The prevalence of pilus islets in Streptococcus pneumoniae isolates from healthy children in Indonesia

Streptococcus pneumoniae produces pili that function as adherence factors to bind to epithelial cells in the human upper respiratory tract. In this study, we investigated the prevalence of pilus islets (PIs) in S. pneumoniae strains carried by healthy children below 5 years of age prior to pneumococcal vaccination in 2012 in Lombok Island, Indonesia. In all, 347 archived S. pneumoniae isolates were screened using polymerase chain reactions for the presence of rrgC and pitB genes representing pilus islet 1 (PI-1) and pilus islet 2 (PI-2), respectively. We found that 40 isolates (11.5 %) contained the PI genes: 5.2% carried both PI-1 and PI-2, and 3.5 and 2.9% carried PI-1 and PI-2, respectively. Furthermore, we found that most of the strains carrying either of the PIs belonged to the vaccine serotypes 19F and 19A and were less susceptible to chloramphenicol and tetracycline.

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Serotypes and antibiotic susceptibility profile of Streptococcus pneumoniae isolated from nasopharynges of children infected with HIV in Jakarta, Indonesia, pre- and post-pneumococcal vaccination

Access Microbiology ◽

10.1099/acmi.0.000215 ◽

2021 ◽

Author(s):

Dina Muktiarti ◽

Miftahuddin Majid Khoeri ◽

Wisnu Tafroji ◽

Lia Waslia ◽

Dodi Safari

Keyword(s):

Antibiotic Susceptibility ◽

Type Species ◽

Pneumococcal Vaccination ◽

Nasopharyngeal Swab ◽

Post Vaccination ◽

Content Type ◽

Link Type ◽

Vaccine Type ◽

Before And After ◽

Type Strains

The aim of this prospective study was to investigate the serotypes and antibiotic susceptibility of S. pneumoniae carried by children infected with HIV before and after vaccination with the seven-valent pneumococcal conjugate vaccine in Jakarta, Indonesia in 2013. We collected nasopharyngeal swab specimens from 52 children pre-vaccination and 6 months post-vaccination. Serotyping was performed by conventional multiplex polymerase chain reaction and Quellung reaction. The antibiotic susceptibility profile was obtained by disc diffusion. We determined that 27 (52%) and 24 (46%) of the 52 children carried S. pneumoniae during pre- and post-vaccination periods, respectively with the majority of the isolates being non-vaccine type strains (85% pre-vaccination and 75% post-vaccination). Serotypes 34, 6C, and 16F (two strains each) were the most commonly identified serotypes at pre-vaccination. Serotypes 23A (three strains) and 19F (two strains) were the most commonly identified serotypes post-vaccination. In general, isolates were most commonly susceptible to chloramphenicol (88%) and clindamycin (88%), followed by erythromycin (84%), trimethoprim-sulphamethoxazole (69%), tetracycline (61%), and penicillin (59%). In conclusion, serotypes of S. pneumoniae isolated from the nasopharynges of children infected with HIV varied and were more likely to be non-vaccine type strains both before and after vaccination.

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Azithromycin resistance mutations in Streptococcus pneumoniae as revealed by a chemogenomic screen

Microbial Genomics ◽

10.1099/mgen.0.000454 ◽

2020 ◽

Vol 6 (11) ◽

Author(s):

Hélène Gingras ◽

Kévin Patron ◽

Philippe Leprohon ◽

Marc Ouellette

Keyword(s):

Streptococcus Pneumoniae ◽

Ribosomal Proteins ◽

Type Species ◽

Chemical Mutagenesis ◽

Resistance Mutations ◽

Content Type ◽

Link Type ◽

Chromosomal Changes ◽

23S Ribosomal Rna ◽

Ribosomal Binding Site

We report on the combination of chemical mutagenesis, azithromycin selection and next-generation sequencing (Mut-Seq) for the identification of small nucleotide variants that decrease the susceptibility of Streptococcus pneumoniae to the macrolide antibiotic azithromycin. Mutations in the 23S ribosomal RNA or in ribosomal proteins can confer resistance to macrolides and these were detected by Mut-Seq. By concentrating on recurrent variants, we could associate mutations in genes implicated in the metabolism of glutamine with decreased azithromycin susceptibility among S. pneumoniae mutants. Glutamine synthetase catalyses the transformation of glutamate and ammonium into glutamine and its chemical inhibition is shown to sensitize S. pneumoniae to antibiotics. A mutation affecting the ribosomal-binding site of a putative ribonuclease J2 is also shown to confer low-level resistance. Mut-Seq has the potential to reveal chromosomal changes enabling high resistance as well as novel events conferring more subtle phenotypes.

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Streptococcus pneumoniae, S. pyogenes and S. agalactiae membrane phospholipid remodelling in response to human serum

Microbiology ◽

10.1099/mic.0.001048 ◽

2021 ◽

Vol 167 (5) ◽

Author(s):

Luke R. Joyce ◽

Ziqiang Guan ◽

Kelli L. Palmer

Keyword(s):

Streptococcus Pneumoniae ◽

Human Serum ◽

Type Species ◽

Cellular Membrane ◽

Defined Medium ◽

Content Type ◽

Link Type ◽

Streptococcal Species ◽

Group A ◽

Group B

Streptococcus pneumoniae , S. pyogenes (Group A Streptococcus ; GAS) and S. agalactiae (Group B Streptococcus ; GBS) are major aetiological agents of diseases in humans. The cellular membrane, a crucial site in host–pathogen interactions, is poorly characterized in streptococci. Moreover, little is known about whether or how environmental conditions influence their lipid compositions. Using normal phase liquid chromatography coupled with electrospray ionization MS, we characterized the phospholipids and glycolipids of S. pneumoniae , GAS and GBS in routine undefined laboratory medium, streptococcal defined medium and, in order to mimic the host environment, defined medium supplemented with human serum. In human serum-supplemented medium, all three streptococcal species synthesize phosphatidylcholine (PC), a zwitterionic phospholipid commonly found in eukaryotes but relatively rare in bacteria. We previously reported that S. pneumoniae utilizes the glycerophosphocholine (GPC) biosynthetic pathway to synthesize PC. Through substrate tracing experiments, we confirm that GAS and GBS scavenge lysoPC, a major metabolite in human serum, thereby using an abbreviated GPC pathway for PC biosynthesis. Furthermore, we found that plasmanyl-PC is uniquely present in the GBS membrane during growth with human serum, suggesting GBS possesses unusual membrane biochemical or biophysical properties. In summary, we report cellular lipid remodelling by the major pathogenic streptococci in response to metabolites present in human serum.

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Co-infection in critically ill patients with COVID-19: an observational cohort study from England

Journal of Medical Microbiology ◽

10.1099/jmm.0.001350 ◽

2021 ◽

Vol 70 (4) ◽

Author(s):

Vadsala Baskaran ◽

Hannah Lawrence ◽

Louise E. Lansbury ◽

Karmel Webb ◽

Shahideh Safavi ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Cohort Study ◽

Streptococcus Pneumoniae ◽

Critically Ill ◽

Type Species ◽

Severe Illness ◽

Gram Negative ◽

Content Type ◽

Link Type ◽

Icu Stay

Introduction. During previous viral pandemics, reported co-infection rates and implicated pathogens have varied. In the 1918 influenza pandemic, a large proportion of severe illness and death was complicated by bacterial co-infection, predominantly Streptococcus pneumoniae and Staphylococcus aureus . Gap statement. A better understanding of the incidence of co-infection in patients with COVID-19 infection and the pathogens involved is necessary for effective antimicrobial stewardship. Aim. To describe the incidence and nature of co-infection in critically ill adults with COVID-19 infection in England. Methodology. A retrospective cohort study of adults with COVID-19 admitted to seven intensive care units (ICUs) in England up to 18 May 2020, was performed. Patients with completed ICU stays were included. The proportion and type of organisms were determined at <48 and >48 h following hospital admission, corresponding to community and hospital-acquired co-infections. Results. Of 254 patients studied (median age 59 years (IQR 49–69); 64.6 % male), 139 clinically significant organisms were identified from 83 (32.7 %) patients. Bacterial co-infections/ co-colonisation were identified within 48 h of admission in 14 (5.5 %) patients; the commonest pathogens were Staphylococcus aureus (four patients) and Streptococcus pneumoniae (two patients). The proportion of pathogens detected increased with duration of ICU stay, consisting largely of Gram-negative bacteria, particularly Klebsiella pneumoniae and Escherichia coli . The co-infection/ co-colonisation rate >48 h after admission was 27/1000 person-days (95 % CI 21.3–34.1). Patients with co-infections/ co-colonisation were more likely to die in ICU (crude OR 1.78,95 % CI 1.03–3.08, P=0.04) compared to those without co-infections/ co-colonisation. Conclusion. We found limited evidence for community-acquired bacterial co-infection in hospitalised adults with COVID-19, but a high rate of Gram-negative infection acquired during ICU stay.

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Population genetic structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in children in Argentina

Microbial Genomics ◽

10.1099/mgen.0.000636 ◽

2021 ◽

Vol 7 (9) ◽

Author(s):

Paula Gagetti ◽

Stephanie W. Lo ◽

Paulina A. Hawkins ◽

Rebecca A. Gladstone ◽

Mabel Regueira ◽

...

Keyword(s):

Streptococcus Pneumoniae ◽

Antimicrobial Resistance ◽

Type Species ◽

Invasive Disease ◽

Multidrug Resistant ◽

Childhood Immunization ◽

Content Type ◽

Sequencing Project ◽

Link Type ◽

Immunization Programme

Invasive disease caused by Streptococcus pneumoniae (IPD) is one of the leading causes of morbidity and mortality in young children worldwide. In Argentina, PCV13 was introduced into the childhood immunization programme nationwide in 2012 and PCV7 was available from 2000, but only in the private market. Since 1993 the National IPD Surveillance Programme, consisting of 150 hospitals, has conducted nationwide pneumococcal surveillance in Argentina in children under 6 years of age, as part of the SIREVA II-OPS network. A total of 1713 pneumococcal isolates characterized by serotype (Quellung) and antimicrobial resistance (agar dilution) to ten antibiotics, belonging to three study periods: pre-PCV7 era 1998–1999 (pre-PCV), before the introduction of PCV13 2010–2011 (PCV7) and after the introduction of PCV13 2012–2013 (PCV13), were available for inclusion. Fifty-four serotypes were identified in the entire collection and serotypes 14, 5 and 1 represented 50 % of the isolates. Resistance to penicillin was 34.9 %, cefotaxime 10.6 %, meropenem 4.9 %, cotrimoxazole 45 %, erythromycin 21.5 %, tetracycline 15.4 % and chloramphenicol 0.4 %. All the isolates were susceptible to levofloxacin, rifampin and vancomycin. Of 1713 isolates, 1061 (61.9 %) were non-susceptible to at least one antibiotic and 235(13.7 %) were multidrug resistant. A subset of 413 isolates was randomly selected and whole-genome sequenced as part of Global Pneumococcal Sequencing Project (GPS). The genome data was used to investigate the population structure of S. pneumoniae defining pneumococcal lineages using Global Pneumococcal Sequence Clusters (GPSCs), sequence types (STs) and clonal complexes (CCs), prevalent serotypes and their associated pneumococcal lineages and genomic inference of antimicrobial resistance. The collection showed a great diversity of strains. Among the 413 isolates, 73 known and 36 new STs were identified belonging to 38 CCs and 25 singletons, grouped into 52 GPSCs. Important changes were observed among vaccine types when pre-PCV and PCV13 periods were compared; a significant decrease in serotypes 14, 6B and 19F and a significant increase in 7F and 3. Among non-PCV13 types, serogroup 24 increased from 0 % in pre-PCV to 3.2 % in the PCV13 period. Our analysis showed that 66.1 % (273/413) of the isolates were predicted to be non-susceptible to at least one antibiotic and 11.9 % (49/413) were multidrug resistant. We found an agreement of 100 % when comparing the serotype determined by Quellung and WGS-based serotyping and 98.4 % of agreement in antimicrobial resistance. Continued surveillance of the pneumococcal population is needed to reveal the dynamics of pneumococcal isolates in Argentina in post-PCV13. This article contains data hosted by Microreact.

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Streptococcus pneumoniae serotypes that frequently colonise the human nasopharynx are common recipients of penicillin-binding protein gene fragments from Streptococcus mitis

Microbial Genomics ◽

10.1099/mgen.0.000622 ◽

2021 ◽

Vol 7 (9) ◽

Author(s):

Akuzike Kalizang'oma ◽

Chrispin Chaguza ◽

Andrea Gori ◽

Charlotte Davison ◽

Sandra Beleza ◽

...

Keyword(s):

Streptococcus Pneumoniae ◽

Type Species ◽

Binding Protein ◽

Pneumococcal Serotypes ◽

Penicillin Binding Protein ◽

Beta Lactam ◽

Streptococcus Mitis ◽

Content Type ◽

Link Type ◽

Close Relatives

Streptococcus pneumoniae is an important global pathogen that causes bacterial pneumonia, sepsis and meningitis. Beta-lactam antibiotics are the first-line treatment for pneumococcal disease, however, their effectiveness is hampered by beta-lactam resistance facilitated by horizontal genetic transfer (HGT) with closely related species. Although interspecies HGT is known to occur among the species of the genus Streptococcus , the rates and effects of HGT between Streptococcus pneumoniae and its close relatives involving the penicillin binding protein (pbp) genes remain poorly understood. Here we applied the fastGEAR tool to investigate interspecies HGT in pbp genes using a global collection of whole-genome sequences of Streptococcus mitis , Streptococcus oralis and S. pneumoniae . With these data, we established that pneumococcal serotypes 6A, 13, 14, 16F, 19A, 19F, 23F and 35B were the highest-ranking serotypes with acquired pbp fragments. S. mitis was a more frequent pneumococcal donor of pbp fragments and a source of higher pbp nucleotide diversity when compared with S. oralis . Pneumococci that acquired pbp fragments were associated with a higher minimum inhibitory concentration (MIC) for penicillin compared with pneumococci without acquired fragments. Together these data indicate that S. mitis contributes to reduced β-lactam susceptibility among commonly carried pneumococcal serotypes that are associated with long carriage duration and high recombination frequencies. As pneumococcal vaccine programmes mature, placing increasing pressure on the pneumococcal population structure, it will be important to monitor the influence of antimicrobial resistance HGT from commensal streptococci such as S. mitis .

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Nasopharyngeal carriage rates and serotype distribution of Streptococcus pneumoniae among school children with acute otitis media in Central Java, Indonesia

Access Microbiology ◽

10.1099/acmi.0.000249 ◽

2021 ◽

Vol 3 (7) ◽

Author(s):

Daniel Joko Wahyono ◽

Mifathuddin Majid Khoeri ◽

Anton Budhi Darmawan ◽

Siwi Pramatama Mars Wijayanti ◽

Aris Mumpuni ◽

...

Keyword(s):

Streptococcus Pneumoniae ◽

Otitis Media ◽

School Children ◽

Type Species ◽

Acute Otitis Media ◽

Nasopharyngeal Carriage ◽

Content Type ◽

Link Type ◽

Central Java ◽

Vaccine Type

Streptococcus pneumoniae is a common bacterial pathogen that causes acute otitis media (AOM) in children. In this study, we investigated nasopharyngeal carriage rates and serotype distributions of S. pneumoniae among school children with AOM in Banyumas Regency, Central Java, Indonesia, from 2018 to 2019. Nasopharyngeal swab specimens and demographic data were collected from 122 children between the ages of 6 and 12. The specimens were cultured for the identification of S. pneumoniae , and serotyping was performed using a sequential multiplex PCR assay. We found that the S. pneumoniae carriage rate was 73 % (89/122) among children with AOM. Serotypes 23A (11 %) and 6A/6B (10 %) were the most common serotypes among the 91 cultured S. pneumoniae strains, followed by 3 (8 %), 14 (7 %), 6C/6D (7 %), 11A/11D (6 %), 15B/15C (4 %) and 35 B (4 %). Moreover, 41 % of the strains could be covered by the 13-valent pneumococcal conjugate vaccine, PCV13. In conclusion, high nasopharyngeal carriage rates of S. pneumoniae were found in school children with AOM, with almost half of the strains being the vaccine-type. This finding provides a baseline for nasopharyngeal carriage of S. pneumoniae in school children with AOM and supports the implementation of pneumococcal conjugate vaccines in Indonesia.

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Control of acetyl phosphate-dependent phosphorylation of the response regulator CiaR by acetate kinase in Streptococcus pneumoniae

Microbiology ◽

10.1099/mic.0.000894 ◽

2020 ◽

Vol 166 (4) ◽

pp. 411-421

Author(s):

Sabrina Kaiser ◽

Lisa Marie Hoppstädter ◽

Kevser Bilici ◽

Kevin Heieck ◽

Reinhold Brückner

Keyword(s):

Streptococcus Pneumoniae ◽

Transcriptional Activation ◽

Type Species ◽

Response Regulator ◽

Acetate Kinase ◽

Acetyl Phosphate ◽

Content Type ◽

Link Type ◽

Cell Extracts

The two-component regulatory system CiaRH of Streptococcus pneumoniae affects a large variety of physiological processes including ß-lactam resistance, competence development, maintenance of cell integrity, bacteriocin production, but also host colonization and virulence. The response regulator CiaR is active under a wide variety of conditions and the cognate CiaH kinase is not always needed to maintain CiaR activity. Using tetracycline-controlled expression of ciaR and variants, acetyl phosphate was identified in vivo as the alternative source of CiaR phosphorylation in the absence of CiaH. Concomitant inactivation of ciaH and the acetate kinase gene ackA led to very high levels of CiaR-mediated promoter activation. Strong transcriptional activation was accompanied by a high phosphorylation status of CiaR as determined by Phos-tag gel electrophoresis of S. pneumoniae cell extracts. Furthermore, AckA acted negatively upon acetyl phosphate-dependent phosphorylation of CiaR. Experiments using the Escherichia coli two-hybrid system based on adenylate cyclase reconstitution indicated binding of AckA to CiaR and therefore direct regulation. Subsequent in vitro CiaR phosphorylation experiments confirmed in vivo observations. Purified AckA was able to inhibit acetyl phosphate-dependent phosphorylation. Inhibition required the presence of ADP. AckA-mediated regulation of CiaR phosphorylation is the first example for a regulatory connection of acetate kinase to a response regulator besides controlling acetyl phosphate levels. It will be interesting to see if this novel regulation applies to other response regulators in S. pneumoniae or even in other organisms.

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

Journal of Medical Microbiology ◽

10.1099/jmm.0.001151 ◽

2020 ◽

Vol 69 (4) ◽

pp. 505-520 ◽

Cited By ~ 1

Author(s):

B. Midouni Ayadi ◽

E. Mehiri ◽

H. Draoui ◽

A. Ghariani ◽

L. Essalah ◽

...

Keyword(s):

Streptococcus Pneumoniae ◽

Type Species ◽

Resistance Mechanisms ◽

Macrolide Resistance ◽

23S Rrna ◽

Serotype Distribution ◽

Antibiotic Resistant ◽

Content Type ◽

Link Type ◽

Resistant Strains

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, Portugal19F ST177 and Spain9V 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.

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Evaluating the use of a 22-pathogen TaqMan array card for rapid diagnosis of respiratory pathogens in intensive care

Journal of Medical Microbiology ◽

10.1099/jmm.0.001218 ◽

2020 ◽

Vol 69 (7) ◽

pp. 971-978

Author(s):

Nick K. Jones ◽

Andrew Conway Morris ◽

Martin D. Curran ◽

Surendra Parmar ◽

Olajumoke Sule ◽

...

Keyword(s):

Intensive Care ◽

Type Species ◽

Pathogen Detection ◽

Laboratory Diagnosis ◽

Fungal Culture ◽

Respiratory Pathogens ◽

Content Type ◽

Chain Reactions ◽

Link Type ◽

Taqman Array

Introduction. Pneumonia is highly prevalent in intensive care units (ICUs), with high associated mortality. Empirical treatment prioritizes breadth of coverage while awaiting laboratory diagnosis, often at the expense of antimicrobial stewardship. Microarrays use multiple parallel polymerase chain reactions to enable a rapid syndromic approach to laboratory diagnosis. Aim. To evaluate the clinical and laboratory implications of introducing a bespoke 22-pathogen TaqMan Array Card (TAC) for rapid pathogen detection in deep respiratory samples from adult ICUs. Methodology. TAC results from all ICU patients prospectively tested over a 9-month period at Cambridge’s Clinical Microbiology and Public Health Laboratory were compared to those of corresponding conventional microbiological assays (culture-, PCR- or serology-based) in terms of result agreement and time-to-result availability. Clinical impact was assessed by retrospective review of medical records. Results. Seventy-one patients were included [45 (63 %) male, median age 59). Overall result agreement was 94 %, with TAC detecting more pathogens than conventional methods. TAC detected Streptococcus pneumoniae more readily than culture (7 vs 0 cases; P=0.02). TAC did not detect Aspergillus spp. in eight culture- or galactomannan-positive cases. The median turnaround time (1 day) was significantly shorter than that of bacterial/fungal culture, Pneumocystis jirovecii PCR and galactomannan testing (each 3 days; P<0.001), atypical bacteria serology (13 days; P<0.001) and Mycobacterium tuberculosis culture (46 days; P<0.001). Earlier result availability prompted discontinuation of unnecessary antimicrobials in 15/71 (21 %) cases, but had no bearing on patient isolation/deisolation. Conclusion. TAC provided greater overall yield of pathogen detection and faster turnaround times, permitting earlier discontinuation of unnecessary antimicrobials.

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