Comparison of the performance of three variations of the Carbapenem Inactivation Method (CIM, modified CIM [mCIM] and in-house method (iCIM)) for the detection of carbapenemase-producing Enterobacterales and non-fermenters.

OBJECTIVE: The objective of this study was to compare the performance of an in-house CIM (iCIM) modification with the CIM and mCIM for the detection of carbapenemase production in 149 well characterised isolates (70 carbapenemase producers and 79 non-carbapenemase producers). METHODS: Isolates were tested using the CIM, mCIM and iCIM procedures. The gold standard was genotypic characterisation by PCR. RESULTS: For Acinetobacter baumannii, the sensitivity was low (10%) for the mCIM, 70% for the CIM but was 100% for the iCIM, with a specificity of 100% for all three. For Enterobacterales, the sensitivity of all three tests was 100% for Ambler class A and B ß-lactamases, while the iCIM also had a sensitivity of 100% for class D ß lactamases. The sensitivity in Enterobacterales was highest for the iCIM at 100% (CIM 98.2%, mCIM 96.2%). The specificity was 100% for the mCIM and 98% for the CIM and iCIM. For Pseudomonas aeruginosa, the sensitivity of the CIM (100%) was higher than the iCIM (85.7%) and the mCIM (71.4%). iCIM exhibited excellent sensitivity (100%) and specificity (98%) for carbapenemase detection in Enterobacterales and was able to detect two OXA-232 producers that the mCIM did not detect and an OXA-181 producer that the CIM did not detect. CONCLUSIONS: In conclusion, iCIM performed better than the CIM and mCIM for carbapenemase detection in A. baumannii and Enterobacterales, however the CIM achieved the highest sensitivity for carbapenemase detection in P. aeruginosa suggesting that different CIM variations should be utilised depending on the organism type.

Haemophilus influenzae type b carriage and novel bacterial population structure among children in urban Kathmandu, Nepal.

Haemophilus influenzae type b (Hib) is a major cause of invasive bacterial infection in children that can be prevented by a vaccine, but there is still uncertainty about its relative importance in Asia. This study investigated the age-specific prevalence of Hib carriage and its molecular epidemiology in carriage and disease in Nepal. Oropharyngeal swabs were collected from children in Kathmandu, Nepal, from 3 different settings: a hospital outpatient department (OPD), schools, and children's homes. Hib was isolated using Hib antiserum agar plates, and serotyping was performed with latex agglutination. Hib isolates from children with invasive disease were obtained during active microbiological surveillance at Patan Hospital, Kathmandu, Nepal. Genotyping of disease and carriage isolates was undertaken using multilocus sequence typing (MLST). Swabs were taken from 2,195 children, including 1,311 children at an OPD, 647 children attending schools, and 237 children in homes. Overall, Hib was identified in 5.0% (110/2,195; 95% confidence interval [95% CI], 3.9% to 6.4%). MLST was performed on 108 Hib isolates from children carrying Hib isolates and 15 isolates from children with invasive disease. Thirty-one sequence types (STs) were identified, and 20 of these were novel STs. The most common ST isolates were sequence type 6 (ST6) and the novel ST722. There was marked heterogeneity among the STs from children with disease and children carrying Hib. STs identified from invasive infections were those commonly identified in carriage. This study provides evidence of Hib carriage among children in urban Nepal with genetically diverse strains prior to introduction of universal vaccination. The Hib carriage rate in Nepal was similar to the rates observed in other populations with documented high disease rates prior to vaccination, supporting implementation of Hib vaccine in Nepal in 2009.

Incidence and characteristics of viral community-acquired pneumonia in adults.

BACKGROUND: In adults, viral causes of community-acquired pneumonia (CAP) are poorly characterised. The aims of this study were to characterise the viral aetiology of CAP in adults by using an extensive array of viral diagnostic tests and to compare the characteristics of viral pneumonia with those of pneumococcal pneumonia. METHODS: Adults admitted to Christchurch Hospital over a 1-year period with CAP were included in the study. Microbiological testing methods included blood and sputum cultures, urinary antigen testing for Streptococcus pneumoniae and Legionella pneumophila, antibody detection in paired sera and detection of respiratory viruses in nasopharyngeal swabs by immunofluorescence, culture and PCR. RESULTS: Of 304 patients with CAP, a viral diagnosis was made in 88 (29%), with rhinoviruses and influenza A being the most common. Two or more pathogens were detected in 49 (16%) patients, 45 of whom had mixed viral and bacterial infections. There were no reliable clinical predictors of viral pneumonia, although several variables were independently associated with some aetiologies. The presence of myalgia was associated with pneumonia caused by any respiratory virus (OR 3.62, 95% CI 1.29 to 10.12) and influenza pneumonia (OR 190.72, 95% CI 3.68 to 9891.91). Mixed rhinovirus/pneumococcal infection was associated with severe disease. CONCLUSIONS: Virus-associated CAP is common in adults. Polymicrobial infections involving bacterial and viral pathogens are frequent and may be associated with severe pneumonia.

Human metapneumovirus in children with bronchiolitis or pneumonia in New Zealand.

OBJECTIVES: To confirm the presence of human metapneumovirus (hMPV) in New Zealand and establish its prevalence in selected paediatric patient groups. METHODS: Nasopharyngeal swabs were collected in two separate paediatric studies enrolling children clinically diagnosed with either bronchiolitis or pneumonia and tested for hMPV by polymerase chain reaction. RESULTS: Nucleic acid detection tests demonstrated 5.3% of paediatric bronchiolitis cases were positive for hMPV RNA and 2.7% of children admitted with pneumonia tested positive for hMPV RNA. CONCLUSIONS: The presence of hMPV in New Zealand has been confirmed in two selected paediatric patient groups, namely children diagnosed with bronchiolitis and pneumonia. These results indicate that hMPV is associated with a minority of cases of bronchiolitis or pneumonia in this patient group.

Prevalence and phylogenetic characterisation of TT-virus in the blood donor population of Auckland, New Zealand.

TT-virus (TTV, patient initials: T.T.), a novel DNA virus, was first isolated in Japan in 1997 from serum of a patient with post-transfusion hepatitis of unknown aetiology. To date, the contribution of TTV to liver disease remains doubtful. The potential for transmission via blood and blood products makes it essential to establish the prevalence of TTV viraemia in the blood donor population. 413 blood donor serum samples were chosen randomly, the DNA was extracted and TTV-specific DNA amplified by nested polymerase chain reaction (PCR). TTV infection was present in 13 out of 413 (3.15%) blood donors in the Auckland region of New Zealand using a set of primers targeting open reading frame (ORF) 1. These 13 amplification products (264 bp) were sequenced and TTV genotypes determined. Alignment with published TTV sequences showed that seven (53.8%) of the thirteen positive serum samples belonged to genotype 1, five (38.5%) belonged to genotype 2 and one (7.7%) could not be classified as either genotype 1 or 2. One hundred twenty-seven blood donor serum samples were retested with a second set of primers targeting the 5' region of the TTV genome in a single round PCR. Forty-three samples were positive for TTV DNA with these primers resulting in a prevalence of 37%. The data demonstrate that TTV is present among New Zealand blood donors and support the need for further investigation into the natural history of TTV infection.