Phenotypic and genotypic characterization of Streptococcus pneumoniae resistant to macrolide in Casablanca, Morocco

Genetic determinants of macrolide and tetracycline resistance in penicillin non-susceptible Streptococcus pneumoniae isolates from people living with HIV in Dar es Salaam, Tanzania

BACKGROUND

Over one million yearly deaths are attributable to Streptococcus pneumoniae and people living with HIV are particularly vulnerable. Emerging penicillin non-susceptible Streptococcus pneumoniae (PNSP) challenges therapy of pneumococcal disease. The aim of this study was to determine the mechanisms of antibiotic resistance among PNSP isolates by next generation sequencing.

METHODS

We assessed 26 PNSP isolates obtained from the nasopharynx from 537 healthy human immunodeficiency virus (HIV) infected adults in Dar es Salaam, Tanzania, participating in the randomized clinical trial CoTrimResist (ClinicalTrials.gov identifier: NCT03087890, registered on 23rd March, 2017). Next generation whole genome sequencing on the Illumina platform was used to identify mechanisms of resistance to antibiotics among PNSP.

RESULTS

Fifty percent (13/26) of PNSP were resistant to erythromycin, of these 54% (7/13) and 46% (6/13) had MLS_B phenotype and M phenotype respectively. All erythromycin resistant PNSP carried macrolide resistance genes; six isolates had mef(A)-msr(D), five isolates had both erm(B) and mef(A)-msr(D) while two isolates carried erm(B) alone. Isolates harboring the erm(B) gene had increased MIC (> 256 µg/mL) towards macrolides, compared to isolates without erm(B) gene (MIC 4-12 µg/mL) p < 0.001. Using the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines, the prevalence of azithromycin resistance was overestimated compared to genetic correlates. Tetracycline resistance was detected in 13/26 (50%) of PNSP and all the 13 isolates harbored the tet(M) gene. All isolates carrying the tet(M) gene and 11/13 isolates with macrolide resistance genes were associated with the mobile genetic element Tn6009 transposon family. Of 26 PNSP isolates, serotype 3 was the most common (6/26), and sequence type ST271 accounted for 15% (4/26). Serotypes 3 and 19 displayed high-level macrolide resistance and frequently carried both macrolide and tetracycline resistance genes.

CONCLUSION

The erm(B) and mef(A)-msr(D) were common genes conferring resistance to MLS_B in PNSP. Resistance to tetracycline was conferred by the tet(M) gene. Resistance genes were associated with the Tn6009 transposon.

Antimicrobial and the Resistances in the Environment: Ecological and Health Risks, Influencing Factors, and Mitigation Strategies

Antimicrobial contamination and antimicrobial resistance have become global environmental and health problems. A large number of antimicrobials are used in medical and animal husbandry, leading to the continuous release of residual antimicrobials into the environment. It not only causes ecological harm, but also promotes the occurrence and spread of antimicrobial resistance. The role of environmental factors in antimicrobial contamination and the spread of antimicrobial resistance is often overlooked. There are a large number of antimicrobial-resistant bacteria and antimicrobial resistance genes in human beings, which increases the likelihood that pathogenic bacteria acquire resistance, and also adds opportunities for human contact with antimicrobial-resistant pathogens. In this paper, we review the fate of antimicrobials and antimicrobial resistance in the environment, including the occurrence, spread, and impact on ecological and human health. More importantly, this review emphasizes a number of environmental factors that can exacerbate antimicrobial contamination and the spread of antimicrobial resistance. In the future, the timely removal of antimicrobials and antimicrobial resistance genes in the environment will be more effective in alleviating antimicrobial contamination and antimicrobial resistance.

An Overview of Macrolide Resistance in Streptococci: Prevalence, Mobile Elements and Dynamics

Streptococcal infections are usually treated with beta-lactam antibiotics, but, in case of allergic patients or reduced antibiotic susceptibility, macrolides and fluoroquinolones are the main alternatives. This work focuses on studying macrolide resistance rates, genetic associated determinants and antibiotic consumption data in Spain, Europe and also on a global scale. Macrolide resistance (MR) determinants, such as ribosomal methylases (erm(B), erm(TR), erm(T)) or active antibiotic efflux pumps and ribosomal protectors (mef(A/E)-mrs(D)), are differently distributed worldwide and associated with different clonal lineages and mobile genetic elements. MR rates vary together depending on clonal dynamics and on antibiotic consumption applying selective pressure. Among Streptococcus, higher MR rates are found in the viridans group, Streptococcus pneumoniae and Streptococcus agalactiae, and lower MR rates are described in Streptococcus pyogenes. When considering different geographic areas, higher resistance rates are usually found in East-Asian countries and milder or lower in the US and Europe. Unfortunately, the availability of data varies also between countries; it is scarce in low- and middle- income countries from Africa and South America. Thus, surveillance studies of macrolide resistance rates and the resistance determinants involved should be promoted to complete global knowledge among macrolide resistance dynamics.

Antimicrobial resistance among GLASS pathogens in Morocco: an epidemiological scoping review

BACKGROUND

Monitoring of antimicrobial resistance (AMR) is of great importance due to the frequency of strains becoming increasingly resistant to antibiotics. This review, using a public health focused approach, which aims to understand and describe the current status of AMR in Morocco in relation to WHO priority pathogens and treatment guidelines.

METHODS

PubMed, ScienceDirect and Google Scholar Databases and grey literature are searched published articles on antimicrobial drug resistance data for GLASS priority pathogens isolated from Morocco between January 2011 and December 2021. Articles are screened using strict inclusion/exclusion criteria. AMR data is extracted with medians and IQR of resistance rates.

RESULTS

Forty-nine articles are included in the final analysis. The most reported bacterium is Escherichia coli with median resistance rates of 90.9%, 64.0%, and 56.0%, for amoxicillin, amoxicillin-clavulanic acid, and co-trimoxazole, respectively. Colistin had the lowest median resistance with 0.1%. A median resistance of 63.0% is calculated for amoxicillin-clavulanic acid in Klebsiella pneumonia. Imipenem resistance with a median of 74.5% is reported for Acinetobacter baumannii. AMR data for Streptococcus pneumonie does not exceed 50.0% as a median.

CONCLUSIONS

Whilst resistance rates are high for most of GLASS pathogens, there are deficient data to draw vigorous conclusions about the current status AMR in Morocco. The recently join to the GLASS system surveillance will begin to address this data gap.

Characterization of Pneumococcal Colonization Dynamics and Antimicrobial Resistance Using Shotgun Metagenomic Sequencing in Intensively Sampled South African Infants

Background: There remains a significant proportion of deaths due to pneumococcal pneumonia in infants from low- and middle-income countries despite the marginal global declines recorded in the past decade. Monitoring changes in pneumococcal carriage is key to understanding vaccination-induced shifts in the ecology of carriage, patterns of antimicrobial resistance, and impact on health. We longitudinally investigated pneumococcal carriage dynamics in PCV-13 vaccinated infants by collecting nasopharyngeal (NP) samples at 2-weekly intervals from birth through the first year of life from 137 infants. As a proof of concept, 196 NP samples were retrieved from a subset of 23 infants to explore strain-level pneumococcal colonization patterns and associated antimicrobial-resistance determinants. These were selected on the basis of changes in serotype and antibiogram over time. NP samples underwent short-term enrichment for streptococci prior to total nucleic acid extraction and whole metagenome shotgun sequencing (WMGS). Reads were assembled and aligned to pneumococcal reference genomes for the extraction of pneumococcal and non-pneumococcal bacterial reads. Pneumococcal contigs were aligned to the Antibiotic Resistance Gene-ANNOTation database of acquired AMR genes. In silico pneumococcal capsular and multilocus sequence typing were performed.

Results: Of the 196 samples sequenced, 174 had corresponding positive cultures for pneumococci, of which, 152 were assigned an in silico serotype. Metagenomic sequencing detected a single pneumococcal serotype in 85% (129/152), and co-colonization in 15% (23/152) of the samples. Twenty-two different pneumococcal serotypes were identified, with 15B/15C and 16F being the most common non-PCV13 serotypes, while 23F and 19A were the most common PCV13 serotypes. Twenty-six different sequence types (STs), including four novel STs were identified in silico. Mutations in the folA and folP genes, associated with cotrimoxazole resistance, were detected in 89% (87/98) of cotrimoxazole-non-susceptible pneumococci, as well as in the pbp1a and pbp2x genes, in penicillin non-susceptible ST7052^15B/15C isolates.

Conclusions: Metagenomic sequencing of NP samples is a valuable culture-independent technique for a detailed evaluation of the pneumococcal component and resistome of the NP microbiome. This method allowed for the detection of novel STs, as well as co-colonization, with a predominance of non-PCV13 serotypes in this cohort. Forty-eight resistance genes, as well as mutations associated with resistance were detected, but the correlation with phenotypic non-susceptibility was lower than expected.

Analysis of multidrug resistance in Streptococcus suis ATCC 700794 under tylosin stress

Streptococcus suis is an important zoonotic pathogen. The massive use of tylosin and other antibiotics in swine production has led to the emergence of resistant phenotypes of S. suis. However, there are no adequate measures available to address the problem of bacterial resistance. This study involved the use of 1/4 MIC (0.125 µg/mL) of tylosin to investigate resistance-related proteins by S. suis ATCC 700794. Our results showed that 171 proteins were differentially expressed in S. suis tested with 1/4 MIC (0.125 µg/mL) of tylosin using iTRAQ-based quantitative proteomic methods. TCS, heat shock protein and elongation factors were differentially expressed at 1/4 MIC (0.125 µg/mL) of tylosin compared to non treated, control cells. Using quantitative RT-PCR analysis, we verified the relationship between the differentially expressed proteins in S. suis with different MIC values. The data showed that expression profile for elongation factor G (fusA), elongation factor Ts (tsf), elongation factor Tu (tuf), putative histidine kinase of the competence regulon, ComD (comD), putative competence-damage inducible protein (cinA) and protein GrpE (grpE), observed in tylosin-resistant S. suis, correlated with that of S. suis ATCC 700794 at 1/4 MIC (0.125 µg/mL). The MIC of tylosin-resistant showed high-level resistance in terramycin, chlortetracycline, ofloxacin and enrofloxacin. Our findings demonstrated the importance of elongation factors, TCS and heat shock protein during development of tylosin resistance in S. suis. Thus, our study will provide insight into new drug targets and help reduce bacterial multidrug resistance through development of corresponding inhibitors.

Phenotypic and molecular characterization of macrolide resistance mechanisms among Streptococcus pneumoniae isolated in Tunisia

Introduction. Streptococcus pneumoniae is responsible for many community infections, with the main ones being pneumonia and meningitis. Pneumococcus has developed increased resistance to multiple classes of antibiotics. The evolution of antibiotic resistance in pneumococcus was influenced by changes in serotype distribution under vaccine selection pressure.Aim. The aim of this study was to determine the genes involved in macrolide resistance, the antimicrobial susceptibility, the serotype distribution and the spread of international antibiotic-resistant clones among clinical isolates of S. pneumoniae.Methodology. We investigated 86 erythromycin-resistant S. pneumoniae strains isolated from respiratory (n=74) or non-respiratory (n=12) samples in Tunisia. Antimicrobial susceptibility was tested using the disk diffusion method. Macrolide-resistant strains were analysed by polymerase chain reaction (PCR) for ermA, ermB, mefA and msrD. We also investigated the macrolide resistance mechanisms in eight isolates (9.3%) by sequencing the L4 and L22 riboprotein-coding genes, plus relevant segments of the three 23S rRNA genes. Capsular serotypes were detected by multiplex PCR. Sequence types (STs) were explored using multilocus sequence typing (MLST).Results. Among the 86 studied strains, 70 (81.4 %) were resistant to penicillin G. The prevalent serotypes were 19F, 14, 19A and 23F. We observed that the cMLSB phenotype (66/86, 76.7%) was the most common in these pneumococci. In addition, ermB was the most frequent resistance gene. No mutation in ribosomal protein L22 or L4 or 23S rRNA was detected. Overall, 44 STs were identified in this study, including 16 that were described for the first time. Resistance to lincomycin, tetracycline and trimethoprim/sulfamethoxazole was observed in 55 (64 %), 34 (39.5 %) and 31 (36 %) isolates, respectively. Furthermore, an increase in fluoroquinolone use in particular may lead to the emergence of levofloxacin-resistant strains. Multidrug resistance was observed in 83 isolates (96.5%). Three global antibiotic-resistant clones were identified: Denmark¹⁴ ST230, Portugal^19F ST177 and Spain^9V ST156.Conclusion. This study shows that macrolide resistance among S. pneumoniae isolated in Tunisia is mainly related to target site modification. Our observations demonstrate a high degree of genetic diversity and capsular types among strains resistant to macrolides.

Antimicrobial Resistance Among Streptococcus pneumoniae

Antibiotic resistance in Streptococcus pneumoniae (pneumococcus), the main pathogen responsible for community-acquired pneumonia (CAP), meningitis, bacteremia, and otitis media, is a major concern for clinicians. This pathogen is associated with high rates of morbidity and mortality, especially among children under 2 years old, immunocompromised persons, and the elderly population. The major anti-pneumococcus agents are β-lactams and macrolides, with fluoroquinolones ranking third. The emergence of antibiotic-resistant pneumococcus due to overuse of antibiotics is a global concern. While the discovery of novel classes of antibiotics for the pneumococcus is at a standstill, significant progress in reducing the problem of resistance is associated with antibacterial vaccines. Nevertheless, the World Health Organization recently considered drug-resistant S. pneumoniae as ranking among the 12 bacteria, for which there is an urgent need for new treatments. A challenge is to slow the evolution of new strains that are resistant to the vaccines.

Molecular characterization of penicillin non-susceptible Streptococcus pneumoniae isolated before and after pneumococcal conjugate vaccine implementation in Casablanca, Morocco

Background

Streptococcus pneumoniae is a major cause of morbidity and mortality worldwide, especially among children and the elderly. The ability to effectively treat pneumococcal infection has been compromised due to the acquisition of antibiotic resistance, particularly to β-lactam drugs. This study aimed to describe the prevalence and molecular evolution of penicillin non-susceptible S. pneumoniae (PNSP) isolated from invasive diseases before and after pneumococcal conjugate vaccine implementation in Casablanca, Morocco.

Methods

Isolates were obtained from the Microbiology Laboratory of Ibn Rochd University Hospital Centre of Casablanca. Serogrouping was done by Pneumotest Kit and serotyping by the Quellung capsular swelling. Antibiotic susceptibility pattern was determined by disk diffusion and E-test methods. The PNSP were analyzed by pulsed-field gel electrophoresis (PFGE) and by genotyping of pbp1a, pbp2b, and pbp2x genes.

Results

A total of 361 S. pneumoniae isolates were collected from 2007 to 2014. Of these isolates, 58.7% were obtained before vaccination (2007–2010) and 41.3% after vaccination (2011–2014). Of the 361 isolates, 80 were PNSP (22.2%). Generally, the proportion of PNSP between pre- and post-vaccination periods were 31 and 13% (p = 0.009), respectively. The proportion of PNSP isolated from pediatric and adult (age > 14 years) patients decreased from 34.5 to 22.9% (p = 0.1) and from 17.7 to 10.2% (p = 0.1) before and after vaccine implementation, respectively. The leading serotypes of PNSP were 14 (33 vs. 57%) and 19A (18 vs. 14%) before and after vaccination among children. For adults, serotypes 19A (53%) and 23F (24%) were the dominant serotypes in the pre-vaccination period, while serotype 14 (22%) was the most prevalent after vaccination. There were 21 pbp genotypes in the pre-vaccination period vs. 12 for post-vaccination period. PFGE clustering showed six clusters of PNSP grouped into three clusters specific to pre-vaccination period (clusters I, II and III), two clusters specific to post-period (clusters V and VI) and a cluster (IV) that contained clones belonging to the two periods of vaccination.

Conclusion

Our observations demonstrate a high degree of genetic diversity among PNSP. Genetic clustering among PNSP strains showed that they spread mainly by a restricted number of PNSP clones with vaccine serotypes. PFGE clustering combined with pbp genotyping revealed that vaccination can change the population structure of PNSP.

Macrolide Resistance in Streptococcus pneumoniae

Streptococcus pneumoniae is a common commensal and an opportunistic pathogen. Suspected pneumococcal upper respiratory infections and pneumonia are often treated with macrolide antibiotics. Macrolides are bacteriostatic antibiotics and inhibit protein synthesis by binding to the 50S ribosomal subunit. The widespread use of macrolides is associated with increased macrolide resistance in S. pneumoniae, and the treatment of pneumococcal infections with macrolides may be associated with clinical failures. In S. pneumoniae, macrolide resistance is due to ribosomal dimethylation by an enzyme encoded by erm(B), efflux by a two-component efflux pump encoded by mef (E)/mel(msr(D)) and, less commonly, mutations of the ribosomal target site of macrolides. A wide array of genetic elements have emerged that facilitate macrolide resistance in S. pneumoniae; for example erm(B) is found on Tn917, while the mef (E)/mel operon is carried on the 5.4- or 5.5-kb Mega element. The macrolide resistance determinants, erm(B) and mef (E)/mel, are also found on large composite Tn916-like elements most notably Tn6002, Tn2009, and Tn2010. Introductions of 7-valent and 13-valent pneumococcal conjugate vaccines (PCV-7 and PCV-13) have decreased the incidence of macrolide-resistant invasive pneumococcal disease, but serotype replacement and emergence of macrolide resistance remain an important concern.