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.

Characterizing Mobilized Virulence Factors and Multidrug Resistance Genes in Carbapenemase-Producing Klebsiella pneumoniae in a Sri Lankan Hospital.

Limited data is available on the epidemiology and characteristics of carbapenem-resistant Enterobacteriaceae (CRE) and their associated plasmids or virulence determinants from Sri Lanka. Through whole genome sequencing of CREs from the intensive care units of a Sri Lankan teaching hospital, we identified a carbapenemase gene, blaOXA-181 in 10 carbapenemase-producing Klebsiella pneumoniae isolates (two strains of ST437 and eight strains of ST147) from 379 respiratory specimens. blaOXA-181 was carried in three variants of ColE-type plasmids. K. pneumoniae strains with ompK36 variants showed high minimum inhibitory concentrations to carbapenem. Furthermore, genes encoding for extended spectrum ß-lactamases (ESBL), plasmid-mediated quinolone resistance (PMQR) determinants (qnr, aac(6')-Ib-cr, and oqxAB) were present in all 10 strains. Amino acid substitution in chromosomal quinolone resistance-determining regions (QRDRs) gyrA (Ser83Ile) and parC (Ser80Ile) were also observed. All strains had yersiniabactin genes on mobile element ICEkp. Strict infection control practices and judicious use of antibiotics are warranted to prevent further spread of multidrug-resistant K. pneumoniae.

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.