Cerebrospinal Fluid Isolates Research Articles

Impact of COVID-19 on the Prevalence and Drug Resistance of Bacteria Isolated From Bacterial Meningitis Cerebrospinal Fluid in Shandong Province: A Multicenter Retrospective Study.

Our objective was to evaluate the ramifications of the 2019 coronavirus disease (COVID-19) pandemic on the microbial profile and antimicrobial resistance patterns of bacteria isolated from cerebrospinal fluid (CSF) specimens of patients with bacterial meningitis. We conducted a retrospective analysis of laboratory results and clinical records about positive CSF cultures reported by the SPARSS network from 2017 to 2023. The study covered three distinct periods: January 2017 to December 2019 (before the COVID-19 pandemic), January 2020 to December 2022 (during the COVID-19 pandemic), and January 2023 to December 2023 (after the COVID-19 pandemic), with a total of 5793 CSF isolates collected. Notably, the proportion of male patients (61.3%) was higher than that of females. After COVID-19, we observed a notable shift in the seasonal peak of CSF pathogens, with a delay of approximately 3 months. Remarkable alterations were evident in both pediatric and adult CSF isolate profiles. In children, the predominant pathogens included coagulase-negative Staphylococcus (CoNS), Streptococcus pneumonia, and Escherichia coli. Notably. After COVID-19, there was a significant decrease in the proportion of CoNS (p = 0.0039) and a notable increase in E. coli (p = 0.0067). In adults, the top three pathogens were CoNS, Acinetobacter baumannii, and Klebsiella pneumoniae. After the pandemic, we observed a significant reduction in the prevalence of A. baumannii (p = 0.0059), while the proportions of K. pneumoniae, Pseudomonas aeruginosa, Enterobacter cloacae, and Enterococcus faecalis increased significantly (p < 0.05). Additionally, among multidrug-resistant bacteria, the detection rate of carbapenem-resistant E. coli escalated (p = 0.0375). Antimicrobial susceptibility analysis indicated a declining trend in resistance rates for CoNS and A. baumannii to certain antibiotics following the pandemic. Conversely, resistance to imipenem in A. baumannii increased. In conclusion, the COVID-19 pandemic has significantly influenced the composition, antimicrobial resistance patterns, and epidemiological dynamics of CSF-isolated bacteria in Shandong province. To effectively address these changes, ongoing and dynamic surveillance of pathogen trends and antimicrobial resistance rate is essential.

High Mortality Rates and Antimicrobial Resistance in Children with Invasive Bacterial Infections in a Tertiary Care Facility in West Africa

Abstract Background Childhood data on infection mortality and antimicrobial resistance in Sub-Saharan Africa are emerging but remain limited. The University of Maryland Center for Vaccine Development (CVD) and CVD-Mali have been conducting a prospective observational study at L’Hopital Gabriel Toure (HGT), a referral hospital in Bamako, Mali, since 2002 to identify causes of invasive bacterial infections (IBI) in children. These data have been used to initiate vaccination programs to decrease the burden of Haemophilus influenzae type b and Streptococcus pneumoniae. Additional demographic and antimicrobial susceptibility data have been collected since 2021, allowing for more detailed resistance and mortality analyses. Methods All children presenting to HGT are screened. Children ages 0-15 years with temperature of at least 39 degrees Celsius and/or suspicion of IBI are eligible. Eligible children have blood cultures collected with additional site-specific cultures when focal infection is suspected. Cultures are performed using the Bactec system; when positive, Gram staining, sub-culturing, and antimicrobial susceptibility testing (by disk diffusion using standard methods) are performed. Organisms thought to be contaminants are excluded. American type culture collection strains are utilized for quality control. Results Between 1/14/2021 and 9/14/2023, 28703 patients were screened. 2156 patients were included. 212 patients (10%) had 235 pathogens isolated. Gram positive organisms were most frequently isolated (N=112), followed by Gram negative Enterobacterales (N=81), non-Enterobacterales Gram negatives (N=36), and yeast (N=6). Staphylococcus aureus was the most frequently isolated Gram positive organism (59 bloodstream isolates, 2 joint isolates, 2 subcutaneous isolates) followed by S.pneumoniae (10 bloodstream isolates, 17 cerebrospinal fluid isolates, 1 joint isolate) and Enterococcus species (16 bloodstream isolates). Klebsiella pneumoniae (28 bloodstream isolates, 2 cerebrospinal fluid isolates) and Escherichia coli (18 bloodstream isolates, 3 cerebrospinal fluid isolates, 2 subcutaneous isolates) were the most frequently isolated Gram negative Enterobacterales, with Pseudomonas species most common among non-Enterobacterales Gram negative organisms (16 bloodstream isolates, 1 cerebrospinal fluid isolate). Mortality rates in both culture-positive and culture-negative patients were high (52% and 28%, respectively), with greater than 50% of deaths occurring within 48 hours in both groups. 88% of Gram negative Enterobacterales were ceftriaxone resistant or intermediate, with 56% ciprofloxacin resistant or intermediate; 55% of isolates were resistant or intermediate to both. 71% of isolates were gentamicin resistant. Imipenem resistance remained low, with 91% of isolates retaining sensitivity. 24% of S. aureus isolates were oxacillin resistant and 34% of isolates were resistant or intermediate to trimethoprim/sulfamethoxazole. 100% of S. aureus isolates tested (14/60) retained sensitivity to clindamycin. Only 54% of pneumococcal isolates had positive oxacillin screens, implying frequent penicillin resistance, and only 60% of enterococcal species were ampicillin sensitive, although 92% retained vancomycin sensitivity. Conclusion We found higher mortality rates in our study than in similar studies; the contribution of issues such as limited access to advanced supportive care and delay in presentation is an area for further study. The high frequency of multidrug-resistant organisms is alarming, suggesting an urgent need to investigate underlying contributing factors, increase access to affordable broad-spectrum antibiotics, and create robust antimicrobial stewardship programs.

Prevalence and antimicrobial resistance of bacterial meningitis in China from 2017 to 2021: a multicenter retrospective study.

This study aims to investigate the changing epidemiology and antimicrobial susceptibility of bacteria isolated from cerebrospinal fluid (CSF) in the Shandong region. We conducted a retrospective analysis of bacterial distribution and resistance patterns in CSF samples, utilizing data from the SPARSS network and analyzed with WHONET 5.6 software. A total of 3968 pathogenic bacterial strains were isolated, consisting of 70.6% Gram-positive bacteria, 27.2% Gram-negative bacteria, and 0.2% fungi. The six most commonly detected bacteria were coagulase-negative staphylococcus, Acinetobacter baumannii, Klebsiella pneumoniae, Streptococcus pneumoniae, Escherichia coli, and staphylococcus aureus. Analysis revealed gender and seasonal variations in the distribution of CSF pathogens, with a higher incidence observed in males and during autumn compared to other seasons. The susceptibility profiles of these bacterial species varied significantly, with many exhibiting multidrug resistances. A. baumannii showed a high resistance rate to cephalosporins and carbapenems but was sensitive to tigecycline and polymyxins. For treating multidrug-resistant A. baumannii infections, polymyxin-based combinations with tigecycline or sulbactam are recommended for adults, while tigecycline combined with meropenem is suggested for children. Enterobacteriaceae species were generally sensitive to carbapenems, such as meropenem and other carbapenems that can penetrate the blood-brain barrier can be recommended. Linezolid and vancomycin are the first choice for treating common gram-positive bacterial infections. The high resistance rates observed among common CSF isolates and their varied distributions across different demographics highlight the necessity for customized treatment strategies.

Phylogenetic position and genetic features of HIV-1 in CNS

Background. Due to the wide coverage with antiretroviral therapy, the life expectancy of HIV infected people has significantly increased. Against the background of a decrease in mortality from HIV infection, HIV-associated neurocognitive disorders, which develop even during effective treatment, are of high importance. The overall prevalence of this pathology among HIV-infected people reaches 42.6%.&#x0D; The objective of the study was to research the genetic features and phylogenetic position of HIV-1 persisting in the central nervous system.&#x0D; Materials and methods. The clinical study group consisted of 38 patients with severe neurocognitive disorders against the background of HIV infection in stage 4B. The viral load of HIV-1 in blood plasma and cerebrospinal fluid (CSF) was measured using the "AmpliSens HIV Monitor-FRT" reagents kit. Sanger sequencing was performed using the AmpliSens HIV-Resist-Seq assay kit on an Applied Biosystems 3500 analyzer. Phylogenetic analysis of the pol gene fragments of HIV-1 strains (the site encoding the viral protease and part of the reverse transcriptase) was carried out using maximum likelihood method with the GTR+G nucleotide substitution model. Comparisons of the tertiary structure of viral proteins were performed according to three-dimensional models of the protease and p51 and p66 reverse transcriptase subunits obtained by homologous reconstruction using the SWISS-MODEL tools.&#x0D; Results. The viral load in the sample of patients with severe CNS lesions in blood plasma was 6.27 times higher than in CSF and amounted to 4.67 and 3.87 lg copies/ml respectively by median (p = 0,004).&#x0D; Phylogenetic analysis with the use of all available HIV-1 genomes from GenBank, which differed from the studied ones by less than 5% showed close genetic relations of viruses circulating in Chelyabinsk region, apart from strains circulating in Russian Federation, with viruses circulating in neighboring countries, in most abundance — from Ukraine and Kyrgyzstan, slightly less — from Belarus, Tajikistan, Kazakhstan and Armenia and also with strains from certain foreign countries: Poland and Germany. Phylogenetic analysis of 38 HIV-1 genomes revealed significant genetic distances between HIV isolates from blood plasma and CSF in 5 patients, 4 of whom were PWID, which may indicate an event of superinfection.&#x0D; The amount of independent amino acid substitutions in protease in isolates from blood plasma ranged from 1 to 3, in isolates from CSF — from 1 to 2. An amount of such substitutions in a fragment of reverse transcriptase in isolates from blood plasma ranged from 1 to 6, while in isolates from CSF, it ranged from 1 to 7. HIV isolates from blood plasma and CSF from 5 patients had differences in the tertiary structure of HIV-1 reverse transcriptase p51 subunit in amino acid positions 16–20 and 210–235. Isolates from 3 other patients differed in the tertiary structure only in amino acid positons 210–235. Isolates from 3 patients differed in the structure of HIV-1 RT p66 subunit in a non-nucleoside reverse transcriptase inhibitor binding pocket (NNRTI) region. Fixed differences in the tertiary structure of p51 subunit required at minimum only 1 amino acid substitution to emerge. Alterations in the tertiary structure of p66 subunit required at least 3 amino acid substitutions.&#x0D; Conclusion. Microevolution of HIV-1 proceeds in parallel within the same patient, in different compartments, which is reflected in the accumulation of amino acid substitutions different from another compartment in the conserved pol gene. There is a weak correlation between the viral load level in plasma and in CSF. The genetic heterogeneity of HIV strains from patients of the Chelyabinsk region indicates a high frequency of reintroduction of HIV infection in the region from other countries. Differences in the tertiary structure of HIV-1 reverse transcriptase between blood plasma and CSF isolates are regularly fixed in certain domens, which also confirms the presence of parallel HIV microevolution during virus persistence in tissues separated by the blood-brain barrier which allows a better understanding of the fixation trends of individual amino acid substitutions during HIV-induced damage to central nervous system.

Incidence, pathogens and antimicrobial resistance of blood and cerebrospinal fluid isolates from a tertiary neonatal unit in South Africa: A 10 year retrospective review.

To determine trends in incidence, etiology and antimicrobial susceptibility of blood and cerebrospinal fluid (CSF) culture confirmed infections in hospitalized infants in a large tertiary neonatal unit in South Africa. Single-center, retrospective review of laboratory records of bacteria and fungi, and their susceptibility profiles, isolated from blood and CSF of infants hospitalized in the neonatal unit at Chris Hani Baragwanath Academic Hospital, Johannesburg, South Africa, from 1st January 2010 to 31st December 2019. Laboratory data on isolates and their antimicrobial susceptibilities were collected. Coagulase-negative Staphylococcus, Corynebacteria and Bacillus spp. were excluded. Patient-level clinical and laboratory data were not available. There were 8,319 significant isolates, giving an infection rate of 14.3/1000 patient-days. Infection rates increased from 12.0 to 15.7/1000 patient-days (estimated average yearly change 0.6[95%CI, 0.5-0.7];p = <0.001). Gram-negative infection rates increased from 4.3 to 10.8/1000 patient-days (estimated average yearly change 0.7[95%CI,0.6-0.8];p = <0.001). The 2 most commonly isolated Gram-negative organisms were Acinetobacter baumannii (44%) and Klebsiella pneumoniae (39%). Carbapenem resistance was seen in 31% of all Gram-negatives and increased over time (estimated average yearly change 4.8%[95%CI,4.2%-5.3%];p<0.001). Gram-positive infection rates decreased (estimated average yearly change -0.1[95%CI,-0.2- -0.05];p = <0.001). Staphylococcus aureus was the most common Gram-positive isolated. Rates of methicillin-resistant Staphylococcus aureus decreased from 91% to 55%(estimated average yearly change -2.8%[95%CI,-3.5%-2%],p< 0.001). Rates of fungal isolates decreased (estimated average yearly change -0.06[95%CI,-0.1 --0.02]);p = 0.007). Candida parapsilosis (52%) and Candida albicans (35%) were the most common fungi isolated. There has been a marked overall increase in rates of blood and/or CSF infections, with an absolute increase in Gram-negative infections observed, replacing Gram-positive and fungal pathogens. Extended spectrum beta-lactamase Gram-negative isolates are being replaced by carbapenem resistance, with around one third of all significant Gram-negative isolates now carbapenem resistant. Research into hospital based novel treatment and prevention interventions for neonatal sepsis should be urgently prioritized.

829. 5-Flucytosine Longitudinal Antifungal Susceptibility Testing of Cryptococcus neoformans: A Sub-study of the EnACT Trial Testing Oral Amphotericin

Abstract Background The EnACT trial was a phase 2 randomized clinical trial conducted in Uganda, which evaluated a novel orally delivered lipid nanocrystal (LNC) amphotericin B for treatment of cryptococcal meningitis. Oral LNC amphotericin B applies nanotechnology, which hopes to improve intracellular drug delivery to affected tissues while reducing extracellular concentrations and thereby adverse events. When flucytosine (5-FC) is used as monotherapy, it can induce stable, highly resistant mutants of Cryptococcus. Since LNC amphotericin is a novel drug delivery mechanism, we assessed whether resistance to 5-FC develops in this context. Results from the ACTA and AMBITION Clinical Trials 10-week mortality by antifungal regimen for cryptococcal meningitis from the clinical trial by Molloy et al. (ACTA) in top section and Jarvis et al. (AMBITION) in bottom section. Mean survival for each group is represented by diamonds and 95% confidence interval represented by error bars. Encapsulation of Amphotericin B in a Lipid nanocrystal Particle Lipid nanocrystal particle encapsulates amphotericin B molecule and delivers the drug to antigen presenting cells. Methods The trial enrolled subjects with HIV who were diagnosed with cryptococcal meningitis and randomized to receive 5-FC and either standard IV amphotericin or LNC amphotericin. Subjects had a lumbar puncture (LP) performed on screening and days 3, 7, and 14. We used broth microdilution methods, standardized by the European Committee on Antimicrobial Susceptibility Testing (EUCAST) to assess the MIC of isolates in each arm of the trial. We tested cryptococcal isolates from the cerebrospinal fluid (CSF) on the day of screening and then on the last positive CSF to contain cryptococcal growth. Statistical analysis included chi-square to test for a difference in MIC between the control and LNC amphotericin groups; and linear regression to compare MIC with early fungicidal activity (EFA), which is a surrogate endpoint. Intervention and Control Gropus for EnACT Phase 2 The EnACT trial phase 2 was completed in 4 cohorts to determine the ideal combination of IV and LNC amphotericin. The MIC analysis was completed in the 4th cohort. In the 4th cohort, participants randomized to the intervention group started LNC amphotericin B from the day of enrollment. Broth Microdilution for 5-Flucytosine Susceptibility Testing A 96-well plate was prepared with serial dilutions of 5-FC ranging from 256 µg/mL to 0.5 µg/mL in columns 1-10. Columns 11 and 12 were drug-free controls. The first and last CSF isolate from each unique participant was inoculated into rows B-D and E-G, respectively. The first row is a negative control and the last row is a positive control. Results The MIC50 was 4 µg/mL and MIC90 was 8 µg/mL for both the control and LNC amphotericin B groups. There was no evidence of 5-FC resistance in any Cryptococcus isolate tested after 2 weeks of therapy. 73% (n=8) of participants in the control group and 73% (n=19) in the LNC amphotericin group had no change or a decrease in MIC from the first to last Cryptococcus isolate. 27% (n=3) in the control group and 19% (n=5) in the LNC amphotericin group had a 2-fold increase in MIC. 9% (n=2) in the LNC amphotericin group had a 4-fold increase in MIC. There was no association with MIC and EFA. 5-FC CSF levels were above the MIC50. Distribution of MIC for flucytosine The MIC for each CSF isolate in the control and oral amphotericin B arms of the trial with the percents of each MIC level in each trial arm. Chi-squared statistic testing for a difference in MIC between each trial arm. Early Fungicidal Activity Compared to MIC for Each Trial Arm The EFA is compared to MIC in the control and oral amphotericin groups. Linear regression comparing EFA and control group shows that there is no correlation between MIC and EFA. Change in MIC During Treatment with Flucytosine and Amphotericin B A) Percent of participants in each trial group who had an increase in MIC over the treatment course. B) Individual participants are represented by a line with the MIC represented by a dot on the end of each line. Conclusion There is no evidence of baseline resistance to 5-FC or incident resistance during therapy in individuals presenting with cryptococcal meningitis in Uganda. LNC amphotericin B can safely be used in combination with 5-FC. Disclosures All Authors: No reported disclosures

Lack of Association between YEASTONE Antifungal Susceptibility Tests and Clinical Outcomes of Cryptococcus Meningitis.

The relation between antifungal susceptibility and treatment outcomes is not well-characterized. There is paucity of surveillance data for cerebrospinal fluid (CSF) isolates of cryptococcus investigated with YEASTONE colorimetric broth microdilution susceptibility testing. A retrospective study of laboratory-confirmed cryptococcus meningitis (CM) patients was conducted. The antifungal susceptibility of CSF isolates was determined using YEASTONE colorimetric broth microdilution. Clinical parameters, CSF laboratory indices, and antifungal susceptibility results were analyzed to identify risk factors for mortality. High rates of resistance to fluconazole and flucytosine were observed in this cohort. Voriconazole had the lowest MIC (0.06 µg/mL) and lowest rate of resistance (3.8%). In a univariate analysis, hematological malignancy, concurrent cryptococcemia, high Sequential Organ Failure Assessment (SOFA) score, low Glasgow coma scale (GCS) score, low CSF glucose level, high CSF cryptococcal antigen titer, and high serum cryptococcal antigen burden were associated with mortality. In a multivariate analysis, meningitis with concurrent cryptococcemia, GCS score, and high CSF cryptococcus burden, were independent predictors of poor prognosis. Both early and late mortality rates were not significantly different between CM wild type and non-wild type species.

Streptococcus pneumoniae Strains Isolated From a Single Pediatric Patient Display Distinct Phenotypes.

Streptococcus pneumoniae is the leading cause of bacterial paediatric meningitis after the neonatal period worldwide, but the bacterial factors and pathophysiology that drive pneumococcal meningitis are not fully understood. In this work, we have identified differences in raffinose utilization by S. pneumoniae isolates of identical serotype and sequence type from the blood and cerebrospinal fluid (CSF) of a single pediatric patient with meningitis. The blood isolate displayed defective raffinose metabolism, reduced transcription of the raffinose utilization pathway genes, and an inability to grow in vitro when raffinose was the sole carbon source. The fitness of these strains was then assessed using a murine intranasal infection model. Compared with the CSF isolate, mice infected with the blood isolate displayed higher bacterial numbers in the nose, but this strain was unable to invade the ears of infected mice. A premature stop codon was identified in the aga gene in the raffinose locus, suggesting that this protein likely displays impaired alpha-galactosidase activity. These closely related strains were assessed by Illumina sequencing, which did not identify any single nucleotide polymorphisms (SNPs) between the two strains. However, these wider genomic analyses identified the presence of an alternative alpha-galactosidase gene that appeared to display altered sequence coverage between the strains, which may account for the observed differences in raffinose metabolic capacity. Together, these studies support previous findings that raffinose utilization capacity contributes to disease progression, and provide insight into a possible alternative means by which perturbation of this pathway may influence the behavior of pneumococci in the host environment, particularly in meningitis.

Shunt Overdrainage: Reappraisal of the Syndrome and Proposal for an Integrative Model.

Although shunt overdrainage is a well-known complication in hydrocephalus management, the problem has been underestimated. Current literature suggests that the topic requires more examination. An insight into this condition is limited by a lack of universally agreed-upon diagnostic criteria, heterogeneity of published series, the multitude of different management options and misunderstanding of relationships among pathophysiological mechanisms involved. We carried out a review of the literature on clinical, radiological, intracranial pressure (ICP), pathophysiological and treatment concepts to finally propose an integrative model. Active prophylaxis and management are proposed according to this model based on determination of pathophysiological mechanisms and predisposing factors behind each individual case. As pathophysiology is progressively multifactorial, prevention of siphoning with gravitational valves or antisiphon devices is mandatory to avoid or minimize further complications. Shunt optimization or transferal and neuroendoscopy may be recommended when ventricular collapse and cerebrospinal fluid isolation appear. Cranial expansion may be useful in congenital or acquired craniocerebral disproportion and shunting the subarachnoid space in communicating venous hydrocephalus and idiopathic intracranial hypertension.

Antimicrobial Resistance and Predictors of Adverse Outcomes in Neonates with Bacterial Meningitis: A Retrospective Study from a Tertiary Care Hospital of Northern India

AbstractThis study aimed to determine antimicrobial resistance pattern and predictors of adverse outcome in neonatal meningitis. A retrospective study by analyzing case files of 134 cases of neonatal meningitis. We noted an alarming degree of multidrug resistance (MDR) among both gram-negative (Klebsiella spp., 50%; Escherichia coli, 100%; and and Acinetobacter spp., 50%), as well as positive (Enterococcus, 100%) isolates in cerebrospinal fluid (CSF) culture. The incidence rate of adverse outcome (i.e., mortality and abnormal neurological examination at discharge) was 8.2 and 17.2%, respectively. On univariate analysis, delayed seeking of medical care, bulging anterior fontanelle, vomiting, positive sepsis screen, shock during hospital course, ventriculitis, diversion procedures for raised intracranial pressure, central line placement, low CSF sugar, and failed hearing screening test at discharge were associated with increased risk of adverse outcome. Further, delayed seeking of medical care, shock during hospital course, positive sepsis screen, thrombocytopenia, and MDR infections were independently found to be associated with adverse outcomes. An alarming degree of antimicrobial resistance among the CSF isolates necessitates the need to understand the pathogenesis of resistance and curtail the irrational prescription of antibiotics in neonatal meningitis. Further, delayed seeking of medical care, shock during hospital course, positive sepsis screen, thrombocytopenia, and MRD infection may have prognostic value in neonatal meningitis

Acinetobacter baumannii strains isolated from cerebrospinal fluid (CSF) and bloodstream analysed by cgMLST: the dominance of clonal complex CC92 in CSF infections

A total of 54 unique clinical Acinetobacter baumannii strains isolated from cerebrospinal fluid (CSF) together with 21 bloodstream isolates collected from five tertiary hospitals in East China between April 2013 and November 2016 were studied for antimicrobial susceptibility patterns and the prevalence of antimicrobial resistance genes. Molecular epidemiological characteristics of CSF isolates and the phylogenetic relationship of isolates from different sources were assessed using multilocus sequence typing (MLST) and core genome MLST (cgMLST). Of the 54 CSF isolates, 51 (94.4%) were blaOXA-23-carrying carbapenem-resistant A. baumannii. Their average resistance rate to different classes of antibiotics was extremely high (>90%), except for tigecycline and colistin. According to the Oxford MLST scheme, all CSF isolates fell into 10 defined sequence types (STs) and 4 novel STs. ST195 and ST208 were the leading STs in isolates from either source. A total of 50 CSF isolates and 20 bloodstream isolates were assigned to clonal complex 92 (CC92), revealing a wild distribution of CC92 in the hospitals of East China. In combination with epidemiological data linked in time and space, cgMLST results elucidated intrahospital and interhospital polyclonal dissemination of A. baumannii causing meningitis. Based on cgMLST, there was no correlation between phylogeny and the source of isolation of A. baumannii. These results emphasise that the genetic potential of this pathogen is vast enough to infect multiple human body sites.

Molecular characterization and antibiotic resistance of Acinetobacter baumannii in cerebrospinal fluid and blood.

The increasing prevalence of carbapenem-resistant Acinetobacter baumannii (CRAB) caused nosocomial infections generate significant comorbidity and can cause death among patients. Current treatment options are limited. These infections pose great difficulties for infection control and clinical treatment. To identify the antimicrobial resistance, carbapenemases and genetic relatedness of Acinetobacter baumannii isolates from cerebrospinal fluid (CSF) and blood, a total of 50 nonrepetitive CSF isolates and 44 blood isolates were collected. The resistance phenotypes were determined, and polymerase chain reaction (PCR) was performed to examine the mechanisms of carbapenem resistance. Finally, multilocus sequence typing (MLST) was conducted to determine the genetic relatedness of these isolates. It was observed that 88 of the 94 collected isolates were resistant to imipenem or meropenem. Among them, the blaOXA-23 gene was the most prevalent carbapenemase gene, with an observed detection rate of 91.5% (86/94), followed by the blaOXA-24 gene with a 2.1% detection rate (2/94). Among all carbapenem-resistant Acinetobacter baumannii (CRAB) observations, isolates with the blaOXA-23 gene were resistant to both imipenem and meropenem. Interestingly, isolates positive for the blaOXA-24 gene but negative for the blaOXA-23 gene showed an imipenem-sensitive but meropenem-resistant phenotype. The MLST analysis identified 21 different sequence types (STs), with ST195, ST540 and ST208 most frequently detected (25.5%, 12.8% and 11.7%, respectively). 80 of the 94 isolates (85.1%) were clustered into CC92 which showed a carbapenem resistance phenotype (except AB13). Five novel STs were detected, and most of them belong to CRAB. In conclusion, these findings provide additional observations and epidemiological data of CSF and blood A. baumannii strains, which may improve future infection-control measures and aid in potential clinical treatments in hospitals and other clinical settings.

Molecular epidemiology and mortality of group B streptococcal meningitis and infant sepsis in the Netherlands: a 30-year nationwide surveillance study

Streptococcus agalactiae (group B streptococcus) causes invasive disease in all age groups. In the Netherlands, the incidence of group B streptococcal sepsis in early infancy is increasing because of a specific genetic subtype, clonal complex (CC) 17-A1. We assessed the molecular epidemiology, incidence, and mortality of group B streptococcal meningitis in the Netherlands over 30 years. We used nationwide surveillance data from Jan 1, 1987, to Dec 31, 2016, on all group B streptococcal meningitis and sepsis cases. The surveillance database of the Netherlands Reference Laboratory for Bacterial Meningitis-which receives approximately 90% of cerebrospinal fluid isolates from all patients with bacterial meningitis in the Netherlands-was the data source for the study. All patients with group B streptococcus-positive cerebrospinal fluid cultures (meningitis) and infants (0-89 days) with group B streptococcus-positive blood cultures (sepsis) were included. Patients with missing date of birth were excluded. Multi-locus sequence typing and clade profiles were extracted from whole genome sequences. Serotyping was done by latex agglutination and genome sequencing. Survival data was obtained through Municipal Personal Records. 1501 episodes in 1490 patients were identified: 626 meningitis cases (in patients of all ages) and 875 sepsis cases (in patients aged 0-89 days). Mean annual group B streptococcal meningitis incidence was 1·32 per 1 000 000 population. CC17-A1 caused 16 (5%) of 307 meningitis cases in the first half of the study and 77 (26%) of 296 meningitis cases in the second half of the observation period (p<0·0001). Because of a simultaneous decline in CC19, the overall meningitis incidence remained stable. 27 (8%) of 323 patients with meningitis younger than 3 months died and 14 (21%) of 66 patients older than 3 months died. Patients older than 65 years with sequence type (ST) 24 disease were independently associated with death. Serotype III and ST17 were associated with meningitis in early infancy, serotype III remained associated with meningitis in children younger than 3 months after correcting for ST17 (odds ratio 3·71, 95%CI 2·75-5·01). Serotype Ia, Ib, II, III, and V accounted for 98% of the meningitis cases in patients younger than 3 months and 92% cases in patients older than 3 months. CC17-A1 is an increasing cause of group B streptococcal meningitis in all age groups. A pentavalent polysaccharide vaccine would cover most meningitis cases. Netherlands Organization for Health Research and Development and Amsterdam University Medical Centres.

Resistance of Streptococcus pneumoniae Strains Isolated from Clinical Samples to Various Antibiotics

Objective: It was aimed to determine the antibiotics resistance rates of Streptococcus pneumoniae (S. pneumoniae) strains which are important causes of mortality and morbidity with increasing resistance rates.&#x0D; Methods: Antibiotic susceptibilities of 80 S. pneumoniae specimens identified from samples sent from various clinics in our hospital were analyzed retrospectively. Isolated strains were identified by classical methods and BD Phoenix 100 system (Becton Dickinson Diagnostic, USA) and their antimicrobial susceptibility was evaluated by Kirby-Bauer disc diffusion method according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) document. Penicillin, cefotaxime and meropenem susceptibilities were examined by gradient test; while erythromycin, clindamycin, trimethoprim-sulfamethoxazole, levofloxacin, tetracycline, vancomycin and linezolid resistances were analyzed by disc diffusion method.&#x0D; Results: A total of 80 isolates including 32 blood samples, 29 respiratory samples, 10 cerebrospinal fluid (CSF), 5 vitreous, 3 pleural fluid and 1 abscess aspiration were included in the study. Penicillin resistance in CSF isolates was 70% and there was no resistance to cefotaxime and meropenem. Of 70 non-CSF isolates, 15 (21.4%) were moderately resistant, 14 (20%) were highly resistant and 41 (58.6%) were susceptible to penicillin. Cefotaxime resistance was detected in 2 (2.9%) of these isolates. Intermediate values were found in 2 (2.9%) isolates and remaining 66 (94.2%) isolates were susceptible to cefotaxime. There was no meropenem resistance in non-CSF isolates. Resistance rates of erythromycin, clindamycin, trimethoprim-sulfamethoxazole, levofloxacin and tetracycline in all isolates were 32.5%, 27.5%, 42.5%, 3.7% ve 30% respectively. There was no resistance to vancomycin and linezolid.&#x0D; Conclusion: Penicillin resistance is high in S. pneumoniae strains and penicillin has no place in empirical treatment of pneumococcal meningitis. Periodic monitoring of infectious agents and antibiotic susceptibilities in certain regions may guide clinicians to initiate empirical treatment.

Changing Epidemiology of Bacterial Meningitis Since Introduction of Conjugate Vaccines: 3 Decades of National Meningitis Surveillance in The Netherlands

BackgroundThe epidemiology of acute bacterial meningitis has changed substantially since the introduction of conjugate vaccines.MethodsWe analyzed nationwide surveillance data of all cerebrospinal fluid isolates received by the Netherlands Reference Laboratory for Bacterial Meningitis in the Netherlands. We assessed the impact of conjugate vaccines on incidence (defined as episodes per 100 000 population per year) and for different age groups using incidence rate ratios (IRRs), comparing incidence before and after conjugate vaccine introduction.ResultsWe analyzed 17 393 episodes, of which 5960 episodes (34%) occurred in preschool children (aged 3 months to 4 years). Overall, bacterial meningitis incidence decreased from 6.37 to 1.58 between 1989–1993 and 2014–2019 (IRR, 0.25 [95% confidence interval {CI}, .23–.26]; P < .001). This decrease was most pronounced in preschool and school-aged children (5–15 years); IRR, 0.10 [95% CI, .09–.12] and 0.08 [95% CI, .06–.10]; both P < .001. The incidence was highest in young infants (<90 days) due to a high incidence of group B Streptococcus and Escherichia coli meningitis (42.48 and 19.49, respectively). Conjugate vaccines effectively reduced the incidence of Haemophilus influenzae type b, Neisseria meningitidis serogroup C, and 10 pneumococcal serotypes (IRRs, .02–.04; P < .001). At the end of the observed period, Streptococcus pneumoniae caused the majority of meningitis cases (829/1616 [51%]), mostly in older adults (aged 45–64 years) and elderly adults (aged ≥65 years; incidence of 1.06 and 1.54, respectively).ConclusionsConjugate vaccines reduced the burden of bacterial meningitis, especially in children. The efforts for new measures to prevent bacterial meningitis should be focused on neonates and elderly, as the residual rate of disease is still high in these age groups.

Ventricular Catheter Tract Hemorrhage as a Risk Factor for Ventriculostomy-Related Infection.

Ventriculostomy-related infection (VRI) is a feared complication of external ventricular drain (EVD) placement. Although many contributing factors to VRI have been examined, little is known whether there is an association between ventriculostomy-related catheter tract hemorrhage (VCTH) and VRI. To evaluate risk factors for VRI and assess possible correlations with VCTH. We performed a retrospective analysis of patients with EVD placement in a neurocritical care unit between 2011 and 2015. VRI was defined as clinical signs of infection with a positive cerebrospinal fluid gram stain and isolation of cerebrospinal fluid culture. VCTH was diagnosed by computed tomography immediately after EVD insertion. A total of 247 patients with EVD were identified during the 5-yr study period. An association between VCTH and gram-negative VRI was identified (P=.02). Ten percent (25 of 247 patients) developed a VRI, and 7% (18 of 247 patients) had a VCTH. Of the 25 patients with VRI, 20% (n=5) had a VCTH, compared to 6% (n=13) of 222 patients who had an EVD placed but did not develop VRI. There were no significant differences in demographic and clinical factors except for multiple EVD insertions (P<.00001), EVD duration (P<.001), and hospital length of stay (P<.001). VCTH is a potentially significant risk factor for VRI. Further analysis will be needed to confirm the strength of this association, and to delineate the possible mechanisms by which tract hemorrhage may serve as a nidus for bacterial penetration into the central nervous system.

Residual Variation Intolerance Score Detects Loci Under Selection in Neuroinvasive Listeria monocytogenes.

Listeria monocytogenes is a Gram-positive bacterium that can be found in a broad range of environments, including soil, food, animals, and humans. L. monocytogenes can cause a foodborne disease manifesting as sepsis and meningo-encephalitis. To evaluate signals of selection within the core genome of neuroinvasive L. monocytogenes strains, we sequenced 122 L. monocytogenes strains from cerebrospinal fluid (CSF) of Dutch meningitis patients and performed a genome-wide analysis using Tajima’s D and ω (dN/dS). We also evaluated the residual variation intolerance score (RVIS), a computationally less demanding methodology, to identify loci under selection. Results show that the large genetic distance between the listerial lineages influences the Tajima’s D and ω (dN/dS) outcome. Within genetic lineages we detected signals of selection in 6 of 2327 loci (<1%), which were replicated in an external cohort of 105 listerial CSF isolates from France. Functions of identified loci under selection were within metabolism pathways (lmo2476, encoding aldose 1-epimerase), putative antimicrobial resistance mechanisms (lmo1855, encoding PBPD3), and virulence factors (lmo0549, internalin-like protein; lmo1482, encoding comEC). RVIS over the two genetic lineages showed signals of selection in internalin-like proteins loci potentially involved in pathogen-host interaction (lmo0549, lmo0610, and lmo1290). Our results show that RVIS can be used to detect bacterial loci under selection.

The current global situation for tuberculous meningitis: epidemiology, diagnostics, treatment and outcomes.

Tuberculous meningitis (TBM) results from dissemination of M. tuberculosis to the cerebrospinal fluid (CSF) and meninges. Ischaemia, hydrocephalus and raised intracranial pressure frequently result, leading to extensive brain injury and neurodisability. The global burden of TBM is unclear and it is likely that many cases are undiagnosed, with many treated cases unreported. Untreated, TBM is uniformly fatal, and even if treated, mortality and morbidity are high. Young age and human immunodeficiency virus (HIV) infection are potent risk factors for TBM, while Bacillus Calmette-Guérin (BCG) vaccination is protective, particularly in young children. Diagnosis of TBM usually relies on characteristic clinical symptoms and signs, together with consistent neuroimaging and CSF parameters. The ability to confirm the TBM diagnosis via CSF isolation of M. tuberculosis depends on the type of diagnostic tests available. In most cases, the diagnosis remains unconfirmed. GeneXpert MTB/RIF and the next generation Xpert Ultra offer improved sensitivity and rapid turnaround times, and while roll-out has scaled up, availability remains limited. Many locations rely only on acid fast bacilli smear, which is insensitive. Treatment regimens for TBM are based on evidence for pulmonary tuberculosis treatment, with little consideration to CSF penetration or mode of drug action required. The World Health Organization recommends a 12-month treatment course, although data on which to base this duration is lacking. New treatment regimens and drug dosages are under evaluation, with much higher dosages of rifampicin and the inclusion of fluoroquinolones and linezolid identified as promising innovations. The inclusion of corticosteroids at the start of treatment has been demonstrated to reduce mortality in HIV-negative individuals but whether they are universally beneficial is unclear. Other host-directed therapies show promise but evidence for widespread use is lacking. Finally, the management of TBM within health systems is sub-optimal, with drop-offs at every stage in the care cascade.

In vivo proteomics identifies the competence regulon and AliB oligopeptide transporter as pathogenic factors in pneumococcal meningitis.

Streptococcus pneumoniae (pneumococci) is a leading cause of severe bacterial meningitis in many countries worldwide. To characterize the repertoire of fitness and virulence factors predominantly expressed during meningitis we performed niche-specific analysis of the in vivo proteome in a mouse meningitis model, in which bacteria are directly inoculated into the cerebrospinal fluid (CSF) cisterna magna. We generated a comprehensive mass spectrometry (MS) spectra library enabling bacterial proteome analysis even in the presence of eukaryotic proteins. We recovered 200,000 pneumococci from CSF obtained from meningitis mice and by MS we identified 685 pneumococci proteins in samples from in vitro filter controls and 249 in CSF isolates. Strikingly, the regulatory two-component system ComDE and substrate-binding protein AliB of the oligopeptide transporter system were exclusively detected in pneumococci recovered from the CSF. In the mouse meningitis model, AliB-, ComDE-, or AliB-ComDE-deficiency resulted in attenuated meningeal inflammation and disease severity when compared to wild-type pneumococci indicating the crucial role of ComDE and AliB in pneumococcal meningitis. In conclusion, we show here mechanisms of pneumococcal adaptation to a defined host compartment by a proteome-based approach. Further, this study provides the basis of a promising strategy for the identification of protein antigens critical for invasive disease caused by pneumococci and other meningeal pathogens.

Pneumococcal meningitis before the introduction of 10-valent pneumococcal conjugate vaccine into the National Childhood Immunization Program in Poland

BackgroundPoland introduced the 10-valent conjugate pneumococcal vaccine (PCV10) into the childhood immunization program in January 2017. During previous decades, considerable changes had occurred in the surveillance system for invasive pneumococcal disease. Therefore, to provide baseline data on pneumococcal diseases before PCV10 introduction, we evaluated the epidemiology of pneumococcal meningitis (PM), the only syndrome monitored consistently since 1970. MethodsBased on laboratory-confirmed cases reported during 2005-2015, we calculated the reported rates, serotypes distribution and antimicrobial resistance of pneumococcal meningitis isolates. Data from the mandatory national surveillance system was linked with data on cerebrospinal fluid isolates submitted to the National Reference Centre for Bacterial Meningitis. We used negative binomial regression with Newey West method to test for trend in rates of pneumococcal meningitis notified during 2005-2015 and Chi-squared test to assess changes in the serotype distribution from 2008-2011 to 2012-2015. ResultsFrom 2005 to 2015, the overall reported incidence of PM increased from 0.21 to 0.47 cases per 100,000 population, average yearly increase of 7% (rate ratio 1.07; 95% CI 1.06–1.08). The increase was primarily due to annual increase of 3% (1.02–1.05) among 15–49 years of age, 12% (95% CI: 1.10–1.13) among 50–64 years of age, 18% (95% CI: 1.16–1.19) among persons 65–74 years of age and 9% (95% CI 1.07–1.10) among persons ≥75 years of age. In children <5 years of age, serotypes included in PCV10 and PCV13 accounted for 75% and 80% of reported isolates, respectively. From 2008-2011 to 2012-2015, the proportion of PM cases caused by PCV10 serotypes decreased from 52% to 41% (p < 0.01). Overall, 28% of isolates were resistant to penicillin and 13% were non-susceptible to cefotaxime. ConclusionsThe introduction of PCV10 into national immunization program may have considerable impact on disease burden, especially on number of cases caused by isolates non-susceptible to antimicrobials.