Whole-genome analysis of extraintestinal Escherichia coli sequence type 73 from a single hospital over a 2 year period identified different circulating clonal groups

Sequence type (ST)73 has emerged as one of the most frequently isolated extraintestinal pathogenic Escherichia coli. To examine the localized diversity of ST73 clonal groups, including their mobile genetic element profile, we sequenced the genomes of 16 multiple-drug resistant ST73 isolates from patients with urinary tract infection from a single hospital in Sydney, Australia, between 2009 and 2011. Genome sequences were used to generate a SNP-based phylogenetic tree to determine the relationship of these isolates in a global context with ST73 sequences (n=210) from public databases. There was no evidence of a dominant outbreak strain of ST73 in patients from this hospital, rather we identified at least eight separate groups, several of which reoccurred, over a 2 year period. The inferred phylogeny of all ST73 strains (n=226) including the ST73 clone D i2 reference genome shows high bootstrap support and clusters into four major groups that correlate with serotype. The Sydney ST73 strains carry a wide variety of virulence-associated genes, but the presence of iss, pic and several iron-acquisition operons was notable.

Association between minimum inhibitory concentration, beta-lactamase genes and mortality for patients treated with piperacillin/tazobactam or meropenem from the MERINO study

INTRODUCTION

This study aims to assess the association of piperacillin/tazobactam and meropenem minimum inhibitory concentration (MIC) and beta-lactam resistance genes with mortality in the MERINO trial.

METHODS

Blood culture isolates from enrolled patients were tested by broth microdilution and whole genome sequencing at a central laboratory. Multivariate logistic regression was performed to account for confounders. Absolute risk increase for 30-day mortality between treatment groups was calculated for the primary analysis (PA) and the microbiologic assessable (MA) populations.

RESULTS

320 isolates from 379 enrolled patients were available with susceptibility to piperacillin/tazobactam 94% and meropenem 100%. The piperacillin/tazobactam non-susceptible breakpoint (MIC > 16 mg/L) best predicted 30-day mortality after accounting for confounders (odds ratio 14.9, 95% CI 2.8 - 87.2). The absolute risk increase for 30-day mortality for patients treated with piperacillin/tazobactam compared with meropenem was 9% (95% CI 3% - 15%) and 8% (95% CI 2% - 15%) for the original PA population and the post-hoc MA populations, which reduced to 5% (95% CI -1% - 10%) after excluding strains with piperacillin/tazobactam MIC values > 16 mg/L. Isolates co-harboring ESBL and OXA-1 genes were associated with elevated piperacillin/tazobactam MICs and the highest risk increase in 30-mortality of 14% (95% CI 2% - 28%).

CONCLUSION

After excluding non-susceptible strains, the 30-day mortality difference was from the MERINO trial was less pronounced for piperacillin/tazobactam. Poor reliability in susceptibility testing performance for piperacillin/tazobactam and the high prevalence of OXA co-harboring ESBLs suggests meropenem remains the preferred choice for definitive treatment of ceftriaxone non-susceptible E. coli and Klebsiella.

The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee

Whole genome sequencing (WGS) offers the potential to predict antimicrobial susceptibility from a single assay. The European Committee on Antimicrobial Susceptibility Testing established a subcommittee to review the current development status of WGS for bacterial antimicrobial susceptibility testing (AST). The published evidence for using WGS as a tool to infer antimicrobial susceptibility accurately is currently either poor or non-existent and the evidence / knowledge base requires significant expansion. The primary comparators for assessing genotypic-phenotypic concordance from WGS data should be changed to epidemiological cut-off values in order to improve differentiation of wild-type from non-wild-type isolates (harbouring an acquired resistance). Clinical breakpoints should be a secondary comparator. This assessment will reveal whether genetic predictions could also be used to guide clinical decision making. Internationally agreed principles and quality control (QC) metrics will facilitate early harmonization of analytical approaches and interpretive criteria for WGS-based predictive AST. Only data sets that pass agreed QC metrics should be used in AST predictions. Minimum performance standards should exist and comparative accuracies across different WGS laboratories and processes should be measured. To facilitate comparisons, a single public database of all known resistance loci should be established, regularly updated and strictly curated using minimum standards for the inclusion of resistance loci. For most bacterial species the major limitations to widespread adoption for WGS-based AST in clinical laboratories remain the current high-cost and limited speed of inferring antimicrobial susceptibility from WGS data as well as the dependency on previous culture because analysis directly on specimens remains challenging. For most bacterial species there is currently insufficient evidence to support the use of WGS-inferred AST to guide clinical decision making. WGS-AST should be a funding priority if it is to become a rival to phenotypic AST. This report will be updated as the available evidence increases.

Predictors and outcome associated with an Enterococcus positive isolate during intensive care unit admission

This study reports the incidence, risk factors and mortality associated with a positive Enterococcus spp. isolate during admission to two tertiary intensive care units participating in an antibiotic cycling study. Incidence was low, with only 4.2% of admissions (36/852) at Royal Brisbane and Women's Hospital and 2.8% (31/1104) at Westmead Hospital developing a positive Enterococcus spp. isolate (P=0.087). A positive enterococcal isolate, while not an independent predictor of mortality (odds ratio [OR]=1.6, 95% confidence interval [CI] 0.80 to 3.2, P=0.18), may be a marker of the underlying severity of illness with higher unadjusted in-hospital mortality (26% or 17/66 vs 14% or 250/1855, P=0.007). Independent risk factors for a positive isolate were use of meropenem/imipenem (OR=5.7, 95% CI 2.4 to 14, P <0.001) and cefepime (OR=2.5, 95% CI 1.2 to 5.3, P=0.017) within 48 hours of intensive care unit admission, the presence of a nasogastric tube (OR=4.1, 95% CI 1.3 to 14, P=0.018), renal replacement therapy (OR=2.2, 95% CI 1.0 to 4.7, P=0.046), operative intervention (OR=1.8, 95% CI 1.0 to 3.2, P=0.035) and age (OR=1.2, 95% CI 1.1 to 1.5, P=0.009). None of these factors, except for the need for renal replacement therapy (OR=6.2, 95% CI 1.4 to 27, P=0.015), was associated with increased mortality. Enterococci-directed empiric therapy in the treatment of sepsis remains of unproven value, although this negative finding must be evaluated against other higher powered studies.

Development of a real-time Staphylococcus aureus and MRSA (SAM-) PCR for routine blood culture

The notification of "Gram-positive cocci, possibly staphylococcus" in a blood culture drawn from a seriously ill patient is responsible for a large amount of vancomycin prescribing in institutions where methicillin-resistant Staphylococcus aureus (MRSA) is an important cause of bacteraemia. A duplex real-time TaqMan polymerase chain reaction targeting the species-specific nuc gene, and the mecA gene encoding methicillin-resistance, was developed as a tool for rapid identification and detection of S. aureus and methicillin-resistance, and optimised for immediate as-needs testing. Three different DNA extraction methods achieved varying DNA quality, with PCR inhibition the main problem. Serial blood cultures (n=120) identified as possible staphylococci on Gram stain from our clinical laboratory were examined. There was one false negative result for a methicillin-resistant Staphylococcus epidermidis, which was positive on repeat testing, and one false negative result due to DNA extraction failure for MRSA from peritoneal dialysate inoculated into blood culture medium. Sensitivity and specificity of 97% and 100%, respectively, were obtained for mecA; and sensitivity and specificity of 98% and 100%, respectively, for nuc. Detection of slow-growing coagulase-negative staphylococci as co-infecting strains may be reduced. The assay quickly and reliably identified S. aureus in mixed infection, and identified methicillin resistance in both S. epidermidis and S. aureus strains.

Antimicrobial susceptibility of Bartonella henselae using Etest methodology

OBJECTIVES

Bartonella henselae is a fastidious slow growing pathogen which is seldom cultured in the laboratory. Previous descriptions of antimicrobial susceptibility have been largely limited to feline isolates and/or laboratory reference strains, with no accounting for genotypic or phenotypic diversity.

METHODS

An optimal method of antimicrobial susceptibility testing by Etest was established to compare the antimicrobial susceptibilities of 12 different isolates of B. henselae, 5 human and 7 feline, which have previously been well characterized by 16S rRNA sequencing, multi-locus sequence typing (MLST), phase variation and passage number.

RESULTS

No difference in susceptibility could be attributed to differences in genotype, source of the isolate or passage number. Where comparisons were drawn with previously published results, these were found to be concordant.

CONCLUSIONS

We conclude that antibiotic susceptibility can be determined by a simple Etest method for B. henselae isolates. This method is reproducible among diverse strains, and is sufficiently predictable that generalizations can be confidently made about optimal antibiotic choices.

Multiplex PCR for screening of integrons in bacterial lysates

Bacterial integrons are a useful PCR amplification target in epidemiological surveys of bacterial antibiotic resistance, and a variety of primers have been published. We describe multiplex PCR methodology to test for classes 1, 2 and 3 integron-associated integrases in boiled lysates of Gram-negative bacteria. We report on performance in Acinetobacter spp. (n=50), Enterobacteriaceae (n=76), Pseudomonas aeruginosa (n=15), Bacteroidesspp. (n=69), and in undifferentiated mixed cultures derived from perineal swabs (n=50) and endotracheal aspirates (n=8). This method achieved 100% sensitivity and specificity in simple lysates made from a range of bacteria, without requiring DNA extraction, and is recommended as an efficient screening tool for surveys of integron cassettes.

Antibiotic resistance in the intensive care unit: a primer in bacteriology

The clinical use of potent, well-tolerated, broad-spectrum antibiotics has been paralleled by the development of resistance in bacteria, and the prevalence of highly resistant bacteria in some intensive care units is despairingly commonplace. The intensive care community faces the realistic prospect of untreatable nosocomial infections and should be searching for new approaches to diagnose and manage resistant bacteria. In this review, we discuss some of the relevant underlying biology, with a particular focus on genetic transfer vehicles and the relationship of selection pressure to their movements. It is an attempt to demystify the relevant language and concepts for the anaesthetist and intensivist, to explain some of the reasons for the emergence of resistance in bacteria, and to provide a contextual basis for discussion of management approaches such as selective decontamination and antibiotic cycling.

Characterization of the natural population of Bartonella henselae by multilocus sequence typing

Investigations of the population genetics of Bartonella henselae have demonstrated a high level of diversity among strains, and the delineation of isolates into one of two subtypes, type I (Houston) and type II (Marseille), represented by specific 16S ribosomal DNA (rDNA) sequences, has long been considered the most significant genotypic division within the species. This belief is challenged by recent work suggesting a role for horizontal gene exchange in generating intraspecies diversity. We attempted to resolve this issue and extend exploration of the population structure of B. henselae by using multilocus sequence typing (MLST) to examine the distribution of polymorphisms within nine different genes in a sample of 37 human and feline isolates. MLST distinguished seven sequence types (STs) that resolved into three distinct lineages, suggesting a clonal population structure for the species, and support for these divisions was obtained by macrorestriction analysis using pulsed-field gel electrophoresis. The distribution of STs among isolates recovered from human infections was not random, and such isolates were significantly more often associated with one particular ST, lending further support to the suggestion that specific genotypes contribute disproportionately to the disease burden in humans. All but one isolate lay on lineages that bore the representative strain of either the Houston or Marseille subtype. However, the distribution of the two 16S rDNA alleles among the isolates was not entirely congruent with their lineage allocations, indicating that this is not a sensitive marker of the clonal divisions within the species. The inheritances of several of the genes studied could not be reconciled with one another, providing further evidence of horizontal gene transfer among B. henselae strains and suggesting that recombination has a role in shaping the genetic character of bartonellae.

Limited diversity among human isolates of Bartonella henselae

A study of 59 isolates of Bartonella henselae reveals relatively limited diversity among those of human origin (n = 28). Either of two distinct alleles of both gltA and 16S ribosomal DNA (rDNA) was found in all isolates, with a high level of congruity between 16S and gltA inheritance among proven human pathogens. Human isolates from all over Eastern Australia were most commonly 16S rDNA (Bergmans) type I, with the same gltA allele as the type strain (Houston-1). Comparable feline isolates were more commonly 16S type II, with less congruity of inheritance between 16S and gltA alleles. Previously described arbitrarily primed PCR and EagI-HhaI infrequent restriction site PCR fingerprinting techniques separated Bartonella species effectively but lacked discriminating power within B. henselae. Examination of the 16-23S intergenic spacer region revealed for several strains several point mutations as well as a repeat sequence of unknown significance which is readily detected by HaeIII restriction fragment length polymorphism analysis. The bacteriophage-associated papA gene was present in all isolates. Enterobacterial repetitive intergenic consensus PCR proved to be a useful and robust typing tool and clearly separated human isolates (including imported strains) from the majority of feline isolates. Our data are consistent with published evidence and with previous suggestions of intragenomic rearrangements in the type strain and suggest that human isolates come from a limited subset of B. henselae strains. They strengthen arguments for careful exploration of genotype-phenotype relationships and for the development of a multilocus enzyme electrophoresis and multilocus sequence typing-based approach to the phylogeny of B. henselae.

Non-bronchoscopic bronchoalveolar lavage in the microbiological diagnosis of pneumonia in mechanically ventilated patients

A prospective study comparing standardized non-bronchoscopic bronchoalveolar lavage (sNB-BAL) and non-specific endotracheal aspirate (NsETA) in the microbiological diagnosis of pneumonia in mechanically ventilated patients is described. One hundred episodes in 82 mechanically ventilated patients with or without radiological and clinical diagnostic criteria of pneumonia were studied. NsETA and sNB-BAL was performed on the day of study. Fifty-one patients had pneumonia (21 ventilator-associated, 12 hospital-acquired, 18 community-acquired) and 49 had no pneumonia as defined by widely accepted clinico-radiological criteria. The sNB-BAL was found to be significantly more specific (0. 73) compared to NsETA (0.35) for the microbiological diagnosis of pneumonia. Colonization rates with NsETA were significantly higher compared to sNB-BAL (P value <0.0001). No patient had complications attributable to the sNB-BAL procedure. We conlude that sNB-BAL is a safe, effective, sensitive, specific and inexpensive procedure for the serial evaluation of pneumonia in mechanically ventilated patients.

Mycobacterium marinum infection: epidemiology and presentation in Queensland 1971-1990

OBJECTIVE

Evaluation of the clinical and epidemiological features of Mycobacterium marinum infection in Queensland.

DESIGN

Laboratory identification and in-vitro susceptibility tests of 29 isolates from the Queensland Health Department Tuberculosis Reference Laboratory were retrospectively gathered and followed up by contacting referring practitioners and obtaining clinical details of patients involved.

SUBJECTS

29 patients from whom M. marinum was isolated, with a male:female ratio of 3.1:1, and a mean age of 47.4 years.

RESULTS

Of 26 patients for whom adequate information was available, 12 had evidence of involvement of deep tissues (including two cases of arthritis) and five suffered sporotrichoid spread of infection. The delay between onset of symptoms and consultation with a medical practitioner was five months (range, two weeks to two years), with a further mean delay to definitive diagnosis of 4.4 weeks. Cure was apparent in 22 of 23 cases. Chemotherapy alone was adequate in 11 cases, as was surgical intervention in three, while a combination approach was successful in eight cases. Trimethoprim/sulfamethoxazole was successful in seven of nine cases and combination rifampicin and ethambutol in six of seven. Tetracyclines were employed as single-agent therapy in nine patients and were effective in seven.

CONCLUSIONS

Synovitis was a common presenting feature of M. marinum infection in Queensland patients. Occupational and recreational exposure to salt or fresh water was common, and although this history was available to practitioners a mean delay to definitive diagnosis of 4.4 weeks still occurred. The data suggest that chemotherapy alone is often adequate, even with deep tissue involvement. Combinations of conventional antimycobacterial drugs may be the therapy of choice, especially for serious infections, although success was recorded with trimethoprim/sulfamethoxazole alone.

Neonatal death: grieving families

This paper examines the stress on a family after a neonatal death. Sixty-seven families who experienced 63 neonatal deaths and four post-neonatal deaths were studied during an interview held eight weeks after the death. Predominant support for the parents was provided by each other (63%), their parents (33%), friends, many of whom had experienced a similar loss (16%), neighbours (15%) and religion (13%). Grief reactions were more commonly reported by mothers than by fathers and included: sleep disturbances (51%); depression or fits of crying (34%); anorexia or weight loss (33%); nervousness and anxiety (19%); social withdrawal (18%); morbid preoccupation (9%); and guilt, anger or hostility (9%). Grief reactions were graded on a scale of I (physically, psychologically and emotionally settled) to IV (serious symptoms that disturbed day-to-day functioning). Pathological grief reactions occurred in 21 families and correlated with a lack of parental support and contact with their critically ill infant and a severe initial grief state (P less than 0.05). There was no correlation with the type of initial grief reaction; the attachment to the baby; the age of the baby; the comprehension of the cause of death; the hospital care or the way that they were informed of the death. The loss of a newborn infant had a major pathological effect on 31% of the families that were studied. This was probably an underestimate as eight weeks is too soon to assess unresolved grief.