated from pregnant women. Tetracycline resistance was predominantly caused by the tetM gene, whilst macrolide resistance was predominantly due to the presence of erm methylase, with the ermB gene being more prevalent. Multi-drug resistance coupled with the recovery of resistant isolates to antimicrobial agents such as penicillins indicates the importance of GBS surveillance and susceptibility tests. It was also observed that in vitro phenotypic resistance is not always accurately predicted by resistance genotypes.

Antibiotics in Food Chain: The Consequences for Antibiotic Resistance

Antibiotics have been used as essential therapeutics for nearly 100 years and, increasingly, as a preventive agent in the agricultural and animal industry. Continuous use and misuse of antibiotics have provoked the development of antibiotic resistant bacteria that progressively increased mortality from multidrug-resistant bacterial infections, thereby posing a tremendous threat to public health. The goal of our review is to advance the understanding of mechanisms of dissemination and the development of antibiotic resistance genes in the context of nutrition and related clinical, agricultural, veterinary, and environmental settings. We conclude with an overview of alternative strategies, including probiotics, essential oils, vaccines, and antibodies, as primary or adjunct preventive antimicrobial measures or therapies against multidrug-resistant bacterial infections. The solution for antibiotic resistance will require comprehensive and incessant efforts of policymakers in agriculture along with the development of alternative therapeutics by experts in diverse fields of microbiology, biochemistry, clinical research, genetic, and computational engineering.

Comparative genomics of vancomycin-resistant Enterococcus spp. revealed common resistome determinants from hospital wastewater to aquatic environments

The rise of vancomycin-resistant Enterococcus spp. (VRE) has led to treatment challenges in hospital settings worldwide. Hospital wastewater (HW) might disseminate this threat to the aquatic environment. Thus, this study elucidates the VRE resistance quotient (RQ) of different environmental matrixes in wastewater and compares genomic determinants of VRE strains recovered from HW to water resources. Presumptive Enterococcus spp. and VRE were quantified and isolated using standard microbiological procedures. Fourteen VRE genomes were then sequenced using an Illumina HiSeq X™ Ten platform. Subsequently, VRE genomes were compared based on antibiotic resistance genes, plasmids, bacteriophages, insertion sequences, transposons, virulence and pathogenicity. Wastewater effluent showed the highest RQ among all sampled matrixes. The phylogeny of vancomycin-resistant E. faecalis (VREfs) and E. faecium (VREfm) revealed a tree structure based on their respective sequence type. A comparative genomic analysis of 14 genomes highlighted regions encoding phage protein, phage holin, phage integrase, integrase and transposase on both query genomes and the reference genome. Acquired resistance to vancomycin was conferred by vanA, vanN, vanL, vanG and the intrinsic resistance vanC operons. Plasmids were dominated by the presence of conserved areas of the replication initiating genes (rep). The Tn3-like and Tn917 transposons were present in all erythromycin-carrying erm(B) isolated VRE genomes. All VRE genomes expect one were putatively predicted as human pathogens with varying degrees of virulence. The presence of such resistant bacteria in African water resource is of great public health concern. It is, therefore, recommended that these bacteria be tracked and characterised from different environments to contribute to improved epidemiological containment action.

Factors that affect the occurrence and distribution of antibiotic resistance genes in soils from livestock and poultry farms

Livestock manure is generally dumped directly onto open soil or used to enhance the soil fertility. However, there are growing concerns regarding the impact of these practices on the development and dissemination of antibiotic resistance genes (ARGs) in soil. In this study, we sampled soils treated with manure from 10 large-scale farms (pig, beef cattle, and chicken farms) and those from farmland without manure. The results showed that the abundance of ARGs was more than 2.62 times higher in the soil samples treated with livestock manure than the farmland soil without manure. The abundances of ARGs and intI1 in all samples were in the following order: pig farms > chicken farms > beef cattle farms. tetX, sul1, sul2, and tetG were the dominant ARGs in farm soil. The concentrations of tetracycline antibiotics and sulfonamide antibiotics were 0.15-4.76 mg/kg and 0-2.62 mg/kg, respectively, in the soils treated with manure, which were higher than those in farmland soils without manure. Redundancy analysis (P < 0.05) and network analysis (P < 0.01, R > 0.80) demonstrated that copper, zinc, actinomycetes, and tetracycline antibiotics were the main factors that affected the distribution of ARGs in soils treated with livestock manure.

Role of Bentonite on the Mobility of Antibiotic Resistance Genes, and Microbial Community in Oxytetracycline and Cadmium Contaminated Soil

The effects of bentonite (BT), a commonly used heavy metal deactivator, on the ARGs and microbial communities in soils and lettuce systems contaminated by heavy metals and antibiotics are unclear. A study was conducted to investigate the effect of BT on the mobility of antibiotic resistance genes in oxytetracycline and cadmium contaminated soil. Results showed that the addition of BT reduced the accumulation of OTC and ARGs in the soil and lettuce roots, but increased the abundance of ARGs in lettuce leaves, and increase the risk of human pathogenic bacteria (HPB) transferring to lettuce leaves. Redundancy analysis showed that environmental factors (OTC, H₂O, SOM, and pH) were the dominant factors that influence the distribution of ARGs and intI1. Network analysis showed that Proteobacteria and Bacteroidetes were the major host bacteria which caused changes in ARGs and intI1. There were significant positive correlations between ermX and ermQ, and a large number of HPB. The co-occurrence of intl1 with some ARGs (tetC, tetG, ermQ, sul1, and sul2), may threaten human health due to the dispersion of ARGs via horizontal gene transfer.

Understanding the impact of antibiotic therapies on the respiratory tract resistome: a novel pooled-template metagenomic sequencing strategy

Determining the effects of antimicrobial therapies on airway microbiology at a population-level is essential. Such analysis allows, for example, surveillance of antibiotic-induced changes in pathogen prevalence, the emergence and spread of antibiotic resistance, and the transmission of multi-resistant organisms. However, current analytical strategies for understanding these processes are limited. Culture- and PCR-based assays for specific microbes require the a priori selection of targets, while antibiotic sensitivity testing typically provides no insight into either the molecular basis of resistance, or the carriage of resistance determinants by the wider commensal microbiota. Shotgun metagenomic sequencing provides an alternative approach that allows the microbial composition of clinical samples to be described in detail, including the prevalence of resistance genes and virulence traits. While highly informative, the application of metagenomics to large patient cohorts can be prohibitively expensive. Using sputum samples from a randomised placebo-controlled trial of erythromycin in adults with bronchiectasis, we describe a novel, cost-effective strategy for screening patient cohorts for changes in resistance gene prevalence. By combining metagenomic screening of pooled DNA extracts with validatory quantitative PCR-based analysis of candidate markers in individual samples, we identify population-level changes in the relative abundance of specific macrolide resistance genes. This approach has the potential to provide an important adjunct to current analytical strategies, particularly within the context of antimicrobial clinical trials.

Respiratory infections due to drug-resistant bacteria

Pneumonia is the most common infection that is the leading cause of death. The increasing antimicrobial resistance in major respiratory pathogens such as Streptococcus pneumoniae, Staphylococcus aureus and gram-negative bacteria has severely restricted the treatment options. Respiratory infections caused by multidrug-resistant bacteria are associated with a greater likelihood of inappropriate antimicrobial therapy and poor clinical outcome. Especially, treatment of infections caused by pandrug-resistant gram-negative bacteria is a major challenge. Continuous efforts to control the global spread of drug-resistant bacteria are essential.

High-level telithromycin resistance in a clinical isolate of Streptococcus pneumoniae

A rare clinical isolate of Streptococcus pneumoniae, highly resistant to telithromycin, contained erm(B) with a truncated leader peptide and a mutant ribosomal protein L4. By transformation of susceptible strains, this study shows that high-level telithromycin resistance is conferred by erm(B), wild type or mutant, in combination with a (69)GTG(71)-to-TPS mutation in ribosomal protein L4.

Characterisation of macrolide-non-susceptible Streptococcus pneumoniae colonising children attending day-care centres in Athens, Greece during 2000 and 2003

Nasopharyngeal Streptococcus pneumoniae isolates colonising young children are representative of isolates causing clinical disease. This study determined the frequency of macrolide-non-susceptible pneumococci, as well as their phenotypic and genotypic characteristics, among pneumococci collected during two cross-sectional surveillance studies of the nasopharynx of 2847 children attending day-care centres in the Athens metropolitan area during 2000 and 2003. In total, 227 macrolide-non-susceptible pneumococcal isolates were studied. Increases in macrolide non-susceptibility, from 23% to 30.3% (p <0.05), and in macrolide and penicillin co-resistance, from 3.4% to 48.6% (p <0.001), were identified during the study period. The M resistance phenotype, associated with the presence of the mef(A)/(E) gene, predominated in both surveys, and isolates carrying both mef(A)/(E) and erm(AM) were identified, for the first time in Greece, among the isolates from the 2003 survey. Pulsed-field gel electrophoresis analysis of the isolates from the 2000 survey indicated the spread of a macrolide- and penicillin-resistant clone among day-care centres. The serogroups identified most commonly in the study were 19F, 6A, 6B, 14 and 23F, suggesting that the theoretical protection of the seven-valent conjugate vaccine against macrolide-non-susceptible isolates was c. 85% during both study periods.

Drug-resistant genes and serotypes of pneumococcal strains of community-acquired pneumonia among adults in Japan

BACKGROUND

A high frequency of drug-resistant pneumococci has been reported in Asian countries. Few data on the drug-resistance or serotype of pneumococcal strains responsible for community-acquired pneumonia (CAP), however, are available for the past two decades in Japan.

METHODOLOGY

Susceptibility to antibiotics and the genotype of antibiotic-resistant genes and serotypes of Streptococcus pneumoniae isolates from 114 adult patients with CAP were examined in a nationwide study in Japan between 2001 and 2003.

RESULTS

Most of the cases were non-bacteraemic pneumonia and the case fatality rate was 4.4%. The most frequent genotype of the pbp gene was pbp1a + 2x + 2b (gPRSP; 36.8%) followed by pbp 2x (28.1%) and of the macrolide-resistant gene, it was ermB (50.0%). The most common serotype was 19F (29.1%), followed by serotype 23F (13.2%), 6B (12.3%) and 3 (11.4%). The coverage of serotypes of isolates by a 23-valent pneumococcal polysaccharide vaccine (PPV) would be 82.5% in these patients with CAP. Most of strains with serotypes 19F and 23F were gPRSP. A cluster of serotype 3 strains associated with the pbp 2x and ermB gene was also noted.

CONCLUSION

A high frequency of altered pbp gene mutations or of macrolide-related genes and a high serotype coverage by the 23-valent PPV found in our study of pneumococcal pneumonia facilitates attempts to increase the coverage rate of the 23-valent PPV in adults older than 65 years in Japan.

In-vitro susceptibility and molecular characterisation of macrolide resistance mechanisms among Streptococcus pneumonia isolates in The Netherlands: the DUEL 2 study

In total, 881 presumptive clinical isolates of Streptococcus pneumoniae collected from throughout The Netherlands were analysed to determine their mechanisms of macrolide resistance. Isolates were identified initially by participating laboratories using their own standard identification technique, followed by determination of MICs with Etests. Only 797 isolates were confirmed as pneumococci following bile-solubility tests, lytA PCR and 16S rRNA sequencing. Of these confirmed pneumococci, 59 (7.4%) isolates were macrolide-resistant. Analysis by PCR indicated that 34 (57.6%) isolates harboured only the erm(B) gene and 16 (27.1%) only the mef gene. Three (5.1%) isolates carried both erm(B) and mef, while six (10.2%) isolates were negative for both mechanisms. Of the six negative isolates, three had a mutation in the 23S rRNA gene, and three were negative for all mechanisms tested. No isolates with the erm(A) subclass erm(TR) gene were detected. Among the 19 mef-positive isolates, 14 (73.7%) carried the mef(A) gene, and only five (26.3%) carried the mef(E) gene. No linezolid cross-resistance or multiresistance (resistance to more than two classes of antibiotics) was observed.