Retrospective analysis of antimicrobial resistance and bacterial spectrum of infection in Gabon, Central Africa

Background: Physicians depend on reliable information on the local epidemiology of infection and antibiotic resistance rates to guide empiric treatment in critically ill patients. As these data are scarce for Central Africa, we performed a retrospective analysis of microbiological findings from a secondary care hospital in Gabon. Methods: Microbiological reports from 2009 to 2012 were used to assess the non-susceptibility rates of the three most common isolates from six major types of infections (bloodstream, ear-eye-nose-throat, surgical site, skin and soft tissue, urinary tract and wound infection). Results: A high diversity of pathogens was found, but Staphylococcus aureus was predominant in the majority of infections. Overall, the three most prevalent pathogens in children were S. aureus (33.7%), Streptococcus pyogenes (8.1%) and Escherichia coli (4.5%) and in adults S. aureus (23.5%), E. coli (15.1%) and Klebsiella pneumoniae (7.4%). In total, 5.8% (n = 19) of all S. aureus isolates were methicillin resistant. The proportion of extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae was 15.4% (n = 78), 49.4% of all K. pneumoniae were ESBL-producer (n = 42). Conclusion: The high diversity of potential pathogens and high resistance rates in Gram-negative bacteria challenge a rational empiric use of antibiotics. Countrywide continuous sentinel surveillance is therefore urgently needed.<br

Staphylococcus aureus pathogenicity in cystic fibrosis patients-results from an observational prospective multicenter study concerning virulence genes, phylogeny, and gene plasticity

Staphylococcus aureus and cystic fibrosis (CF) are closely interlinked. To date, however, the impact of S. aureus culture in CF airways on lung function and disease progression has only been elucidated to a limited degree. This analysis aims to identify bacterial factors associated to clinical deterioration. Data were collected during an observational prospective multi-center study following 195 patients from 17 centers. The average follow-up time was 80 weeks. S. aureus isolates (n = 3180) were scanned for the presence of 25 virulence genes and agr-types using single and multiplex PCR. The presence of specific virulence genes was not associated to clinical deterioration. For the agr-types 1 and 4, however, a link to the subjects' clinical status became evident. Furthermore, a significant longitudinal decrease in the virulence gene quantity was observed. Analyses of the plasticity of the virulence genes revealed significantly increased plasticity rates in the presence of environmental stress. The results suggest that the phylogenetic background defines S. aureus pathogenicity rather than specific virulence genes. The longitudinal loss of virulence genes most likely reflects the adaptation process directed towards a persistent and colonizing rather than infecting lifestyle

Factors associated with worse lung function in cystic fibrosis patients with persistent staphylococcus aureus

Background Staphylococcus aureus is an important pathogen in cystic fibrosis (CF). However, it is not clear which factors are associated with worse lung function in patients with persistent S. aureus airway cultures. Our main hypothesis was that patients with high S. aureus density in their respiratory specimens would more likely experience worsening of their lung disease than patients with low bacterial loads. Methods Therefore, we conducted an observational prospective longitudinal multi-center study and assessed the association between lung function and S. aureus bacterial density in respiratory samples, co-infection with other CF-pathogens, nasal S. aureus carriage, clinical status, antibiotic therapy, IL-6- and IgG-levels against S. aureus virulence factors. Results 195 patients from 17 centers were followed; each patient had an average of 7 visits. Data were analyzed using descriptive statistics and generalized linear mixed models. Our main hypothesis was only supported for patients providing throat specimens indicating that patients with higher density experienced a steeper lung function decline (p<0.001). Patients with exacerbations (n = 60), S. aureus small-colony variants (SCVs, n = 84) and co-infection with Stenotrophomonas maltophilia (n = 44) had worse lung function (p = 0.0068; p = 0.0011; p = 0.0103). Patients with SCVs were older (p = 0.0066) and more often treated with trimethoprim/sulfamethoxazole (p = 0.0078). IL-6 levels positively correlated with decreased lung function (p<0.001), S. aureus density in sputa (p = 0.0016), SCVs (p = 0.0209), exacerbations (p = 0.0041) and co-infections with S. maltophilia (p = 0.0195) or A. fumigatus (p = 0.0496). Conclusions In CF-patients with chronic S. aureus cultures, independent risk factors for worse lung function are high bacterial density in throat cultures, exacerbations, elevated IL-6 levels, presence of S. aureus SCVs and co-infection with S. maltophilia

Staphylococcus aureus and Cystic Fibrosis—A Close Relationship. What Can We Learn from Sequencing Studies?

'Staphylococcus aureus' is next to 'Pseudomonas aeruginosa' the most isolated pathogen from the airways of cystic fibrosis (CF) patients, who are often infected by a dominant 'S. aureus' clone for extended periods. To be able to persist, the pathogen has to adapt to the hostile niche of the airways to counteract host defence, antibiotic therapy and the competition with coinfecting pathogens. 'S. aureus' is equipped with many virulence factors including adhesins, toxins that are localized on the chromosome, on plasmids or are phage-related. 'S. aureus' is especially versatile and adaptation and evolution of the pathogen occurs by the acquisition of new genes by horizontal gene transfer (HGT), changes in nucleotides (single nucleotide variations, SNVs) that can cause a selective advantage for the bacteria and become fixed in subpopulations. Methicillin-resistant 'S. aureus' are a special threat to CF patients due to the more severe lung disease occurring in infected patients. Today, with decreasing costs for sequencing, more and more studies using 'S. aureus' isolates cultured from CF patients are being published, which use whole genome sequencing (WGS), multilocus sequence typing (MLST) or spa-sequence typing ('spa'-typing) to follow the population dynamics of 'S. aureus', elucidate the underlying mechanisms of phenotypic variants, newly acquired resistance or adaptation to the host response in this particular niche. In the first part of this review, an introduction to the genetic make-up and the pathogenesis of 'S. aureus' with respect to CF is provided. The second part presents an overview of recent studies and their findings using genotypic methods such as single or multilocus sequencing and whole genome sequencing, which identify factors contributing to the adaptation of 'S. aureus' and its evolution in the airways of individuals with CF

Correlations of Host and Bacterial Characteristics with Clinical Parameters and Survival in Staphylococcus aureus Bacteremia

'Staphylococcus aureus' bacteremia (SAB) is a frequent, severe condition that occurs in patients of all age groups and affects clinical departments of all medical fields. It is associated with a high mortality rate of 20–30%. In this study, we analyzed patient mortality associated with SAB at our tertiary care university hospital, assessed the clinical management in terms of administered antimicrobial therapy, and determined which factors have an impact on the clinical course and outcome of patients with this disease. We collected clinical data and blood culture isolates of 178 patients diagnosed with SAB between May 2013 and July 2015. For this study, bacteria were cultured and analyzed concerning their phenotype, hemolysis activity, biofilm formation, nuclease activity, prevalence of toxin genes, 'spa' and 'agr' type. Overall mortality was 24.2% and 30-day mortality was 14.6%. Inadequate initial therapy was administered to 26.2% of patients and was associated with decreased survival (p = 0.041). Other factors associated with poor survival were patient age (p = 0.003), 'agr' type 4 (p ≤ 0.001) and pathological leukocyte counts (p = 0.029 if elevated and p = 0.003 if lowered). The type of infection focus, 'spa' clonal complex and enterotoxin genes 'seg' and 'sei' had an impact on severity of inflammation. Our results indicate that mortality and burden of disease posed by SAB are high at our university hospital

Male kidney allograft recipients at risk for urinary tract infection?

Background: Urinary tract infection (UTI) is the most common infection after renal transplantation (RTx). Although female sex is a well-known risk factor for the development of UTI after RTx, the role of the donor sex in this context remains unclear. Methods: In this case control study 6,763 RTx cases were screened for UTI when presenting at our transplant outpatient clinics. 102 different RTx patients fulfilled the inclusion criteria and were compared to 102 controls. Data on renal function was prospectively followed for 12 months. Results were compared to a previous RTx cohort from our transplant center. Additionally, we assessed the immunological response of leukocytes from 58 kidney recipients and 16 controls to lipopolysaccharide stimulation. Result: After identification by univariate analysis, multivariate logistic regression analysis indicated female sex, minor height, advanced age and male kidney allograft sex to be associated with the occurrence of UTI after RTx. Female recipients who received male grafts had the best renal function 12 months after presentation. However, leukocyte response of recipients to lipopolysaccharide was impaired irrespective of donor and recipient sex to the same extend. Conclusions: We conclude from our data that male kidney allografts are associated with the occurrence of UTI after RTx but did not influence the response of leukocytes to lipopolysaccharide. Further prospective studies are needed to identify the underlying mechanisms of higher male kidney donor dependent UTI

Phenotypic and Genotypic Characterization of 'Escherichia coli' Causing Urinary Tract Infections in Kidney-Transplanted Patients

Urinary tract infection (UTI), frequently caused by uropathogenic Escherichia coli (UPEC), is the most common infection after kidney transplantation (KTx). Untreated, it can lead to urosepsis and impairment of the graft function. We questioned whether the UPEC isolated from KTx patients differed from the UPEC of non-KTx patients. Therefore, we determined the genome sequences of 182 UPEC isolates from KTx and control patients in a large German university clinic and pheno- and genotypically compared these two isolated groups. Resistance to the β-lactams, trimethoprim or trimethoprim/sulfamethoxazole was significantly higher among UPEC from KTx than from control patients, whereas both the isolated groups were highly susceptible to fosfomycin. Accordingly, the gene content conferring resistance to β-lactams or trimethoprim, but also to aminoglycosides, was significantly higher in KTx than in control UPEC isolates. E. coli isolates from KTx patients more frequently presented with uncommon UPEC phylogroups expressing higher numbers of plasmid replicons, but interestingly, less UPEC virulence-associated genes than the control group. We conclude that there is no defining subset of virulence traits for UPEC from KTx patients. The clinical history and immunocompromised status of KTx patients enables E. coli strains with low uropathogenic potential, but with increased antibiotic resistance to cause UTIs

Staphylococcus aureus Pathogenicity in Cystic Fibrosis Patients—Results from an Observational Prospective Multicenter Study Concerning Virulence Genes, Phylogeny, and Gene Plasticity

Staphylococcus aureus and cystic fibrosis (CF) are closely interlinked. To date, however, the impact of S. aureus culture in CF airways on lung function and disease progression has only been elucidated to a limited degree. This analysis aims to identify bacterial factors associated to clinical deterioration. Data were collected during an observational prospective multi-center study following 195 patients from 17 centers. The average follow-up time was 80 weeks. S. aureus isolates (n = 3180) were scanned for the presence of 25 virulence genes and agr-types using single and multiplex PCR. The presence of specific virulence genes was not associated to clinical deterioration. For the agr-types 1 and 4, however, a link to the subjects’ clinical status became evident. Furthermore, a significant longitudinal decrease in the virulence gene quantity was observed. Analyses of the plasticity of the virulence genes revealed significantly increased plasticity rates in the presence of environmental stress. The results suggest that the phylogenetic background defines S. aureus pathogenicity rather than specific virulence genes. The longitudinal loss of virulence genes most likely reflects the adaptation process directed towards a persistent and colonizing rather than infecting lifestyle