High prevalence of multi-drug resistant Streptococcus pneumoniae among healthy children in Thailand

Integrated genomic analysis of antibiotic resistance and virulence determinants in invasive strains of Streptococcus pneumoniae

Introduction

Streptococcus pneumoniae is an important human pathogen that may cause severe invasive pneumococcal diseases (IPDs) in young children and the elderly. A comprehensive comparative whole-genome analysis of invasive and non-invasive serotype strains offers great insights that are applicable to vaccine development and disease control.

Methods

In this study, 58 invasive (strains isolated from sterile sites) and 71 non-invasive (serotypes that have not been identified as invasive in our study) pneumococcal isolates were identified among the 756 pneumococcal isolates obtained from seven hospitals in Zhejiang, China (2010-2022). Serotyping, antimicrobial resistance tests, and genomic analyses were conducted to characterize these strains.

Results and discussion

The three most invasive serotypes were 23F, 14, and 6B. The invasive pneumococcal isolates' respective resistance rates against penicillin, ceftriaxone, tetracycline, and erythromycin were 34.5%, 15.5%, 98.3%, and 94.7%. Whole-genome sequencing indicated that the predominant invasive clonal complexes were CC271, CC876, and CC81. The high rate of penicillin non-susceptible Streptococcus pneumoniae (PNSP) is related to the clonal distribution of resistance-conferring penicillin-binding proteins (PBP). Interestingly, we found a negative correlation between invasiveness and resistance in the invasive pneumococcal serotype strains, which might be due to the proclivity of certain serotypes to retain their β-lactam resistance. Moreover, the mutually exclusive nature of zmpC and rrgC+srtBCD suggests their intricate and potentially redundant roles in promoting the development of IPD. These findings reveal significant implications for pneumococcal vaccine development in China, potentially informing treatment strategies and measures to mitigate disease transmission.

Prevalence, Antimicrobial Drug Resistance and Associated Risk Factors of Streptococcus Pneumoniae Bacteria Infection Among Under-Five Children With Acute Lower Respiratory Tract Infection Attending Sheik Hassan Yebere Referral Hospital, Jig-Jiga, Ethiopia

Background

Pneumonia is inflammation of the lung. The Streptococcus pneumoniae (S. pneumoniae) is commensal in the upper airway and can cause infection to under-five children. The bacteria is gram-positive diplococci, catalase negative, and optochin sensitive. The bacteria is the leading cause of bacterial pneumonia among under-five children. No similar data is reported from the current study area.

Objective

To determine prevalence, antimicrobial drug resistance and associated factors of S. pneumoniae infection among under-five children with acute lower respiratory tract infection attending Sheck Hassan Yebere Referral Hospital from March 1 to April 30, 2021 Jig-Jiga, Ethiopia.

Methods

A cross-sectional study was conducted among 374 study participants selected by convenience sampling method. A structured questionnaire was used to collect child data. Nasopharyngeal/oropharyngeal swabs were collected and diagnosed to isolate S. pneumoniae by using culture then identified by biochemical examination. Later antimicrobial drug resistance testing was performed by Kirby-Bauer disk diffusion method. All data were entered on epi-data 3.1 then exported to SPSS version 22 to calculate analysis. Statistically significant value was found by calculating an adjusted odds ratio with p-value ≤ 0.05 in a multivariate logistic regression model.

Results

Among 374 under-five children, 180 (48.1%) were males and 109 (29.2%) were from low income families. The overall prevalence of S. pneumoniae infection in the study was 18% (95% CI 14.4-22.2). No window (AOR=2.8 CI 1.1-7.6), no/non-exclusive breast-feeding (AOR= 2.1 CI 1.1-4.1), and previous URTI (AOR= 3.2 CI 1.7-6.1) were significantly associated with S. pneumoniae infection. The isolated organism showed drug resistance for Cotrimoxazole (35%), and Tetracycline (34%).

Conclusion

The prevalence and antimicrobial resistance in this study were comparatively high. No window, non-exclusive breast-feeding and previous URTI were associated with S. pneumoniae infection. The isolated S. pneumoniae showed high drug resistance to cotrimoxazole and tetracycline.

Antibiotic Resistance of Streptococcus pneumoniae in the Nasopharynx of Healthy Children Less than Five Years Old after the Generalization of Pneumococcal Vaccination in Marrakesh, Morocco

Streptococcus pneumoniae (S. pneumoniae) remains one of the most important pathogens causing childhood infections. The spread of antibiotic-resistant bacteria is a leading cause of treatment failure in children. The purpose of this investigation is to report the antibiotic and multidrug resistance (MDR) of S. pneumoniae strains isolated from healthy children throughout the years 2020–2022. Antimicrobial susceptibility testing of S. pneumoniae strains in selected antimicrobials was performed using disk diffusion and E-test methods on bloodMueller–Hinton agar. The antimicrobials tested included oxacillin, amoxicillin, ceftriaxone, norfloxacin, gentamicin, vancomycin, erythromycin, clindamycin, pristinamycin, tetracycline, chloramphenicol, and trimethoprim-sulfamethoxazole. A total of 201 S. pneumoniae strains were isolated from the nasopharynx of healthy children in Marrakesh, Morocco. The highest rate of resistance of S. pneumoniae was found in penicillin (57.2%), followed by tetracycline (20.9%), and erythromycin (17.9%). The rates of resistance to clindamycin, trimethoprim-sulfamethoxazole, and chloramphenicol were 14.9%, 4%, and 1.5%, respectively. All isolates were susceptible to norfloxacin, gentamicin, vancomycin, and pristinamycin. Approximately 17% of all S. pneumoniae strains were resistant to at least three different antibiotic families. This study showed a low rate of antibiotics resistance among nasopharyngeal S. pneumoniae strains, and it is thus essential to monitor S. pneumoniae susceptibility in healthy children.

High Prevalence of Asymptomatic Nasopharyngeal Carriage Rate and Multidrug Resistance Pattern of Streptococcus pneumoniae Among Pre-School Children in North Showa Ethiopia

Background

Streptococcus pneumoniae infection is still the world’s most serious public health problem among children under the age of five. Nasopharyngeal carriage rate of Streptococcus pneumoniae has been identified as an important risk factor for the acquisition of community acquired respiratory tract infection. To date, little is known about the nasopharyngeal infection and antimicrobial susceptibility pattern of Streptococcus pneumoniae among preschool children in Ethiopia.

Objective

The aim of this study was to assess the prevalence of nasopharyngeal carriage and antimicrobial susceptibility pattern of Streptococcus pneumoniae among preschool children.

Methods

A cross-sectional study was conducted from September 2021 to April 2022. A total of 418 preschool children were enrolled using a multistage sampling technique. Nasopharyngeal swab was collected and transported to Medical Microbiology Laboratory at Debre Berhan comprehensive specialized hospital using skim-milk tryptone glucose glycerol transport media. The swab was inoculated on blood agar plates supplemented with 5µg/mL gentamycin and incubated at 37°C for 24–48 hours under 5% CO2 using a candle jar. Identification of Streptococcus pneumoniae was performed using Gram stain, catalase test, optochin test and bile solubility test. Antimicrobial sensitivity tests were done using a modified Kirby-Bauer disk diffusion method. Data were entered into the statistical package Epi data 4.0.0.6 and transferred to and analyzed using SPSS software version-23. A P-value ≤0.05 with 95% CI was considered to be statistically significant.

Results

The prevalence of Streptococcus pneumoniae nasopharyngeal carriage was 29.9% (125/418). The overall rate of multidrug resistance was 86 (68.8%), with tetracycline (68.8%) and TMP-SMX (68%). Among risk factors, young age and passive smoking were associated with pneumococcal carriage.

Conclusion

The present study revealed a substantially lower prevalence of Streptococcus pneumoniae nasopharyngeal carriage. High antimicrobial resistance was observed for most antimicrobial drugs tested. Younger age groups and passive smokers were at risk of Streptococcus pneumoniae nasopharyngeal carriage.

Molecular Characterization of Predominant Serotypes, Drug Resistance, and Virulence Genes of Streptococcus pneumoniae Isolates From East China

Streptococcus pneumoniae is a common diplococcus pathogen found worldwide. The characterization of predominant serotypes, drug resistance, and virulence genes of S. pneumoniae isolates prevailing in different areas and countries is clinically important for choice of antibiotics and improvement of vaccines. In this study, pneumonia (78.7%) and meningitis (37.0%) were the predominant diseases observed in the 282 (children) and 27 (adults) S. pneumoniae-infected patients (p < 0.05) from seven hospitals in different areas of East China. Of the 309 pneumococcal isolates, 90.3% were classified by PCR into 15 serotypes, with serotypes 19F (27.2%) and the 6A/B (19.1%) being most predominant (p < 0.05). Importantly, serotypes 15A and 15B/C combined for a total of 10.4% of the isolates, but these serotypes are not included in the 13-valent pneumococcal capsule conjugate vaccine used in China. Antimicrobial susceptibility analysis by the E-test showed that >95% of the 309 pneumococcal isolates were susceptible to moxifloxacin and levofloxacin, as well as 18.4, 85.8, and 81.6% of the isolates displayed susceptibility to penicillin, cefotaxime, and imipenem, respectively. A significant correlation between the prevalence of predominant serotypes and their penicillin resistance was observed (p < 0.05). In particular, >95% of all the pneumococcal isolates showed resistance to erythromycin and azithromycin. Of the nine detected virulence genes, the lytA, ply, hysA, and nanA were the most common with 95–100% positive rates in the 309 pneumococcal isolates, while the pavA and psaA genes displayed a significant correlation with pneumococcal bacteremia and meningitis (p < 0.05). Overall, our data suggested that the predominant serotypes, drug resistance, and virulence genes of the S. pneumoniae isolates prevailing in East China are distinct from those observed in other areas of China and adjacent countries.

Rapid, Simple, and Highly Specific Detection of Streptococcus pneumoniae With Visualized Recombinase Polymerase Amplification

Streptococcus pneumoniae is a major pathogen that causes microbiological illness in humans. The introduction of polyvalent vaccines has resulted in a significant decrease in pneumococcal-related mortality. However, pneumococcal infections continue to be a leading cause of death in children under the age of 5 and adults over the age of 65 worldwide. A speedy and highly sensitive diagnostic tool is necessary for routine adoption to adequately manage patients and control the spread of infection. In this study, we investigated a new nucleic acid amplification technique, isothermal recombinase polymerase amplification (RPA), which amplifies DNA at 37°C under isothermal conditions with high specificity, efficiency, and rapidity. Using the autolysin gene lytA as the molecular diagnostic target, an RPA primer-probe combination was designed and optimized for the detection of S. pneumoniae. This RPA reaction produced amplification products labeled with specific chemical markers, to be detected with gold-nanoparticle-based lateral flow strips (LFS), reducing the reliance on equipment and trained personnel. The high specificity of the RPA-LFS technique was demonstrated with the specific detection of 22 strains of S. pneumoniae but not 25 closely related pathogenic bacteria. The assay showed good sensitivity, and detected S. pneumoniae down to 3.32 colony-forming units/μL. When used on clinical samples, the assay provided accurate and consistent results compared with PCR. The compliance with the culture-biochemistry method was 98.18% and the kappa index was 0.977. These results reveal that the RPA–LFS test significantly improved S. pneumoniae identification, particularly in resource-limited areas.

Comparison of pneumococcal colonization density among healthy children and children with respiratory symptoms using real time PCR (RT-PCR)

Background

Nasopharyngeal colonization is considered a necessary step in the initiation of pneumococcal diseases. Real time PCR (RT-PCR) is an alternative approach for the identification and quantification of pneumococci directly from samples.

Objectives

To compare pneumococcal detection rates using culture-based method versus RT-PCR direct detection and to quantify pneumococcal colonization in two study cohorts (healthy children and hospitalized children with respiratory symptoms) using quantitation through RT-PCR.

Methodology

A total of 101 nasopharyngeal swabs (NPS) from healthy children and 183 NPSs from hospitalized children with respiratory symptoms were included in the study. None of the children were vaccinated. All children were between 2 months to 2 years. In parallel to routine culture and identification, a RT-PCR assay targeting the lytA gene was done.

Results

Considering all 284 samples tested, colonization rate by conventional culture was 41.2% (n = 117) while positive colonization using RT-PCR was 43.7% (n = 124). The colonization rate detected by RT-PCR in the healthy cohort was 33.7% (n = 34) and it was 49.2% (n = 90) in the hospitalized cohort. It was 37.6% (n = 38) and 43.2% (n = 79) for the two cohorts by culture. The mean Cq value for the healthy cohort is 29.61 (SD 2.85) and 28.93 (SD 3.62) for the hospitalized cohort.

With the standard curve obtained from amplifying a dilution series of control DNA, the mean amount of genomic DNA copy numbers detected in children with respiratory symptoms was log10 7.49 (SD 1.07) while it was log10 7.30 (SD 0.23) in healthy children and the difference was not statistically significant.

Conclusions

The overall colonization rate was higher when detected using RT-PCR compared to culture. However, it was lower in the healthy group when detected with RT-PCR compared to culture. Even though there was a higher detection of pneumococcal colonization density in children with respiratory symptoms, this was not significantly higher unlike many previous studies. Therefore, the use of RT-PCR to detect pneumococcal colonization needs further evaluation with careful analysis of interpretation and confounders.

Prevalence and risk factors associated with multi-drug resistant organisms (MDRO) carriage among pediatric patients at the time of admission in a tertiary care hospital of a developing country. A cross-sectional study

Background

The rise of Multidrug-resistant organisms (MDROs) poses a considerable burden on the healthcare systems, particularly in low-middle income countries like Pakistan. There is a scarcity of data on the carriage of MDRO particularly in the pediatrics population therefore, we aimed to determine MDRO carriage in pediatric patients at the time of admission to a tertiary care hospital in Karachi, Pakistan, and to identify the risk factors associated with it.

Methods

A cross-sectional study conducted at the pediatric department of Aga Khan University Hospital (AKUH) from May to September 2019 on 347 children aged 1–18 years. For identification of MDRO (i.e., Extended Spectrum Beta-Lactamase (ESBL) producers, Carbapenem Resistant Enterobacteriaceae (CRE), Vancomycin Resistant Enterococci (VRE), Methicillin Resistant Staphylococcus aureus (MRSA), Multidrug-resistant (MDR) Acinetobacter species and MDR Pseudomonas aeruginosa), nasal swabs and rectal swabs or stool samples were cultured on specific media within 72 h of hospitalization. Data was collected on a predesigned structured questionnaire on demographics, prior use of antibiotics for > 48 h in the last 6 months, history of vaccination in last 6 months, exposure to health care facility regardless of the time of exposure, ICU stay for > 72 h, and about the prior use of medical devices (urinary catheter, central venous lines etc.) in last 1 year. Statistical analysis was performed by Standard statistical software.

Results

Out of 347 participants, 237 (68.3%) were found to be MDRO carriers. Forty nine nasal swabs from 346 children (14.2%) showed growth of MRSA. The majority of the stool/rectal swabs (n = 222 of 322; 69%) collected were positive for MDRO. The most isolated species were ESBL Escherichia coli 174/222 (78.3%) followed by ESBL Enterobacter species 37/222 (16.7%) and ESBL Klebsiella pneumoniae 35/222 (15.8%). On univariate analysis, none of the risk factors showed statistically significant association with MDRO carriage.

Conclusion

Overall, a high prevalence of MDRO carriage was identified among admitted pediatric patients. Implementation of systematic screening may help to identify true burden of MDROs carriage in the health care settings.

Homology analysis of 51 penicillin-intermediate Streptococcus pneumoniae isolates from Wenzhou City, China

Objective

To investigate drug resistance features and homology among penicillin-intermediate Streptococcus pneumoniae isolates from Wenzhou City, China.

Methods

Fifty-one penicillin-intermediate S. pneumoniae isolates were obtained from respiratory samples of infants and children hospitalized with lung infections. An antimicrobial susceptibility test was used to assess drug resistance. Polymerase chain reaction and agarose gel electrophoresis were used to identify S. pneumoniae isolates and pulsed-field gel electrophoresis (PFGE) was used to analyze molecular subtypes. Hierarchical cluster analysis of PFGE fingerprints was used to compare genetic diversity and relatedness of S. pneumoniae isolates. The Quellung test was used for serotyping.

Results

Fifty-one penicillin-intermediate S. pneumoniae isolates showed evidence of multi-drug resistance and polyclonal origins. The isolates were classified into 25 subtypes through hierarchical cluster analysis of PFGE fingerprints. Three of these subtypes formed a supertype (15/51, 16/51 and 8/51 isolates), while the remaining subtypes occurred sporadically (12/51 isolates).

Conclusions

Transmission of penicillin-intermediate S. pneumoniae is mostly vertical and to a lesser extent horizontal. Effective prevention strategies, including respiratory tract management and contact isolation, are essential to control nosocomial S. pneumoniae infection. Once susceptibility is confirmed, vancomycin, high-dose penicillin or third-generation cephalosporins (cefotaxime and ceftriaxone) may be used to treat penicillin-intermediate S. pneumoniae.

Serotypes and Vaccine Coverage of Streptococcus Pneumoniae Colonization in the Nasopharynx of Thai Children in Congested Areas in Chiang Mai

Streptococcus pneumoniae causes around 10% of all deaths in children younger than five years of age. This study aimed to examine the serogroups/serotypes of S. pneumoniae colonization and vaccine serotype coverage of this organism among Thai children. Nasopharyngeal swabs of children less than or equal to 15 years of age were obtained in congested areas in Chiang Mai from 1 February 2013 to 1 August 2013. The serotyping of S. pneumoniae isolates was performed using the ImmuLex™ kit and the vaccine serotype coverage for this organism was evaluated. A total of 292 children were enrolled. One hundred and thirty children (44.5%) had nasopharyngeal colonization with Streptococcus pneumoniae. Eighty-seven (66.9%) isolates were from children younger than five years of age, seventeen (13.1%) were from children aged 6-10 years, and twenty-six (20%) were from children aged 11-15 years. The five most common serogroups/serotypes isolated were 6 (6A, 6B, 6C) (46.1%), 23 (23F, 23A, 23B) (14.6%), 19 (19F, 19A, 19B, 19C) (8.5%), 15 (15F, 15A, 15B, 15C) (6.9%), and 14 (6.1%). Vaccine serotype coverages in pneumococcal conjugate vaccines (PCV):PCV7, PCV10, and PCV13 were 79.1%, 83.6%, and 85.9%, respectively. There were significant increases in coverage between PCV7 and PCV10 (from 79.1% to 83.6%, p < 0.001), PCV7 and PCV13 (from 79.1% to 85.9%, p < 0.001), and PCV10 and PCV13 (from 83.6% to 85.9%, p < 0.001). The majority of pneumococcal serogroup/serotype colonization in the nasopharynx of Thai children in the studied areas was included in the current licensed pneumococcal conjugated vaccines (PCVs). PCV vaccination should be considered for high-risk children to reduce the incidence of invasive pneumococcal disease among Thai children.

Pneumococcal disease in Thailand

This review examines the epidemiology of pneumococcal disease, serotype prevalence, antibiotic resistance, and national vaccination recommendations in Thailand. The incidence of invasive pneumococcal disease (IPD) and annualized hospitalization rates for pneumococcal bacteremia in Thailand were highest in children aged <5years and the elderly. The most prevalent serotype is serotype 6B, which is included in both the 10- and 13-valent pneumococcal conjugate vaccines (PCV10 [also known as PHiD-CV] and PCV13, respectively) registered in Thailand. Other common serotypes are 14, 18C, 19F, and 23F (included in both PCVs) and 6A and 19A (only included in PCV13). PCV10/PHiD-CV and PCV13 should cover 48.8%-74% and 73.2%-92% of isolates among children aged ≤5 years, respectively, and 40.0%-47.9% and 58.3%-60.9% of isolates among adults aged ≥65 years. Only PCV13 is licensed for adults in Thailand. Pneumococcal isolates were most commonly resistant to erythromycin, cefuroxime, and penicillin. Despite their demonstrated cost effectiveness and efficacy in reducing nasopharyngeal carriage and IPD, PCVs are not included in the Thai national immunization program. The serotype-specific IPD incidence in Thailand suggests that PCVs will reduce the disease burden in all age groups, but particularly in children and older adults.

Current status of resistance to antibiotics in the Democratic Republic of the Congo: A review

A review of literature was conducted to assess the prevalence and mechanisms of antibiotic resistance to date, mainly to β-lactam antibiotics, cephalosporins, carbapenems, colistin, and tigecycline in the Democratic Republic of the Congo (DRC). English and French publications were listed and analysed using PubMed/Medline, Google Scholar, and African Journals database between 1 January 1990 and 31 December 2019. For the 30 published articles found: (1) bacterial resistance to antibiotics concerned both Gram-negative and Gram-positive bacteria; (2) multidrug resistance prevalence was the same in half of Streptococcus pneumoniae isolates; (3) a worrying prevalence of methicillin-resistant Staphylococcus aureus (MRSA) was noted, which is associated with co-resistance to several other antibiotics; and (4) resistance to third-generation cephalosporins was very high in Enterobacteriaceae, mainly because of bla_CTX-M-1 group and bla_SHV genes. Data on carbapenem and colistin resistance were not available in DRC until recently. Further work is required to set up a surveillance system for antibiotic resistance in DRC.

Manganese complex [Mn(CO)3(tpa-κ3N)]Br increases antibiotic sensitivity in multidrug resistant Streptococcus pneumoniae

OBJECTIVES

The emergence of multidrug-resistance (MDR) in Streptococcus pneumoniae clones and non-vaccine serotypes necessitate the development of novel treatment strategies. This work aimed to determine the efficacy of the Mn complex [Mn(CO)³(tpa-κ³N)]Br against clinically important MDR strains of S. pneumoniae.

METHODS

Twenty MDR clinicalS. pneumoniae strains were included in this study. Minimum inhibitory concentrations (MICs) of [Mn(CO)₃(tpa-κ³N)]Br were determined via broth microdilution alone and in combination with other antimicrobial agents using checkerboard assays and/or disc diffusion tests. In vitro efficacy was assessed by time-kill assays while in vivo efficacy was tested using the insect model Galleria mellonella.

RESULTS

[Mn(CO)₃(tpa-κ³N)]Br showed moderate in vitro efficacy against S. pneumoniae coupled with bactericidal activity. Checkerboard and disc diffusion assays showed synergy between [Mn(CO)₃(tpa-κ³N)]Br and tetracycline, and the combination of both agents caused rapid kill-kinetics and reduced the MIC below the susceptibility breakpoint of 1 mg/L even for tetracycline-resistant strains of S. pneumoniae. Similar results were observed for the erythromycin- and the co-trimoxazole-Mn complex combination. In the G. mellonella infection model, mortality and morbidity rates at 96 h were significantly lower in larvae treated with [Mn(CO)₃(tpa-κ³N)]Br than phosphate buffered saline, while treatment with the tetracycline-Mn complex combination was superior to monotherapy, resulting in significantly lower mortality and morbidity rates (p < 0.049).

CONCLUSIONS

We show that [Mn(CO)₃(tpa-κ³N)]Br has in vitro and in vivo antibacterial activity against clinically relevant strains of S. pneumoniae and has the potential to be used in combination with currently available antibiotics to increase their effectiveness against MDR S. pneumoniae.

Pneumococcal colonization prevalence and density among Thai children with severe pneumonia and community controls

Background

Pneumococcal colonization prevalence and colonization density, which has been associated with invasive disease, can offer insight into local pneumococcal ecology and help inform vaccine policy discussions.

Methods

The Pneumonia Etiology Research for Child Health Project (PERCH), a multi-country case-control study, evaluated the etiology of hospitalized cases of severe and very severe pneumonia among children aged 1–59 months. The PERCH Thailand site enrolled children during January 2012–February 2014. We determined pneumococcal colonization prevalence and density, and serotype distribution of colonizing isolates.

Results

We enrolled 224 severe/very severe pneumonia cases and 659 community controls in Thailand. Compared to controls, cases had lower colonization prevalence (54.5% vs. 62.5%, p = 0.12) and lower median colonization density (42.1 vs. 210.2 x 10³ copies/mL, p <0.0001); 42% of cases had documented antibiotic pretreatment vs. 0.8% of controls. In no sub-group of assessed cases did pneumococcal colonization density exceed the median for controls, including cases with no prior antibiotics (63.9x10³ copies/mL), with consolidation on chest x-ray (76.5x10³ copies/mL) or with pneumococcus detected in whole blood by PCR (9.3x10³ copies/mL). Serotype distribution was similar among cases and controls, and a high percentage of colonizing isolates from cases and controls were serotypes included in PCV10 (70.0% and 61.8%, respectively) and PCV13 (76.7% and 67.9%, respectively).

Conclusions

Pneumococcal colonization is common among children aged <5 years in Thailand. However, colonization density was not higher among children with severe pneumonia compared to controls. These results can inform discussions about PCV introduction and provide baseline data to monitor PCV impact after introduction in Thailand.

Novel Antibiotics for Multidrug-Resistant Gram-Positive Microorganisms

Increasing multidrug-resistance to Gram-positive pathogens, particularly to staphylococci, enterococci and streptococci, is a major problem, resulting in significant morbidity, mortality and healthcare costs. In recent years, only a small number of novel antibiotics effective against Gram-positive bacteria has been approved. This review will discuss the current evidence for novel branded antibiotics that are highly effective in the treatment of multidrug-resistant infections by Gram-positive pathogens, namely ceftobiprole, ceftaroline, telavancin, oritavancin, dalbavancin, tedizolid, besifloxacin, delafloxacin, ozenoxacin, and omadacycline. The mechanism of action, pharmacokinetics, microbiological spectrum, efficacy and safety profile will be concisely presented. As for any emerging antibiotic agent, resistance is likely to develop against these highly effective antibiotics. Only through appropriate dosing, utilization and careful resistance development monitoring will these novel antibiotics continue to treat Gram-positive pathogens in the future.

Trends in Antimicrobial Drug Resistance of Streptococcus pneumoniae Isolates at Jordan University Hospital (2000⁻2018)

Antimicrobial drug resistance (AMR) in pneumococci complicates the treatment of serious pneumococcal infections. Country-specific AMR patterns can help to establish guidelines for empiric therapy. The aim of the current study was to analyze the distribution of AMR among Streptococcus pneumoniae isolates at Jordan University Hospital (JUH) during 2000⁻2018. Paper-based and electronic clinical data registry records from 2000 to 2018 were retrospectively analyzed to study the AMR among pneumococcal isolates at JUH. Temporal trend analysis was done using two-tailed linear-by-linear test for association. The total number of unique pneumococcal isolates that were identified was 556, of which 544 isolates had antimicrobial susceptibility testing results. The most frequent specimens were eye (n = 117, 21.0%), bloodstream (n = 93, 16.7%) and sputum (n = 81, 14.6%). Invasive infections represented 23.6% of all unique isolates. The overall susceptibility of S. pneumoniae isolates during the study period to different antimicrobials was: 100% to vancomycin, 97.7% to ceftriaxone, 97.1% to cefotaxime, 94.9% to chloramphenicol, 89.7% to penicillin, 83.8% to levofloxacin, 67.7% to clindamycin and 52.1% to erythromycin. The prevalence of multi-drug resistance (MDR) was 8.6% (95% confidence interval: 6.4⁻11.5%). Trend analysis showed an increase in the prevalence of non-susceptibility to erythromycin, clindamycin and levofloxacin (p < 0.001). MDR prevalence increased from 1.6% in the first quarter to 14.6% in the fourth quarter (p < 0.001). The incidence of invasive infections declined over the study period (p < 0.001). The increase in the prevalence of AMR and MDR among pneumococcal isolates in Jordan demands judicious use of antimicrobials and regular surveillance of resistance.

Molecular Characterization of Colistin-Resistant Escherichia coli Isolated from Chickens: First Report from Nepal

Dissemination of mcr-1 encoding colistin resistance in Gram-negative bacteria has created critical situation in poultry, livestock farming, and public health. In Nepal, for the first time, we initiated surveillance of colistin-resistant Escherichia coli in broilers from seven different chicken farms. A total of 324 cloacal swabs were collected and 118 E. coli were isolated, of which 27 (22.8%) were colistin resistance all harboring mcr-1 gene, but lacking ISApI1. Colistin-resistant isolates were characterized by antibiotic susceptibility testing, detecting antibiotic resistance genes, phylogenetic analysis, and plasmid replicon typing. These isolates belonged to the phylo-group A (70.37%) and phylo-group D (29.63%). In addition, most isolates (>80%) were resistant to ciprofloxacin, tetracycline, and sulfamethoxazole-trimethoprim. As much as 3 of the 27 mcr-1 encoding isolates were confirmed as extended-spectrum β-lactamase (ESBL) producer, all 3 isolates carrying bla_CTX-M gene. We performed the conjugation experiment to check transferability of mcr-1, tet, and bla_CTX-M genes, and only two donors were found to have transferred resistance to ticarcillin. The transfer of colistin and tetracycline resistance was not detected, which suggests the chromosomal location of mcr-1 and tet genes. The prevalence of Inc K/B and Inc I1 was 96.3% and 81.48%, respectively. This study shows the co-existence of mcr-1 with tet, sul, qnr, dfr, and bla_CTX-M genes and dissemination of these resistant isolates in Nepalese chicken farms, which may pose huge threat to the livestock, especially chickens, and public health in Nepal.

Association Between Pneumococcal Surface Protein A Family and Genetic/Antimicrobial Resistance Traits of Non-Invasive Pneumococcal Isolates from Adults in Northern Japan

Pneumococcal isolates from adult patients in northern Japan in 2016 were subjected to molecular investigation related to pneumococcal surface protein A (PspA) and drug resistance determinants. Of the 51 isolates, serotype 3/ST180 was the most prevalent (17.6%), followed by 35B (ST2755/ST558) (11.8%) and 15A (ST63/ST7874/ST13068/ST13785) (9.8%). Coverage of serotypes by 13-valent conjugate vaccine and 23-valent polysaccharide vaccine was 27.5% and 49%, respectively. All the isolates expressed PspA family 1 or 2 (51% and 49%, respectively). Each serotype was associated with either of the PspA families (e.g., serotype 3, PspA family 1; serotypes 35B and 15A, PspA family 2). Multidrug resistance (MDR) was found in 84.3% of the isolates. Minimum of one altered penicillin-binding protein gene was detected in 82.4% of isolates, indicating 25.5% non-susceptibility to penicillin. Serotypes 15A and 35B were predominant and demonstrated MDR. An isolate of serotype 15A/ST13785 (single-locus variant of ST242) was resistant to fluoroquinolones associated with double mutation in the quinolone resistance-determining regions of gyrA and parC. The present study indicates the spread of MDR pneumococci represented by isolates of serotypes 3, 15A, and 35B, and prevalence of both PspA family 1 and 2 in isolates obtained from adult patients.

Acquisition and transfer of antibiotic resistance genes in association with conjugative plasmid or class 1 integrons of Acinetobacter baumannii

Conjugation is a type of horizontal gene transfer (HGT) that serves as the primary mechanism responsible for accelerating the spread of antibiotic resistance genes in Gram-negative bacteria. The present study aimed to elucidate the mechanisms underlying the conjugation-mediated gene transfer from the extensively drug-resistant Acinetobacter baumannii (XDR-AB) and New Delhi Metallo-beta-lactamase-1-producing Acinetobacter baumannii (NDM-AB) to environmental isolates of Acinetobacter spp. Conjugation experiments demonstrated that resistance to ticarcillin and kanamycin could be transferred from four donors to two sodium azide-resistant A. baumannii strains, namely, NU013R and NU015R. No transconjugants were detected on Mueller-Hinton Agar (MHA) plates containing tetracycline. Plasmids obtained from donors as well as successful transconjugants were characterized by PCR-based replicon typing and S1-nuclease pulsed-field gel electrophoresis (S1-PFGE). Detection of antibiotic resistance genes and integrase genes (int) was performed using PCR. Results revealed that the donor AB364 strain can transfer the blaOXA-23 and blaPER-1 genes to both recipients in association with int1. A 240-kb plasmid was successfully transferred from the donor AB364 to recipients. In addition, the aphA6 and blaPER-1 genes were co-transferred with the int1 gene from the donor strains AB352 and AB405. The transfer of a 220-kb plasmid from the donors to recipient was detected. The GR6 plasmid containing the kanamycin resistance gene (aphA6) was successfully transferred from the donor strain AB140 to both recipient strains. However, the blaNDM-1 and tet(B) genes were not detected in all transconjugants. Our study is the first to demonstrate successful in vitro conjugation, which indicated that XDR-AB contained combination mechanisms of the co-transfer of antimicrobial resistance elements with integron cassettes or with the plasmid group GR6. Thus, conjugation could be responsible for the emergence of new types of antibiotic-resistant strains.

Pharyngeal colonization and drug resistance profiles of Morraxella catarrrhalis, Streptococcus pneumoniae, Staphylococcus aureus, and Haemophilus influenzae among HIV infected children attending ART Clinic of Felegehiwot Referral Hospital, Ethiopia

Background

Asymptomatic pharyngeal colonization by potential bacteria is the primary reservoir for bacterial species within a population and is considered a prerequisite for development of major childhood diseases such as sinusitis, otitis media, pneumonia, bacteremia, and meningitis. However, there is dearth of data on the colonization and drug resistance pattern of the main bacterial pathogens in the pharynx of HIV infected children in Ethiopia. Therefore, this study determined the pharyngeal colonization and drug resistance profile of bacterial pathogens in HIV infected children attending ART clinic of Felegehiwot Referral Hospital (FHRH), Amhara Region, Ethiopia.

Methods

A hospital based cross-sectional study was conducted from May 2016 to June 2017 at the ART clinic of FHRH. A total of 300 HIV infected children were enrolled in the study. Data on socio-demographic characteristics of the study participants were collected with face-to-face interview and patient—card review using structured questionnaire. Bacterial species were identified using standard bacteriological techniques. Drug susceptibility testing was performed using disk diffusion technique. Chi-square test was done to determine associations among variables.

Results

The median age of the participants was 11 years. Overall, 153 (51%) of children were colonized by respiratory bacteria in their pharynx. Colonization rate was higher in children from mothers who had attained college and above levels of education than others (P = 0.04). It was also higher in children without the sign of malnutrition than others (P = 0.004). The colonization rate of S.aureus, M.catarrhalis, S.pneumoniae and H.influenzae were 88 (29%), 37 (12.3%), 31 (10.3%) and 6 (2%), respectively. S.aureus—M.catarrhalis concurrent colonization was found in 14 (4.7%) of children. Age (P = 0.03), schooling (P = 0.045) and history of running nose (P = 0.043) were significantly associated with S.aureus colonization. Living in urban setting (P = 0.042) and children from mothers with college and above levels of education (P = 0.002) were significantly associated with M.catarrhalis colonization. Majority of the isolates were resistant to penicillin (68.5%) and cotrimoxazole (52.5%).S.aureus isolates were resistant to penicillin (84.1%) and cotrimoxazole (51.1%).M.catarrhalis isolates were resistant to penicillin (94.6%), erythromycin (86.5%)and cotrimoxazole (78.4%). Overall, 99 (59.3%) of the isolates were multi-drug (MDR) resistant. The overall MDR rates among S.aureus, M.catarrhalis and S.pneumoniae isolates were 65.9%, 78.4% and 22.6%, respectively.

Conclusions

Pharyngeal colonization of respiratory bacteria in HIV infected children is a major public health problem. Single and multiple antibiotic resistant is alarmingly high among respiratory colonizers. Therefore, regular screening of HIV infected children for culture and antimicrobial susceptibility testing is recommended to prevent the development of severe opportunistic infections.

Distance to health services modifies the effect of an 11-valent pneumococcal vaccine on pneumonia risk among children less than 2 years of age in Bohol, Philippines

Background

Both vaccine trials and surveillance studies typically use passive surveillance systems to monitor study outcomes, which may lead to under-reporting of study outcomes in areas with poor access to care. This detection bias can have an adverse effect on conventional estimates of pneumonia risk derived from vaccine trials.

Methods

We conducted a secondary analysis of a randomized, placebo-controlled, double-blind vaccine trial that examined the efficacy of an 11-valent pneumococcal vaccine (PCV) among children less than 2 years of age in Bohol, Philippines. Trial data were linked to the residential location of each participant using a geographical information system. The study was conducted using 11 729 children who received three doses of any study vaccine (PCV11) or placebo. Multivariate Cox proportional hazards models were used to examine major risk factors for pneumonia diagnosis and the relationship between distance to Bohol Regional Hospital (BRH) and vaccination with PCV with risk for pneumonia diagnosis.

Results

There was a significant interaction effect between distance from BRH and vaccination with PCV11 on pneumonia risk. Among children living 12 km from BRH, vaccination with PCV11 was associated with a decreased hazard ratio for radiographic pneumonia, compared with vaccination with the study placebo [0.57, 95% confidence interval (CI) 0.37-0.86). However, for children living 1 km from BRH, there was little difference in risk of radiographic pneumonia diagnosis between children vaccinated with PCV11 and those given the study placebo.

Conclusion

Children living close to BRH had no documented reduction in the primary study outcome from PCV11, whereas those at greater distance experienced a substantial reduction. Because of detection bias caused by distance to BRH, in spatial analysis of vaccine trial results it may be necessary to adjust estimates of pneumonia risk and vaccine efficacy. Failure to consider the geographical dimension of trials may lead to underestimates of efficacy which might influence public health planning efforts.

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.

High Prevalence of Antibiotic-Resistant Otitis Media-Associated Bacterial Flora of Asymptomatic People Living with HIV at Morogoro Hospital, Tanzania

OBJECTIVES

The study aimed to determine the prevalence of otitis media (OM)-associated bacterial flora of asymptomatic people living with HIV (PLH) on antiretroviral therapy (ART) and assess antibiotic resistance profiles of the bacteria.

METHODOLOGY

Ear secretion specimens were collected by syringe or cotton swabs. Isolated bacteria were subjected to antibiotic sensitivity tests.

RESULTS

Of 290 recruited PLH, 81.7% were females and 18.3% males; their CD4+ counts ranged from 0 to 1770. Staphylococcus aureus, Klebsiella pneumonia, and Escherichia coli were the predominant bacteria. High antibiotic resistance was detected on Streptococcus pyogenes and Streptococcus pneumoniae. The prevalence rate of OM-associated bacteria (OAB) was 93.4%, and majority of the bacteria were resistant to multiple antibiotics. Linear association between the prevalence of OAB with both duration of ART and CD4+ counts was observed.

CONCLUSION

High prevalence rates of OAB and antibiotic resistance were observed. Negative correlation between CD4+ counts and prevalence of OAB was revealed.

Bacterial genomic epidemiology, from local outbreak characterization to species-history reconstruction

Bacteriology has embraced the next-generation sequencing revolution, swiftly moving from the time of single genome sequencing to the age of genomic epidemiology. Hundreds and now even thousands of genomes are being sequenced for single bacterial species, allowing unprecedented levels of resolution and insight in the evolution and epidemic diffusion of the main bacterial pathogens. Here, we present a review of some of the most recent and groundbreaking studies in this field.

Nasal carriage of common bacterial pathogens among healthy kindergarten children in Chaoshan region, southern China: a cross-sectional study

BACKGROUND

Nasal colonization with bacterial pathogens is associated with risk of invasive respiratory tract infections, but the related information for Chinese healthy children is scarce.

METHODS

This cross-sectional study was conducted with healthy children from 6 kindergartens in the Chaoshan region, southern China during 2011-2012. Nasal swabs were examined for five common bacterial pathogens: Streptococcus pneumoniae, Haemophilus influenzae, Haemophilus parainfluenzae, Moraxella catarrhalis, and Staphylococcus aureus.

RESULTS

Among 1,088 children enrolled, 79.6 % (866) were target-bacterial carriers, of which 34.4 % (298/866) were positive for ≥2 bacteria species. The most common pathogen in the bacterial carriers was M. catarrhalis (76.6 %), followed by S. pneumoniae (26.6 %), S. aureus (21.8 %), H. parainfluenzae (12.7 %), and H. influenzae (2.3 %). Multiple logistic regression analyses showed negative associations between age and the overall or multiple bacterial carriage, and between the father's education level and multiple bacterial carriage (all p < 0.05). Age was negatively associated with the carriage of M. catarrhalis and S. pneumoniae, and positively associated with the S. aureus carriage (all p < 0.0001).

CONCLUSIONS

This study shows high nasal carriage of common pathogenic bacteria and coexistence of multiple pathogens in healthy Chaoshan kindergarten children, with M. catarrhalis as the commonest colonizer. Increasing age of children and higher paternal education are associated with lower risk of bacterial carriage. Longitudinal follow-up studies would be helpful for better understanding the infection risk in bacterial pathogen carriers.

Characterisation of Invasive Streptococcus pneumoniae Isolated from Cambodian Children between 2007 - 2012

BACKGROUND

The 13-valent pneumococcal vaccine (PCV13) was introduced in Cambodia in January 2015. There are limited data concerning the common serotypes causing invasive pneumococcal disease (IPD). Knowledge of the circulating pneumococcal serotypes is important to monitor epidemiological changes before and after vaccine implementation.

METHODS

All episodes of IPD defined by the isolation of Streptococcus pneumoniae from blood, cerebrospinal fluid or other sterile site in Cambodian children admitted to the Angkor Hospital for Children in Siem Reap, Northwestern Cambodia, between 1st January 2007 and 1st July 2012 were retrospectively studied. Streptococcus pneumoniae isolates that could be retrieved underwent phenotypic typing and whole genome sequencing.

RESULTS

There were 90 Cambodian children hospitalized with IPD with a median (IQR) age of 2.3 years (0.9-6.2). The case fatality was 15.6% (95% CI 8-23). Of 50 Streptococcus pneumoniae isolates available for further testing, 46% were penicillin non-susceptible and 8% were ceftriaxone non-susceptible, 78% were cotrimoxazole resistant, 30% were erythromycin resistant and 30% chloramphenicol resistant. There were no significant changes in resistance levels over the five-year period. The most common serotypes were 1 (11/50; 22%), 23F (8/50; 16%), 14 (6/50; 12%), 5 (5/50; 10%) and 19A (3/50; 6%). Coverage by PCV7, PCV10 and PCV13 was 44%, 76% and 92% respectively. We identified novel multilocus sequence types and resistotypes using whole genome sequencing.

CONCLUSIONS

This study suggests IPD is an important disease in Cambodian children and can have a significant mortality. PCV13 coverage of the serotypes determined in studied strains was high and consistent with another recent study. The phenotypic resistance patterns observed were similar to other regional studies. The use of whole genome sequencing in the present study provides additional typing and resistance information together with the description of novel sequence types and resistotypes.

Pneumococcal Infection among Children before Introduction of 13-Valent Pneumococcal Conjugate Vaccine, Cambodia

Vaccination of children with pneumococcal conjugate vaccine (PCV13) was initiated in Cambodia in 2015. To determine baseline data, we collected samples from children in 2013 and 2014. PCV13 serotypes accounted for 62.7% of colonizing organisms in outpatients and 88.4% of invasive pneumococci overall; multidrug resistance was common. Thus, effectiveness of vaccination should be high.