Colonization with selected antibiotic resistant bacteria among a cohort of Sri Lankan university students.

BACKGROUND: Antibiotic Resistance is an imminent global public health threat. Antibiotic resistance emerged in healthcare settings and has now moved on to the community settings. This study was conducted to identify the rates of asymptomatic colonization with selected antibiotic resistant organisms, (Methicillin Resistant Staphylococcus aureus (MRSA), Extended Spectrum Beta Lactamase (ESBL) producing Escherichia coli and Klebsiella spp and carbapenem resistant E.coli and Klebsiella spp) - among a group of university students in Sri Lanka. Identification of genetic determinants of MRSA and ESBL was an additional objective of the study. METHODS: A self - collected nasal swab and a peri-rectal swab collected after passing stools were obtained. Routine microbiological methods were used for the isolation S.aureus from the nasal swab and E.coli and Klebsiella species from the peri-rectal swab. Antibiotic sensitivity testing was performed as recommended by clinical and laboratory standard institute (CLSI). Three (3) genes that are responsible for ESBL production; blaCTX-M, blaSHV, and blaTEM were tested using previously described primers and PCR procedures. Identification of MecA and PVL genes attributed to MRSA was also done with PCR. RESULTS: A total of 322 participants between 21 and 28 years were recruited representing 5 different faculties of study. Seventy one (22.0%) were colonized with S.aureus and 14 among them with MRSA, making the MRSA colonization rate of 4.3%. Forty five (15%) of the participants were colonized with an ESBL producing E.coli or Klebsiella spp. No one was colonized with carbapenem resistant E.coli or Klebsiella species. Of the 45 ESBL producers the commonest genetic determinant identified was blaCTX-M (n = 36), while 16 isolates had blaTEM and 7 had blaSHV. Similarly, of the 14 isolates identified as MRSA, 3 (21.4%) were found to be PVL positive while 11 (78.6%) were MecA positive. CONCLUSIONS: A high rate of colonization with ESBL producing E.coli and Klebsiella species was noted in our study group.

Identification of bacterial aetiology in acute meningitis.

Background: The lack of rapid and sensitive test remains a key issue in diagnosing meningitis and affordability impedes using the molecular techniques. However, conventional PCR is currently becoming more affordable. Objectives: Optimize and establish a multiplex PCR and to compare the above PCR to Cerebrospinal fluid (CSF) culture and antigen detection in sensitivity and specificity for the detection of bacterial meningitis. Methods: CSF specimens were collected from patients with suspected acute meningitis admitted to Teaching Hospital, Peradeniya from December 2016 to March 2017. A multiplex PCR was used to detect Neisseria meningitides, Streptococcus pneumonia and Haemophilus influenzae. Results: Eighty specimens of CSF were collected during the study period. The mean duration to sample collection was 4.78(SD 2.6) from the onset of symptoms. None of the samples given positive CSF culture. CSF antigen detection was performed on 50 specimens and all were negative. Of the total samples, eight yielded positive PCR results. In two of the positives, the full report was normal, one was suggestive of viral aetiology and five were suggestive of bacterial aetiology. Three were positive for S.pneumoniae and five for H.influenzae. positive PCR results were associated with a shorter time gap between hospitalization and sample collection and a larger CSF volume. Conclusion: Findings of the study highlight the usefulness and recommendation of multiplex PCR in the diagnosis of pathogens causing acute bacterial meningitis. Collection of an adequate volume of CSF early in the illness, without delay may improve the diagnosis.

Synergistic activity between Triphala and selected antibiotics against drug resistant clinical isolates.

BACKGROUND: Triphala is an indigenous medical product used for a variety of diseases. This study was conducted to determine the effect of Triphala on antibiotic properties of gentamicin and oxacillin against multi-drug resistant organisms. METHODS: The checkerboard method was used to determine the synergy of Triphala with gentamicin and oxacillin against multi-drug resistant (MDR) Gram negative bacilli and methicillin-resistant Staphylococcus aureus (MRSA) using 2,3,5-triphenyltetrazolium chloride (TTC) assay. Fractional inhibitory concentration (FIC) index was calculated. RESULTS: When tested alone, the minimum inhibitory concentration (MIC) values of gentamicin for Gram negative isolates ranged from 8 to > 64 µg/ml. The MIC values of gentamicin for the Gram negative isolates ranged from 1 to 32 µg/ml when tested with Triphala. The FIC index was < 1 indicating a synergistic interaction in 10 of the 11 isolates and it was 1 indicating an additive effect in one isolate. The MIC values of oxacillin for MRSA isolates ranged from 4 to > 16 µg/ml with all MICs being equal to or higher than the resistance cut-off level. The MIC level with the addition of Triphala ranged from 0.25 to 4 µg/ml. FIC index was < 1 for all tested isolates indicating a synergistic interaction. CONCLUSIONS: Triphala has synergistic activity with gentamicin against the selected MDR Gram negative bacilli and with oxacillin against MRSA isolates warranting further studies on the possibility of clinical use.

Maternal vaginal colonization with selected potential pathogens of neonatal sepsis in the era of antimicrobial resistance, a single center experience from Sri Lanka.

BACKGROUND: Maternal vaginal colonization with antibiotic resistant organisms is a growing concern in countries with high antibiotic resistance rates. METHODS: A low vaginal swab was collected from mothers on admission, on discharge and a peri-rectal swab was collected from the neonates born to these mothers on discharge. Routine microbiological methods were used to identify the colonization rates for Escherichia coli, Klebsiella spp. and Streptococcus agalactiae. RESULTS: The pre-delivery colonization rate among the 250 participants for total Enterobacteriaceae was 18.8%. The colonization rates for Klebsiella spp., E. coli and S. agalactiae were, 12.4, 5.6 and 14.8% respectively. Two Klebsiella spp. and two E. coli isolates were confirmed to be exentend spectrum ß lactamase (ESBL) producers with the commonest resistant determinant being blaCTX-M. Post-delivery swabs were collected from 130 participants and the colonization rates were 41.5% for Enterobacteriaceae, 25.4% for Klebsiella spp., 10.8% for E. coli, and 10.8% for S. agalacteiae. Three Klebsiella isolates and one E. coli isolate were confirmed to be ESBL producers with the commonest resistant determinant being blaCTX-M. Considering the 130 participants with both samples, there was a significant increase in the colonization with any Enterobacteriaceae and Klebsiella spp. (p < 0.05). Peri-rectal swabs were collected from neonates in 159 instances. The isolation rates for Enterobacteriaceae was 34%. The genus specific isolation rate for Klebsiella was 21.4% while the rates for E. coli and S.agalactiae were 10.1 and 5.7% respectively. Two of the E. coli were confirmed to be ESBL producers while none of the klebsiellae were identified to be so. Considering these 159 instances where both the mother and baby were sampled, random amplification of polymorphic DNA (RAPD) analysis revealed that Enterbacteriaceae with same strain type was present in 6.9% of the instances, indicating possible transfer between the mother and neonate. The transfer rate for ESBL producers were 0.6%. CONCLUSIONS: The lower level of antimicrobial resistance among these potentially community acquired isolates is encouraging. However, in view of the increasing level of resistance reported elsewhere in the region, regular monitoring is warranted.

Terminalia bellirica fruit extracts: in-vitro antibacterial activity against selected multidrug-resistant bacteria, radical scavenging activity and cytotoxicity study on BHK-21 cells.

BACKGROUND: Identification of novel sources for developing new antibiotics is imperative with the emergence of antibiotic resistant bacteria. The fruits of Terminalia bellirica (Gaertn) Roxb., widely used in traditional medicine, were evaluated for antibacterial activity against multidrug-resistant (MDR) bacteria, antioxidant activity and cytotoxicity. METHODS: Twelve solvent extracts of T. bellirica fruits were prepared by direct aqueous extraction and sequential extraction with dichloromethane, methanol and water using Soxhlet, bottle-shaker and ultrasound sonicator methods. Antibacterial activity of the extracts was tested against 16 strains MDR bacteria-methicillin-resistant Staphylococcus aureus (MRSA), extended spectrum ß-lactamase (ESBL) producing Escherichia coli and MDR Acinetobacter spp., Klebsiella pneumoniae and Pseudomonas aeruginosa-and 4 control organisms, using the cut-well diffusion method. The minimum inhibitory concentration (MIC) was determined using an agar dilution method. The radical scavenging activity of six antibacterial extracts was screened against 2,2'-diphenyl-2-picrylhydrazyl (DPPH) and correlation was established between EC50 (50% effective concentration) values and the total phenolic content (TPC). Cytotoxicity was determined for the most potent antibacterial extract on baby hamster kidney (BHK-21) cells by Tryphan Blue exclusion method. Statistical analysis was carried out by one-way analysis of variance at significant level p < 0.05 using "SigmaPlot 10" and "R 3.2.0" software. RESULTS: All aqueous and methanol extracts displayed antibacterial activity (MIC 0.25-4 mg/mL) against all strains of MRSA, MDR Acinetobacter spp. and MDR P. aeruginosa. The sequential aqueous extracts (MIC, 4 mg/mL) inhibited ESBL producing-E. coli. None of the extracts exhibited activity against MDR K. pneumoniae (MIC > 5 mg/mL). The sequential methanol extract (Soxhlet) recorded high antibacterial activity and the highest DPPH radical scavenging activity (EC50, 6.99 ± 0.15 ppm) and TPC content (188.71 ± 2.12 GAE mg/g). The IC50 (50% inhibition concentration) values of the most potent antibacterial extract-the direct aqueous extract from reflux method-on BHK-21 cells were 2.62 ± 0.06 and 1.45 ± 0.08 mg/ml with 24 and 48 h exposure, respectively. CONCLUSIONS: Results indicate that T. bellirica fruit is a potential source for developing broad-spectrum antibacterial drugs against MDR bacteria, which are non-toxic to mammalian cells and impart health benefits by high antioxidant activity.

Spread of resistant gram negatives in a Sri Lankan intensive care unit.

BACKGROUND: Infections with multi drug resistant (MDR) organisms are a major problem in intensive care units (ICUs). Proper infection control procedures are mandatory to combat the spread of resistant organisms within ICUs. Well stablished surveillance programmes will enhance the adherence of the staff to infection control protocols. The study was conducted to assess the feasibility of using basic molecular typing methods and routine hospital data for laboratory surveillance of resistance organisms in resource limited settings. METHODS: A retrospective study was conducted using consecutive Gram negative isolates obtained from an ICU over a six month period. Antibiotic sensitivity patterns and random amplified polymorphic DNA (RAPD) based typing was performed on the given isolates. RESULTS: Of the seventy isolates included in the study, seven were E.coli. All E.coli were MDRs and Extended Spectrum ß lactamse (ESBL) producers carrying bla CTX-M. Fourteen isolates were K.pneumoniae, and all were MDRs and ESBL producers. All K.pneumoniae harboured bla SHV while 13 harboured bla CTX-M. The MDR rate among P.aeruginosa was 13% (n=15) while all acinetobacters (n=30) were MDRs. Predominant clusters were identified within all four types of Gram negatives using RAPD and the ICU stay of patients overlapped temporally. CONCLUSION: We propose that simple surveillance methods like RAPD based typing and basic hospital data can be used to convince hospital staff to adhere to infection control protocols more effectively, in low and middle income countries.

Hypervirulent Clone of Group B Streptococcus Serotype III Sequence Type 283, Hong Kong, 1993-2012.

We describe a hypervirulent clone of group B Streptococcus serotype III, subtype 4, sequence type 283, that caused invasive disease with a predilection for meningitis in Hong Kong during 1993-2012. The organism is associated with high mortality and increased summer prevalence and is linked to diseased fish from freshwater fish farms.

Genetic analyses of penicillin binding protein determinants in multidrug-resistant Streptococcus pneumoniae serogroup 19 CC320/271 clone with high-level resistance to third-generation cephalosporins.

We describe the dissemination of a multidrug-resistant (MDR) serogroup 19 pneumococcal clone of representative multilocus sequence type 271 (ST271) with high-level resistance to cefotaxime in Hong Kong and penicillin binding protein (pbp) genes and its relationships to Taiwan(19F)-14 and the prevalent multidrug-resistant 19A clone (MDR19A-ST320). A total of 472 nonduplicate isolates from 2006 and 2011 were analyzed. Significant increases in the rates of nonsusceptibility to penicillin (PEN) (MIC ≥ 4.0 µg/ml; 9.9 versus 23.3%; P = 0.0005), cefotaxime (CTX) (MIC ≥ 2.0 µg/ml; 12.2 versus 30.3%; P < 0.0001 [meningitis MIC ≥ 1.0 µg/ml; 30.2 versus 48.7%; P = 0.0001]), and erythromycin (ERY) (69.2 versus 84.0%; P = 0.0003) were noted when rates from 2006 and 2011 were compared. The CTX-resistant isolates with MICs of 8 µg/ml in 2011 were of serotype 19F, belonging to ST271. Analyses of the penicillin binding protein 2x (PBP2x) amino acid sequences in relation to the corresponding sequences of the R6 strain revealed M339F, E378A, M400T, and Y595F substitutions found within the ST271 clone but not present in Taiwan(19F)-14 or MDR19A. In addition, PBP2bs of ST271 strains and that of the Taiwan(19F)-14 clone were characterized by a unique amino acid substitution, E369D, while ST320 possessed the unique amino acid substitution K366N, as does that of MDR19A in the United States. We hypothesize that ST271 originated from the Taiwan(19F)-14 lineage, which had disseminated in Hong Kong in the early 2000s, and conferred higher-level ß-lactam and cefotaxime resistance through acquisitions of 19 additional amino acid substitutions in PBP2b (amino acid [aa] positions 538 to 641) and altered PBP2x via recombination events. The serogroup 19 MDR CC320/271 clone warrants close monitoring to evaluate its effect after the switch to expanded conjugate vaccines.

Direct detection and prediction of all pneumococcal serogroups by target enrichment-based next-generation sequencing.

Despite the availability of standard methods for pneumococcal serotyping, there is room for improvement in the available methods, in terms of throughput, multiplexing capacity, and the number of serotypes identified. We describe a target enrichment-based next-generation sequencing method applied to nasopharyngeal samples for direct detection and serogroup prediction of all known serotypes of Streptococcus pneumoniae, 32 to the serotype level and the rest to the closely related serogroup level. The method was applied to detect and to predict the serogroups of pneumococci directly in clinical samples and from sweeps of primary culture DNA, with increased detection rates versus culture-based identification and agreement with the serotypes/serogroups determined by conventional serotyping methods. We propose this method, in conjunction with traditional serotyping methods, as an alternative to rapid detection and serotyping of pneumococci.

Application of a target enrichment-based next-generation sequencing protocol for identification and sequence-based prediction of pneumococcal serotypes.

BACKGROUND: The use of whole-genome sequencing in microbiology at a diagnostic level, although feasible, is still limited by the expenses associated and by the complex bioinformatics pipelines in data analyses. We describe the use of target enrichment-based next-generation sequencing for pneumococcal identification and serotyping as applied to the polysaccharide 23 valent vaccine serotypes as an affordable alternative to whole genome sequencing. RESULTS: Correct identification of Streptococcus pneumoniae and prediction of common vaccine serotypes: 12 to serotype level and the rest to serogroup levels were achieved for all serotypes with >500 reads mapped against serotypes sequences. A proportion-based criterion also enabled the identification of two serotypes present in the same sample, thus indicating the possibility of using this method in detecting co-colonizing serotypes. The results obtained were comparable to or an improvement on the currently existing molecular serotyping methods for S. pneumoniae in relation to the polysaccharide vaccine serotypes. CONCLUSION: We propose that this method has the potential to become an affordable and adaptable alternative to whole-genome sequencing for pneumococcal identification and serotyping.

Global epidemiology of asymptomatic colonisation of methicillin-resistant Staphylococcus aureus in the upper respiratory tract of young children: a systematic review and meta-analysis.

OBJECTIVE: To estimate the global prevalence of asymptomatic colonisation, and determine the associated risk factors, antibiotic resistance and genotypes of methicillin-resistant Staphylococcus aureus (MRSA) in the upper respiratory tract of young children. DESIGN: Four bibliometric databases were searched for publications between 2010 and 2022 according to the protocol registered in PROSPERO. Cross-sectional or cohort studies describing the prevalence of asymptomatic colonisation of S. aureus and MRSA in young children were included. Data extraction and analysis were carried out by two reviewers independently according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses 2020 statement. Pooled prevalence was estimated using a random effects model. SETTING AND STUDIES: We included studies where children without respiratory tract infection or Staphylococcal infection were recruited from the community, children's institutions (ie, nurseries, kindergartens, daycare centres and preschools) and healthcare centre visits and assessed for asymptomatic colonisation with S. aureus and MRSA. MAIN OUTCOME MEASURES: The pooled prevalence of asymptomatic colonisation of S. aureus and MRSA of young children globally. RESULTS: In this systematic review and meta-analysis of 21 416 young children, the pooled global prevalence of asymptomatic S. aureus colonisation was 25.1% (95% CI 21.4 to 28.8) and MRSA colonisation was 3.4% (95% CI 2.8 to 4.1). The clones of MRSA strains included healthcare-associated MRSA, community-associated MRSA and livestock-associated MRSA. CONCLUSION: This study provides evidence of increased MRSA colonisation globally among young children, underlining the critical role of asymptomatic carriers in MRSA transmission and the need for control measures. PROSPERO REGISTRATION NUMBER: CRD 42022328385.

Characterization of group A streptococci causing invasive diseases in Sri Lanka.

Group A ß haemolytic streptococcus (GAS) or Streptococcus pyogenes is a human pathogen that causes an array of infections, including pharyngitis, cellulitis, impetigo, scarlet fever, toxic shock syndrome, and necrotizing fasciitis. The present study characterizes 51 GAS isolates from invasive infections in Sri Lanka, focusing on resistance profiles, genetic determinants of resistance, and virulence markers. Isolates were tested for sensitivity to penicillin, erythromycin, clindamycin, and tetracycline. The presence of erm(A), erm(B), and mef(A) was detected in erythromycin-resistant isolates, while tet(M) was detected in the tetracycline-resistant isolates. PCR was used to identify SpeA, SpeB, SpeC, SpeF, SpeG, smez, and ssa as virulence markers. Selected GAS isolates were emm-typed using the updated CDC protocol. All 51 isolates were susceptible to penicillin. The number of isolates non-susceptible to erythromycin was 16. The commonest resistance determinant identified was erm(B) (11/16). Tetracycline non-susceptibility was found in 36 (70.6 %) isolates and 26 of them contained the tet(M) gene. Thirteen (25.5 %) isolates were resistant to both tetracycline and erythromycin, while 12 (23.5 %) isolates were sensitive to both antibiotics. The commonest virulence markers detected among the isolates were SpeB (44, 86.3 %), SpeG (36, 70.6 %), and SpeF (35, 68.6 %), while SpeJ (15, 29.4 %), SpeA (10, 19.6 %), and ssa (5,9.8 %) were less common. The emm types were diverse. In conclusion, the GAS isolates studied showed resistance to erythromycin and tetracycline, while retaining universal susceptibility to penicillin. Additionally, these isolates exhibited diverse genetic backgrounds, displaying varying patterns of virulence genes and emm types.

Brief Report: Nasal colonization with Staphylococcus aureus and methicillin resistant Staphylococcus aureus among community-dwelling older adults with comorbidities seeking follow-up medical care in Central Sri Lanka.

Older adults are more severely affected by infections caused by drug-resistant bacteria including Methicillin-Resistant Staphylococcus aureus (MRSA). We aimed to identify the MRSA colonization rates and associated factors among older adults aged more than 65-years-old. Among the 309 recruited, 152 (49.2 %) were males. Self-collected nasal swabs were used to isolate Staphylococcus aureus and MRSA with routine microbiological methods. Staphylococcus aureus was isolated from 36 (11.7 %) participants while 11 (3.6 %) were colonized with MRSA. We identified a significant association between the male sex and MRSA colonization (P=0.028, Chi-square test). However, this needs careful interpretation given the smaller number of outcome events. Other factors studied had no statistically significant association with MRSA colonization.

Investigating the drivers for antibiotic use and misuse amongst medical undergraduates-perspectives from a Sri Lankan medical school.

Medical undergraduates are a unique group who gain the theoretical knowledge on prescribing antibiotics but are not authorized to prescribe till full licensure. This unique situation may result in self-medication and unauthorized prescription of antibiotics. This cross-sectional study was conducted among medical students of the Faculty of Medicine, University of Peradeniya, Sri Lanka in 2021 to identify patterns and drivers for antibiotic use and misuse among medical undergraduates. A validated, self-administered Google forms-based online questionnaire was used to gather information on antibiotic use, misuse, and associated factors: demographics, knowledge and perceptions. Two scores; a practice score and a knowledge score were calculated to compare with the associated factors. The study population consisted of 347 medical students with a mean age of 24 (SD1.7) years and 142/347 (40.9%) were male participants. The patterns of misuses identified included; use of antibiotics without a prescription (161/347, 46.4%), keeping left-over antibiotics for future use (111/347, 32.0%), not completing the course of antibiotics (81/347, 23.3%), use of left-over antibiotics (74/347, 21.3%), prescribing to animals (61/347, 17.6%), prescribing antibiotics to family members or friends (51/347, 14.7%), antibiotic self-medication (25/347, 7.2%) and not following the dosage regime prescribed (24/347, 6.9%). The practice score ranged from 33% to 100% (median 87%, IQR 80.0-93.3) and did not differ significantly with either the gender or the year of study. The knowledge score ranged from 4% to 100% (median 87%, IQR: 71.5-95.4) differing significantly according to the year of study. Antibiotic prescription by medical undergraduates was perceived as unacceptable (329/347, 94.8%) by the majority. Individual misuse patterns were associated favourably or unfavourably with gender, year of study, having a health care worker at home and knowledge score. The knowledge score increased with the advancement in training at the medical school while the practice score remained indifferent, highlighting the need to identify the additional drivers of antibiotic misuse among medical undergraduates.

Knowledge, perceptions and practices on antibiotic use among Sri Lankan doctors.

INTRODUCTION: Prescribers have a major role in preventing antimicrobial resistance (AMR) through appropriate prescribing. However, in countries like Sri Lanka, where continuous professional development is not mandatory for license renewal and antimicrobial stewardship is not implemented, prescribing practices go largely unchecked. OBJECTIVES: To identify the knowledge on antibiotic use and practices related to antibiotic prescribing among Sri Lankan doctors. METHODS: This cross-sectional study was conducted in 2020. We used a validated, pretested Google-form based questionnaire with multiple choices, single best answer questions, polar questions (Yes/No) and five-point Likert scale questions. The Google-sheet generated was used for data analysis. Knowledge and practice scores were calculated. RESULTS: Of the 262 respondents, 40.1% were males. Majority (61.8%) were aged 25-35-years and in medical practice for 0-5 years (48.9%) while 46.2% had or were engaged in post graduate studies. Knowledge scores ranged from 98.31% to 46.55% [mean:71.27% (SD±10.83); median:71.18% (IQR 64.4-79.7)]. Most (98.09%) obtained ≥50 marks while 45.8% scored more than the mean. The practice scores ranged from 100% to 0% [mean:65.33% (SD±18.16), median:66.67% (IQR53.3-80)]. The majority (81.3%) scored ≥50 in the practice score while 52.3% achieved more than the mean practice score. The knowledge score and the practice score differed significantly (p<0.001, related sample Wilcoxon Signed Rank Test) but the knowledge and practice scores were significantly correlated [Spearman correlation, p<0.001, r = 0.343 (Bias corrected 95% CI 0.237-0.448)]. Knowledge scores and the practice scores were significantly higher in those with or undergoing postgraduate training. CONCLUSIONS: While the knowledge and practice scores were high, and knowledge and practice scores were correlated, the practices score was lower than that of knowledge indicating the need to encourage correct practices through means other than solely promoting knowledge.

Colonization of Group B Streptococcus in Pregnant Women and Their Neonates from a Sri Lankan Hospital.

We investigated the molecular epidemiology of Streptococcus agalactiae (Group B Streptococcus, GBS) from carriage in a cohort of pregnant mothers and their respective newborns in a Teaching Hospital in Sri Lanka. GBS vaginal carriage was assessed on pregnant mothers at pre-delivery (n = 250), post-delivery (n = 130), and from peri-rectal swabs of neonates (n = 159) in a prospective study. All colonizing, non-duplicate GBS isolates (n = 60) were analyzed for antimicrobial susceptibilities, capsular serotyping, and whole-genome sequencing (WGS). The percentage of GBS carriage in mothers in the pre-delivery and post-delivery cohorts were 11.2% (n = 28) and 19.2% (n = 25), respectively, and 4.4% (n = 7) in neonates. GBS isolates predominantly belonged to serotype VI (17/60, 28.3%). The isolates spanned across 12 sequence types (STs), with ST1 (24/60, 40%) being the most predominant ST. Concomitant resistance to erythromycin, tetracyclines, and gentamicin was observed in eight strains (13.3%). WGS revealed the presence of antimicrobial resistance genes including ermA (5/60), mefA (1/60), msrD (1/60), and tetLMO (2/60, 28/60, and 1/60, respectively) among 60 strains. The study provides insight into the diversity of vaccine targets of GBS since serotype VI is yet to be covered in the vaccine development program.

Seroepidemiology of rickettsioses in Sri Lanka: a patient based study.

BACKGROUND: Rickettsioses are emerging infections in Sri Lanka as shown by the increase in the number of clinically diagnosed rickettsial patients being reported to the Epidemiology Unit, Sri Lanka. However, mapping the disease for the whole island with laboratory confirmed cases has not been previously carried out. METHODS: 615 samples received from 23 hospital representing 8 provinces were tested using ELISA or IFA methods and clinical data was collected using a validated questionnaire. RESULTS: Rash was found among more spotted fever seropositive patients than scrub typhus seropositive patients while the opposite was true for the presence of eschar. Spotted fever and scrub typhus was found in a geographically restricted manner. Consistent temporal patterns were seen for the presentation of patients with rickettsioses in Kandy and Kurunegala districts for 2009 and 2010. CONCLUSIONS: This study expanded knowledge on the distribution of rickettsioses in Sri Lanka and their clinical profiles which in turn helps in the clinical diagnosis of these infections.

Persistence of Pneumococcal Serotype 3 in Adult Pneumococcal Disease in Hong Kong.

The epidemiology of hospitalised pneumococcal disease in adults following the introduction of universal childhood pneumococcal immunisation in 2009 was assessed. Culture-confirmed Streptococcus pneumoniae (SP) from adults hospitalised between 2009 to 2017 were examined. The cases were categorised into invasive pneumococcal disease (IPD) and pneumonia (bacteraemic, non-bacteraemic, and that associated with other lung conditions). The isolates were serotyped and antimicrobial susceptibilities were determined by microbroth dilution. Patient characteristics, comorbidities, and outcomes were analysed. Seven hundred and seventy-four patients (mean age, 67.7 years, SD ± 15.6) were identified, and IPD was diagnosed in 110 (14.2%). The most prevalent serotype, 19F, was replaced by serotype 3 over time. Penicillin and cefotaxime non-susceptibilities were high at 54.1% and 39.5% (meningitis breakpoints), 19.9% and 25.5% (non-meningitis breakpoints), respectively. The overall 30-day mortality rate was 7.8% and 20.4% for IPD. Age ≥ 75 years (OR:4.6, CI:1.3-17.0, p < 0.02), presence of any complications (OR:4.1, CI:1.02-16.3, p < 0.05), pleural effusion (OR:6.7, CI:1.2-39.4, p < 0.03) and intensive care unit (ICU) admission (OR:9.0, CI:1.3-63.4, p < 0.03) were independent predictors of 30-day mortality. Pneumococcal disease by PCV 13 covered serotypes; in particular, 19F and 3 are still prominent in adults. Strengthening targeted adult vaccination may be necessary in order to reduce disease burden.

Longitudinal Genomic Characterization of Carbapenemase-producing Enterobacteriaceae (CPE) Reveals Changing Pattern of CPE Isolated in Hong Kong Hospitals.

An active, territory-wide, CPE surveillance program implemented from 2011 showed increasing levels of carbapenemase-producing Enterobacteriaceae (CPE) isolates from patients in Hong Kong hospitals. The molecular epidemiology of 567 CPE from patients of three of seven public hospital clusters in Hong Kong are described. During a 7-year period, the incidence of CPE isolation increased from 0.05 to 9.6/100 000 patient-days. The carbapenemase genes identified were polyclonal, including blaKPC, blaNDM and blaIMP, which were mainly associated with hospitalization overseas in previous years. However, increasing CPE isolation from patients without hospitalization overseas occurred in 2015, with blaNDM (52.6%) predominant followed by blaIMP (30.0%). Escherichia coli (46.4%) and Klebsiella spp. (38.3%) were the dominant species. Whole-genome sequencing was performed on 169 representative isolates with a combination of short and long reads using Illumina and Nanopore technology. Two distinct lineages of blaKPC-2-positive Klebsiella pneumoniae (ST11 and ST258) were identified with ST11 carrying yersiniabactin gene ybt-9 on ICEKp3. ST131 E. coli producing IMP-4 was present throughout the study period. The blaNDM and blaIMP genes were mainly carried in IncX3 and IncN-ST7 plasmids, respectively. blaOXA-48-like gene was carried in the IncX3 plasmid in E. coli and in the ColKP3 plasmid in K. pneumoniae. A lineage of K. pneumoniae with blaNDM-1 plus blaOXA-232 in distinct plasmids of IncF1B/IncHI1B was identified and associated with prior hospitalization overseas. This study highlights the threat of multiple types of CPE, with the predominance of blaNDM and blaIMP among CPE in our hospitals. Enhanced containment strategies are needed to mitigate the trend of rapidly rising CPE in healthcare settings.

Pneumococcal colonization among healthy and hospitalized vaccine-naive Sri Lankan children.

BACKGROUND: Streptococcus pneumoniae continues to cause mortality and morbidity despite availability of effective vaccines. Pneumococcal colonization is considered a pre-requisite for disease. Identifying the serotypes circulating in a given locale is important for surveillance purposes as well as for assessing the need for vaccination. Aim of the present study was to identify nasopharyngeal pneumococcal colonization rates in healthy children and children with respiratory tract infections in central Sri Lanka. METHOD: A total of 450 nasopharyngeal swabs (NPS) of children aged between 2 months and 2 years were collected from two groups; healthy children and children hospitalized with respiratory symptoms. NPS samples were processed using conventional laboratory techniques to isolate S. pneumoniae. Antibiotic susceptibility patterns of pneumococcal isolates were identified using CLSI disc diffusion method and minimum inhibitory concentration (MIC) was determined by micro-broth dilution method. RESULTS: Pneumococcal colonization rate among healthy children was 31.8% (143/450) it was 39.8% (179/450) in children hospitalized with respiratory symptoms. MIC for penicillin and cefotaxime ranged between 0.015 to 4 µg/ml and <0.015 to 16 µg/ml respectively. All isolates were susceptible to levofloxacin, vancomycin, linezolid and rifampicin. Erythromycin and tetracycline non-susceptibility rates were >50% in both groups. The predominant serotypes identified were 19F (n = 66, 20.5%), 6B (n = 43, 13.4%), 6A (n = 30, 9.3%), 23F (n = 28, 8.7%) and 14 (n = 20, 6.2%). Among healthy children, presence of school going children at home and the number of household members were significantly associated with pneumococcal colonization while in hospitalized children, pneumococcal colonization was significantly associated with presence of school going children at home. CONCLUSION: Pneumococcal colonization rates were considerably higher in both study cohorts and the commonest serotypes were 19F, 6B, 6A, 23F and 14. Antibiotic resistance rates were also relatively higher among the pneumococcal isolates.