Plasmid interference for curing antibiotic resistance plasmids in vivo

Antibiotic resistance increases the likelihood of death from infection by common pathogens such as Escherichia coli and Klebsiella pneumoniae in developed and developing countries alike. Most important modern antibiotic resistance genes spread between such species on self-transmissible (conjugative) plasmids. These plasmids are traditionally grouped on the basis of replicon incompatibility (Inc), which prevents coexistence of related plasmids in the same cell. These plasmids also use post-segregational killing (‘addiction’) systems, which poison any bacterial cells that lose the addictive plasmid, to guarantee their own survival. This study demonstrates that plasmid incompatibilities and addiction systems can be exploited to achieve the safe and complete eradication of antibiotic resistance from bacteria in vitro and in the mouse gut. Conjugative ‘interference plasmids’ were constructed by specifically deleting toxin and antibiotic resistance genes from target plasmids. These interference plasmids efficiently cured the corresponding antibiotic resistant target plasmid from different Enterobacteriaceae in vitro and restored antibiotic susceptibility in vivo to all bacterial populations into which plasmid-mediated resistance had spread. This approach might allow eradication of emergent or established populations of resistance plasmids in individuals at risk of severe sepsis, enabling subsequent use of less toxic and/or more effective antibiotics than would otherwise be possible, if sepsis develops. The generalisability of this approach and its potential applications in bioremediation of animal and environmental microbiomes should now be systematically explored.

Quantitative multiplexed-tandem PCR for direct detection of bacteraemia in critically ill patients

Culture remains the gold standard for diagnosis of blood stream infections (BSI), but its clinical utility is limited by slow turnaround times. Here we describe a method for rapid quantitative detection of bacterial DNA directly extracted from whole blood using a multiplexed tandem real-time PCR (MT-PCR) assay targeting Staphylococcus, Streptococcus, Pseudomonas, Enterococcus and Enterobacteriaceae 16S rDNA genes. Results were available less than 3.5 hours after blood collection with all five bacterial targets having limits of detection between 10¹ and 10³ CFU/mL. A small-scale clinical evaluation of the assay using blood samples collected from 15 patients admitted to the Intensive Care Unit at our institution demonstrated 93.3% (14/15) concordance between MT-PCR and blood culture when detection of persistent bacterial DNAemia by MT- PCR was considered a true result. Further evaluation with clinical samples is needed; however, this method has potential as an effective rule-in diagnostic tool for bacteraemic sepsis and septic shock.

In vitro volatile organic compound profiling using GC×GC-TOFMS to differentiate bacteria associated with lung infections: a proof-of-concept study

Chronic pulmonary infections are the principal cause of morbidity and mortality in individuals with cystic fibrosis (CF). Due to the polymicrobial nature of these infections, the identification of the particular bacterial species responsible is an essential step in diagnosis and treatment. Current diagnostic procedures are time-consuming, and can also be expensive, invasive and unpleasant in the absence of spontaneously expectorated sputum. The development of a rapid, non-invasive methodology capable of diagnosing and monitoring early bacterial infection is desired. Future visions of real-time, in situ diagnosis via exhaled breath testing rely on the differentiation of bacteria based on their volatile metabolites. The objective of this proof-of-concept study was to investigate whether a range of CF-associated bacterial species (i.e. Pseudomonas aeruginosa, Burkholderia cenocepacia, Haemophilus influenzae, Stenotrophomonas maltophilia, Streptococcus pneumoniae and Streptococcus milleri) could be differentiated based on their in vitro volatile metabolomic profiles. Headspace samples were collected using solid phase microextraction (SPME), analyzed using comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC×GC-TOFMS) and evaluated using principal component analysis (PCA) in order to assess the multivariate structure of the data. Although it was not possible to effectively differentiate all six bacteria using this method, the results revealed that the presence of a particular pattern of VOCs (rather than a single VOC biomarker) is necessary for bacterial species identification. The particular pattern of VOCs was found to be dependent upon the bacterial growth phase (e.g. logarithmic versus stationary) and sample storage conditions (e.g. short-term versus long-term storage at  -18 °C). Future studies of CF-associated bacteria and exhaled breath condensate will benefit from the approaches presented in this study and further facilitate the production of diagnostic tools for the early detection of bacterial lung infections.

Characterization of multidrug-resistant Klebsiella pneumoniae from Australia carrying blaNDM-1

blaNDM genes, encoding metallo-β-lactamases providing resistance to carbapenems, have been reported in many locations since the initial report in 2008, including in several Enterobacteriaceae isolates in Australia/New Zealand. Here, we compare 4 additional carbapenem-resistant Klebsiella pneumoniae carrying blaNDM-1 isolated in Australia. Two are sequence type ST147, previously associated with blaNDM in Australia and elsewhere. They carry blaNDM-1 and different 16S rRNA methylase genes (armA or rmtC) on different conjugative plasmids, in 1 case with an IncFIIY replicon. One isolate belongs to the globally important ST11 but did not transfer a plasmid to Escherichia coli. The fourth isolate belongs to the novel ST1068 and transferred blaNDM-1, armA, and an IncA/C plasmid. Amplification and sequencing of ompK porin genes suggest that, unlike the case for other carbapenemase genes, ompK36 defects may not be required for NDM to cause clinically relevant levels of carbapenem resistance.

Dependency of caspase-1 activation induced in macrophages by Listeria monocytogenes on cytolysin, listeriolysin O, after evasion from phagosome into the cytoplasm

Listeriolysin O (LLO), an hly-encoded cytolysin from Listeria monocytogenes, plays an essential role in the entry of this pathogen into the macrophage cytoplasm and is also a key factor in inducing the production of IFN-gamma during the innate immune stage of infection. In this study, we examined the involvement of LLO in macrophage production of the IFN-gamma-inducing cytokines IL-12 and IL-18. Significant levels of IL-12 and IL-18 were produced by macrophages upon infection with wild-type L. monocytogenes, whereas an LLO-deficient mutant (the L. monocytogenes Deltahly) lacked the ability to induce IL-18 production. Complementation of Deltahly with hly completely restored the ability. However, when Deltahly was complemented with ilo encoding ivanolysin O (ILO), a cytolysin highly homologous with LLO, such a restoration was not observed, although ILO-expressing L. monocytogenes invaded and multiplied in the macrophage cytoplasm similarly as LLO-expressing L. monocytogenes. Induction of IL-18 was diminished when pretreated with a caspase-1 inhibitor or in macrophages from caspase-1-deficient mice, suggesting the activation of caspase-1 as a key event resulting in IL-18 production. Activation of caspase-1 was induced in macrophages infected with LLO-expressing L. monocytogenes but not in those with Deltahly. A complete restoration of such an activity could not be observed even after complementation with the ILO gene. These results show that the LLO molecule is involved in the activation of caspase-1, which is essential for IL-18 production in infected macrophages, and suggest that some sequence unique to LLO is indispensable for some signaling event resulting in the caspase-1 activation induced by L. monocytogenes.

Haemophilus influenzae type-b and non-b-type invasive diseases in urban children (<5years) of Bangladesh: implications for therapy and vaccination

OBJECTIVE

To prospectively study the epidemiology and antibiotic resistance of Haemophilus infuenzae isolates from invasive infections in children.

METHODS

Children (<5years) with pneumonia, meningitis and septicemia from three hospitals in Dhaka, Bangladesh were enrolled (1999-2003); clinical and laboratory data, and blood for cultures were collected. Cerebrospinal fluid (CSF) of meningitis cases was analyzed (Gram stain, culture and biochemical tests). Hib antigen was detected by latex agglutination (LA) in culture-negative pyogenic CSF and PCR was done for bexA gene in culture- and LA-negative pyogenic CSF. Antibiotic susceptibility was determined by E-Tests and beta-lactamase by nitrocefin stick.

RESULTS

Seventy-three cases of H. influenzae infections (46 of 293 meningitis cases, 25 of 1493 pneumonia cases, 2 of 48 septicemia cases) were detected; 63%, 34% and 3% of them had meningitis, pneumonia and septicemia respectively. H. influenzae type b (Hib) caused infections in 80.8% of cases (60.3% meningitis, 20.5% pneumonia). Most (86%) infections clustered in 4-12month infants. The case-fatality in pneumonia was 8% compared to 19% in meningitis. H. influenzae isolates from pneumonia and meningitis children were equally resistant to antibiotics (46% vs 43%). Of 10 drugs tested, isolates were resistant to ampicillin (31%), chloramphenicol (42%), trimethoprim-sulfamethoxazole (44%) and azithromycin (1.4%). Multidrug-resistant (MDR) strains were equally prevalent in Hib (31%) and non-b-type (29%) isolates, and in pneumonia (31%) and meningitis (34%) cases. None was resistant to amoxicillin-clavulanate, ceftriaxone, ciprofloxacin, levofloxacin, moxifloxacin, and gatifloxacin. Of all H. influenzae infections, 40%, 4.4% and 100% of pneumonia, meningitis and septicemia cases were caused by other serotypes or non-typeable strains. All ampicillin-resistant-strains produced beta-lactamase without detection of beta-lactamase-negative-ampicillin-resistant (BLNAR) strains.

CONCLUSION

Hib is a leading cause of invasive bacterial infections in infants. Multidrug-resistant H. influenzae is common and requires amoxicillin-clavulanate, ceftriaxone or azithromycin as empirical therapy with specific recommendation for use of ceftriaxone for treatment of meningitis particularly MDR cases. New fluoroquinolines has potential utility. An effective national Hib vaccination programme is essential in Bangladesh although non-Hib infections will remain an issue.

Increasing spectrum in antimicrobial resistance of Shigella isolates in Bangladesh: resistance to azithromycin and ceftriaxone and decreased susceptibility to ciprofloxacin

Antimicrobial resistance of Shigella isolates in Bangladesh, during 2001-2002, was studied and compared with that of 1991-1992 to identify the changes in resistance patterns and trends. A significant increase in resistance to trimethoprim-sulphamethoxazole (from 52% to 72%, p < 0.01) and nalidixic acid (from 19% to 51%, p < 0.01) was detected. High, but unchanged, resistance to tetracycline, ampicillin, and chloramphenicol, low resistance to mecillinam (resistance 3%, intermediate 3%), and to emergence of resistance to azithromycin (resistance 16%, intermediate 62%) and ceftriaxone/cefixime (2%) were detected in 2001-2002. Of 266 recent isolates, 63% were resistant to > or =3 anti-Shigella drugs (multidrug-resistant [MDR]) compared to 52% of 369 strains (p < 0.007) in 1991-1992. Of 154 isolates tested by E-test in 2001-2002, 71% were nalidixic acid-resistant (minimum inhibitory concentration [MIC] > or =32 microg/mL) and had 10-fold higher MIC90 (0.25 microg/mL) to ciprofloxacin than that of nalidixic acid-susceptible strains exhibiting decreased ciprofloxacin susceptibility, which were detected as ciprofloxacin-susceptible and nalidixic acid-resistant by the disc-diffusion method. These strains were frequently associated with MDR traits. High modal MICs were observed to azithromycin (MIC 6 microg/mL) and nalidixic acid (MIC 128 micdrog/mL) and low to ceftriaxone (MIC 0.023 microg/mL). Conjugative R-plasmids-encoded extended-spectrum beta-lactamase was responsible for resistance to ceftriaxone/cefixime. The growing antimicrobial resistance of Shigella is worrying and mandates monitoring of resistance. Pivmecillinam or ciprofloxacin might be considered for treating shigellosis with caution.

Emergence of multidrug-resistant Salmonella enterica serotype Typhi with decreased ciprofloxacin susceptibility in Bangladesh

During 1989-2002, we studied the antimicrobial resistance of 3928 blood culture isolates of Salmonella enterica serotype Typhi (S. Typhi) in Dhaka, Bangladesh. Overall 32% (1270) of the strains were multidrug-resistant (MDR, resistant to chloramphenicol, ampicillin and trimethoprim-sulphamethoxazole); first detected in 1990 (rate of 8%), increased in 1994 (44%), declined in 1996 (22%, P<0.01 compared to 1994) and re-emerged in 2001 (36%) and 2002 (42%, P<0.01 compared to 1996). An increased MIC of ciprofloxacin (0.25 microg/ml) indicating decreased susceptibility to ciprofloxacin was detected in 24 (18.2%) out of 132 randomly selected strains during 1990-2002; more frequently in MDR than susceptible strains (46.3% vs. 5.5%, P<0.001), and the proportion of them rose to 47% in 2002 from 8% in 2000 (P<0.01). Ciprofloxacin (5 microg) disk diffusion zone diameters of < or =24 mm as break-point had 98% sensitivity and 100% specificity when compared with a ciprofloxacin MIC of 0.25 microg/ml as break-point for decreased susceptibility; being a useful and easy screen test. All strains were susceptible to ceftriaxone. The emergence of MDR S. Typhi with decreased ciprofloxacin susceptibility will further complicate the therapy of typhoid fever because of the lack of optimum treatment guidelines.

Decline in epidemic of multidrug resistant Salmonella typhi is not associated with increased incidence of antibiotic-susceptible strain in Bangladesh

Since 1987, multidrug resistant (MDR) strains of Salmonella Typhi, resistant simultaneously to ampicillin, chloramphenicol and trimethoprim-sulfamethoxazole, have caused epidemics of severe typhoid fever in Asia and Africa. A retrospective analysis of blood culture results (1989-96) in a Diarrhoea Treatment Centre in Dhaka, Bangladesh detected MDR strains in 0.3% (8 of 2793) of samples in 1990. The isolation rate peaked to 3.2% (240 of 7501) in 1994 (P < 0.01) and decreased to 1.8% (165 of 9348) in 1995 and further to 1.0% (82 of 8587) in 1996 (P < 0.01 compared to 1994) indicating the emergence and decline of MDR typhoid epidemic. Ten of 15 MDR strains tested had a 176 kb conjugative R plasmid that mediates resistance to ampicillin, chloramphenicol and trimethoprim-sulfamethoxazole to Escherichia coli K12. Unlike MDR strains, the isolation rate (approximately 3.3%) of susceptible S. Typhi remained remarkably unchanged during the study. The significant decrease in isolation of MDR strains suggests that cheaper and effective first-line antibiotics may re-emerge as drugs of choice for the treatment of typhoid fever in Bangladesh.

First outbreak of dengue hemorrhagic fever, Bangladesh

During the first countrywide outbreak of dengue hemorrhagic fever in Bangladesh, we conducted surveillance for dengue at a hospital in Dhaka. Of 176 patients, primarily adults, found positive for dengue, 60.2% had dengue fever, 39.2% dengue hemorrhagic fever, and 0.6% dengue shock syndrome. The Dengue virus 3 serotype was detected in eight patients.

Rapid detection of Haemophilus influenzae type b in Bangladeshi children with pneumonia and meningitis by PCR and analysis of antimicrobial resistance

A polymerase chain reaction (PCR) assay with primers from 'bexA' gene was compared with culture for the detection of Haemophilus influenzae type b (Hib) in clinical samples from children with pneumonia and meningitis. Of 200 sera (180 from pneumonia, 20 from non-pneumonia patients) tested by PCR (serum-PCR), Hib was detected in 15 of 16 blood culture-positive and in 6 blood culture-negative pneumonia cases. When compared with the results of blood culture, serum-PCR had sensitivity, specificity, and accuracy index of 93.7%, 96.7%, and 96.5% respectively. Of 120 cerebrospinal fluid (CSF) samples from meningitis patients tested by culture and PCR (CSF-PCR), the latter method could detect Hib in all 15 culture-positive and in 8 of 105 culture-negative cases, showing sensitivity, specificity, and accuracy index of 100%, 92.4%, and 94.4% respectively. The PCR result was available within a day. Antimicrobial susceptibility of Hib was determined by the disc-diffusion method. High rate of resistance to ampicillin (54.8%), chloramphenicol (48.4%), and co-trimoxazole (80.6%) was observed among 31 invasive Hib isolates with resistance to all 3 drugs (multiresistance) in 48.4% of the isolates. All the Hib isolates were susceptible to ceftriaxone. The study has shown that PCR is a rapid, sensitive and specific diagnostic test for Hib from clinical samples, and a combination of culture and PCR is necessary for the detection of Hib infections to the maximum extent for case management to reduce morbidity, mortality, and complications of the invasive Hib infections. A high prevalence of multiresistant Hib strains is a matter of concern.