Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 15-18 March 2016

[This corrects the article DOI: 10.1186/s13054-016-1208-6.].

Non-tuberculous mycobacteria: a retrospective review of Scottish isolates from 2000 to 2010

There is growing recognition of the clinical importance of non-tuberculous mycobacteria (NTM), a group of versatile opportunistic bacterial pathogens. We describe the characteristics of NTM isolates in Scotland over an 11-year period using data held by the Scottish Mycobacteria Reference Laboratory. American Thoracic Society microbiological criteria were used to evaluate the clinical significance of isolates. Data presented include analysis of trends across time, species/body site associations, gender and age differences, geographical variations and the association between cystic fibrosis and Mycobacterium abscessus. We emphasise the need for standardised reporting criteria for NTM isolates to ensure optimal surveillance of NTM disease.

Deep resequencing of serial sputum isolates of Mycobacterium tuberculosis during therapeutic failure due to poor compliance reveals stepwise mutation of key resistance genes on an otherwise stable genetic background

OBJECTIVES

It has generally been held that the repeated emergence of resistance in Mycobacterium tuberculosis is due to the effects of large population sizes, slow replication, and prolonged colonization and treatment. However, there have been suggestions that its emergence is facilitated by high mutation rates due to a lack of mismatch repair, error-prone polymerases, and a potentially mutagenic host niche. Genome re-sequencing has indicated higher variability in strains with emergent resistance, but these studies have not been performed in serial isolates in which drug resistance has emerged. We have used genome re-sequencing to address the mutational processes that occur during the evolution of drug resistance during a clinical infection.

METHODS

Serial isolates from a patient obtained over a 12 month period, and spanning the transition of the colonizing population from fully drug sensitive, to isoniazid resistant, to isoniazid and rifampicin (multiply drug) resistant, spanning an estimated minimum of 100 generations within the host, were deep sequenced using Illumina sequencing. The genomes were compared, and all mutations in non-repetitive sequences were identified.

RESULTS

Specific mutations conferring resistance were identified. No additional mutations in non-repetitive regions were present. The mutations observed were kat S315T and rpoB D516Y.

CONCLUSIONS

M. tuberculosis is relatively stable genetically within the host, and demonstrates greater stability than is suggested by in vitro studies of emergent drug resistance, or by models of hypermutability. This indicates that it is primarily the nature and duration of the infection that are sufficient to lead to the repeated emergence of drug resistance in this infection if improperly managed, and that the selective pressure of the drugs limits additional diversification. This emphasizes the central importance of maintaining therapeutic concentrations of at least two effective antibiotics for the duration of treatment to prevent the emergence of resistance.

Characterising transmission of a tuberculosis genotype in Scotland: a qualitative approach to social network enquiry

SETTING

Contact investigation resulting from specimens sent to the Scottish Mycobacteria Reference Laboratory.

OBJECTIVE

To characterise patients and types of exposures associated with transmission of a prevalent Mycobacterium tuberculosis genotype in Scotland.

DESIGN

A combined approach using molecular epidemiology and semi-structured patient interviews for social network enquiry.

RESULTS

We investigated social connections between 64 patients diagnosed between 1994 and 2004. Fifty-five per cent had > or = 1 identifiable contact. One third (n = 14, 32.6%) of the 43 epidemiological links detected were discerned as a result of patient interviews and were not previously recorded on surveillance reports, nor recognised by nurse specialists (all were non-household contacts). Sixteen putative sites of exposure were identified, 11 were public houses. Rather than a single-source outbreak, eight pockets of transmission were identified, the largest involving UK-born alcohol-misusing males frequenting several public houses.

CONCLUSIONS

Using a standardised approach to explore themes around which individuals may have been exposed to TB resulted in the detection of previously unrecognised epidemiological links. Epidemiological data obtained from cluster investigations, e.g., risk and social behaviours that increase the risk of infection and sites of putative exposure, can enhance the development of more appropriate questions for the contact tracing interview.

Human and animal infections with Mycobacterium microti, Scotland

During 1994-2005, we isolated Mycobacterium microti from 5 animals and 4 humans. Only 1 person was immunocompromised. Spoligotyping showed 3 patterns: vole type, llama type, and a new variant llama type.

Meta-analysis of pancreaticojejunostomy versus pancreaticogastrostomy reconstruction after pancreaticoduodenectomy

Background

Pancreaticoduodenectomy is the primary treatment for periampullary cancer. Associated morbidity is high and often related to pancreatic anastomotic failure. This paper compares rates of pancreatic fistula, morbidity and mortality after pancreaticoduodenectomy in patients having reconstruction by pancreaticogastrostomy with those in patients having reconstruction by pancreaticojejunostomy.

Methods

A meta-analysis was performed of all large cohort and randomized controlled trials carried out since 1990.

Results

Eleven articles were identified for inclusion: one prospective randomized trial, two non-randomized prospective trials and eight observational cohort studies. The meta-analysis revealed a higher rate of pancreatic fistula associated with pancreaticojejunostomy reconstruction (relative risk (RR) 2·62 (95 per cent confidence interval (c.i.) 1·91 to 3·60)). A higher overall morbidity rate was also demonstrated in this group (RR 1·43 (95 per cent c.i. 1·26 to 1·61)), as was a higher mortality rate (RR 2·51 (95 per cent c.i. 1·61 to 3·91)).

Conclusion

Current literature suggests that the safer means of pancreatic reconstruction after pancreaticoduodenectomy is pancreaticogastrostomy, but much of the evidence comes from observational cohort study data.

An extremely rapid and simple DNA-release method for detection of M. tuberculosis from clinical specimens

A single-step, 5-min lysis method was investigated as a rapid technique to extract genomic DNA from mycobacteria for PCR detection of M. tuberculosis directly from clinical specimens. Of 67 smear-positive clinical specimens, 64 (95.5%) were positive by PCR after this rapid extraction method.

Analysis of multidrug-resistant Mycobacterium bovis from three clinical samples from Scotland

OBJECTIVE

To determine whether multidrug-resistant (MDR) strains of Mycobacterium bovis isolated from patients in Scotland were genotypically related.

DESIGN

Genotypes of MDR strains were determined using three molecular fingerprinting techniques: pulsed-field gel electrophoresis (PFGE), spoligotyping and restriction fragment length polymorphism (RFLP). PFGE profiles were also obtained for all medical and veterinary isolates occurring in Scotland in 1997-1998.

RESULTS

MDR strains showed individual Dra I PFGE profiles. Case III/98 had a profile represented in both veterinary and medical populations, Case I/94 had a profile observed in medical but not veterinary isolates, and Case II/98 had a profile unique to this study. Afl II PFGE discriminated the resistant strains. Spoligotyping grouped Cases I/94 and II/98 (ST-134). Case III/98 had a spoligotype ST-140, which is commonly observed in veterinary isolates. Similarly, DRr-RFLP analysis grouped cases I/94 and II/98, whereas Case III/98 had a common veterinary profile. DRX(PGRS) RFLP gave three unique profiles.

CONCLUSION

Three resistant strains were discriminated by PFGE and DRX(PGRS) RFLP, indicating that the three strains are not related in an epidemiologically relevant time scale. However, Cases I/94 and II/98 were more closely linked by spoligotyping and DRr-RFLP data. PFGE and DRr-RFLP linked Case III/98 profiles to the most common veterinary isolate.

Locating transposable element polymorphisms in bacterial genomes

Although whole-genome sequencing is greatly extending our knowledge of the genetic capacity of those bacterial species, it is only directly informative for the particular strain sequenced. Many bacterial species exhibit more or less genetic polymorphism within their populations and characterising this variety is an extremely important way of elucidating the biology of these species. Often genomic polymorphisms are associated with multicopy elements, particularly transposable elements. We describe a novel method that efficiently characterises the sequences of such polymorphisms. We have optimised heminested inverse PCR (hINVPCR) to assess the diversity of insertional polymorphisms of a transposable element (IS6110) in clinical isolates of Mycobacterium tuberculosis. To increase the yield of information, genomic DNA was digested with different endonucleases (Bsp1286I, HaeII or PvuI), and primers based on both the 5' and 3' ends of IS6110 were used to amplify and determine the genomic sequence upstream (or downstream) of the transposable element. We found that both the choice of restriction enzyme and the use of primers at both ends of the transposable element significantly increased the diversity of the insertion sites identified. Band stabbing was incorporated into the method as an alternative to cloning in order to screen large number of isolates at a sequence level in a rapid and labour-efficient fashion. We describe some of the purposes to which such data can be put.

The efficacy of the heat killing of Mycobacterium tuberculosis

There is concern that current procedures for the heat inactivation of Mycobacterium tuberculosis may not be adequate. This raises serious safety issues for laboratory staff performing molecular investigations such as IS6110 restriction fragment length polymorphism typing. This paper confirms that the protocol of van Embden et al, as performed routinely in this laboratory, is safe and effective for the heat inactivation of M tuberculosis. This procedure involves complete immersion of a tube containing a suspension of one loopfull of growth in a water bath at 80 degrees C for 20 minutes. Seventy four isolates were included in this investigation. Despite prolonged incubation for 20 weeks, none of the heat killed M tuberculosis suspensions produced visible colonies or gave a positive growth signal from liquid culture. This method did not affect the integrity of the DNA for subsequent molecular investigations.

Molecular epidemiology of Mycobacterium malmoense infections in Scotland

Clinical isolates of Mycobacterium malmoense collected over 5 years from patients across Scotland with a variety of diseases have been characterized by pulsed-field gel electrophoresis (PFGE), ribotyping, and 16S ribosomal DNA gene sequencing. Results indicate that this species harbors little genetic diversity and that the different strain types that were identified by PFGE showed no correlation with geographical origin or date of isolation.

Molecular evidence for independent occurrence of IS6110 insertions at the same sites of the genome of Mycobacterium tuberculosis in different clinical isolates

Several characteristics of Mycobacterium tuberculosis (e.g., conserved genome and low growth rate) have severely restricted the study of the microorganism. The discovery of IS6110 raised hopes of overcoming these obstacles. However, our knowledge of this IS element is relatively limited; even its two basic characteristics (transposition mechanism and target site selection) are far from well understood. In this study, IS6110 insertions in ipl loci (iplA and iplB) in two collections of clinical isolates of M. tuberculosis from different geographic locations, one from Scotland and the other from Thailand, were investigated. Five different IS6110 insertions in the loci were identified: ipl-4::IS6110, ipl-5::IS6110, ipl-11::IS6110, ipl-12::IS6110, and ipl-13::IS6110. An attempt to establish the phylogenetic relationship of the isolates containing these insertions was unsuccessful, suggesting that some of these insertions may have arisen from more than one event. This possibility is further supported by the observation that IS6110 copies existed in the same site but with different orientations in different isolates, and the insertion site of ipl-1::IS6110 harbored IS6110 copies in both iplA and iplB in different strains. All these suggest the independent occurrence of IS6110 insertions at the same sites of the genome of M. tuberculosis in different clinical isolates. The implications of this finding are discussed.

Functional alpha4-integrin: a newly identified pathway of neutrophil recruitment in critically ill septic patients

Using a novel flow chamber assay system and whole blood, we show that leukocytes from septic individuals have a four-fold elevation of adhesion, but not rolling, on a P-selectin/beta2-integrin substrate. Most leukocytes from septic patients (but not healthy controls) that bound vascular cell adhesion molecule 1 (VCAM-1) were neutrophils. All adhesion was inhibited with an antibody specific for the VCAM-1 ligand alpha4-integrin. The alpha4-integrin was present on neutrophils from septic patients but not on neutrophils from patients with localized bacterial infections. The plasma milieu of septic patients was sufficient to induce neutrophils from healthy subjects to bind VCAM-1 under flow conditions. This is the first description of alpha4-integrin/VCAM-1 pathway of neutrophil recruitment in human disease. This pathway may provide a new therapeutic target to reduce inappropriate neutrophil adhesion without altering the normal yet critical beta2-integrin-mediated adhesive function of neutrophils.

Duodenal versus gastric feeding in ventilated blunt trauma patients: a randomized controlled trial

OBJECTIVE

To evaluate transpyloric feeds as they have been proposed as a means of providing enteric nutrition more rapidly and minimizing morbidity in ventilated trauma patients.

METHODS

Between July of 1994 and June of 1997, 80 adult ventilated trauma patients were enrolled in a randomized controlled trial of duodenal versus gastric feeds. Feeding was initiated within 72 hours of injury.

RESULTS

Forty-three patients received gastric feeds (G), and 37 patients received duodenal feeds (D). Mean age was 34.7+/-15.7 years (G) and 33.6+/-17.5 years (D); the difference in age was not significant (NS). Mean Injury Severity Score was 30.0+/-11 (G), 33.0+/-9.7 (D), NS. Mean Acute Physiology and Chronic Health Evaluation (APACHE II) score was 18.0+/-6.0 (G) and 18.0+/-7.4 (D), NS. Thirty-four of 43 patients were men (G) and 28 of 37 patients were men (D), NS. Use of narcotics and paralytics between the two groups was not significantly different. Energy requirements were 1.4 times basal energy expenditure at 2,127+/-304 Kcal (G) and 2,089+/-274 Kcal (D), NS. Intensive care unit length of stay was a median of 7 days (range, 3-32 days) (G) and 10 days (range, 3-24 days) (D), NS. Number of days on ventilator was a median of 5 days (range, 3-15 days) (G) and 9 days (range, 2-13 days) (D), NS. Hospital length of stay was a median of 25 days (range, 9-88 days) (G) and 30 days (range, 16-47 days) (D), NS. Recorded morbidity was not significantly different. Pneumonia rates were 42% (G) and 27% (D), NS. Time to tolerate full-strength feeds for 24 consecutive hours was 43.8 hours +/-22.6 (G) and 34.3 hours +/-7.1 (D), difference significant at p = 0.02.

CONCLUSION

Length of stay and ventilator days were not significantly different. A larger trial would be required to determine differences in the rates of pneumonia <20%. Transpyloric-duodenal feeds significantly reduce the time required to achieve targeted enteric nutrition.

Molecular evidence for heterogeneity of the multiple-drug-resistant Mycobacterium tuberculosis population in Scotland (1990 to 1997)

Multiple-drug-resistant Mycobacterium tuberculosis (MDR-MTB) has been well studied in hospitals or health care institutions and in human immunodeficiency virus-infected populations. However, the characteristics of MDR-MTB in the community have not been well investigated. An understanding of its prevalence and circulation within the community will help to estimate the problem and optimize the strategies for control and prevention of its development and transmission. In this study, MDR-MTB isolates from Scotland collected between 1990 and 1997 were characterized, along with non-drug-resistant isolates. The results showed that they were genetically diverse, suggesting they were unrelated to each other and had probably evolved independently. Several new alleles of rpoB, katG, and ahpC were identified: rpoB codon 525 (ACC-->AAC; Thr525Asn); katG codon 128 (CGG-->CAG; Arg128Gln) and codon 291 (GCT-->CCT; Ala291Pro); and the ahpC synonymous substitution at codon 6 (ATT-->ATC). One of the MDR-MTB isolates from an Asian patient had an IS6110 restriction fragment length polymorphism pattern very similar to that of the MDR-MTB W strain and had the same drug resistance-related alleles but did not have any epidemiological connection with the W strains. Additionally, a cluster of M. tuberculosis isolates was identified in our collection of 715 clinical isolates; the isolates in this cluster had genetic backgrounds very similar to those of the W strains, one of which had already developed multiple drug resistances. The diverse population of MDR-MTB in Scotland, along with a low incidence of drug-resistant M. tuberculosis, has implications for the control of the organism and prevention of its spread.

Characterization of IS1547, a new member of the IS900 family in the Mycobacterium tuberculosis complex, and its association with IS6110

Unlike classically defined insertion sequence (IS) elements, which are delimited by their inverted terminal repeats, some IS elements do not have inverted terminal repeats. Among this group of atypical IS elements, IS116, IS900, IS901, and IS1110 have been proposed as members of the IS900 family of elements, not only because they do not have inverted terminal repeats but also because they share other features such as homologous transposases and particular insertion sites. In this study, we report a newly identified IS sequence, IS1547, which was first identified in a clinical isolate of Mycobacterium tuberculosis. Its structure, insertion site, and putative transposase all conform with the conventions of the IS900 family, suggesting that it is a new member of this family. IS1547 was detected only in isolates of the M. tuberculosis complex, where it had highly polymorphic restriction fragment length polymorphism patterns, suggesting that it may be a useful genetic marker for identifying isolates of the M. tuberculosis complex and for distinguishing different strains of M. tuberculosis. ipl is a preferential locus for IS6110 insertion where there are eight known different insertion sites for IS6110. Surprisingly, the DNA sequence of ipl is now known to be a part of IS1547, meaning that IS1547 is a preferential site for IS6110 insertion.

IS6110-mediated deletions of wild-type chromosomes of Mycobacterium tuberculosis

The ipl locus is a site for the preferential insertion of IS6110 and has been identified as an insertion sequence, IS1547, in its own right. Various deletions around the ipl locus of clinical isolates of Mycobacterium tuberculosis were identified, and these deletions ranged in length from several hundred base pairs up to several kilobase pairs. The most obvious feature shared by these deletions was the presence of an IS6110 copy at the deletion sites, which suggested two possible mechanisms for their occurrence, IS6110 transposition and homologous recombination. To clarify the mechanism, an investigation was conducted; the results suggest that although deletion transpositionally mediated by IS6110 was a possibility, homologous recombination was a more likely one. The implications of such chromosomal rearrangements for the evolution of M. tuberculosis, for IS6110-mediated mutagenesis, and for the development of genetic tools are discussed. The deletion of genomic DNA in isolates of M. tuberculosis has previously been noted at only a few sites. This study examined the deletional loss of genetic material at a new site and suggests that such losses may occur elsewhere too and may be more prevalent than was previously thought. Distinct from the study of laboratory-induced mutations, the detailed analysis of clinical isolates, in combination with knowledge of their evolutionary relationships to each other, gives us the opportunity to study mutational diversity in isolates that have survived in the human host and therefore offers a different perspective on the importance of particular genetic markers in pathogenesis.

The use of spring-eye needles in neurosurgery: a survey of neurosurgical theatres in the United Kingdom

Spring-eye needles were commonly used in neurosurgery as a method of closure of craniotomy incisions because of the perceived, but not proven, advantages of easy handling, fast wound closure and reduced infection rate. However, these needles produce more tissue trauma and are more fragile. We surveyed 33 neurosurgical operating theatres in the UK to find out if spring eyed needles are still in use and, if they are not why not. We had a 91% response. The survey involved 117 British neurosurgeons, of whom spring-eye needles were used by 38 (13%). Both round body and cutting needles were used, but the cutting needles have a higher breakage rate. The use of 'eyed' needles is rare in other surgical specialties but they are still in use in neurosurgical theatres; however, their use has declined because of changes in surgical practice, the increased breakage rate of these needles, and reduction of their availability.

IS6110 transposition and evolutionary scenario of the direct repeat locus in a group of closely related Mycobacterium tuberculosis strains

In recent years, various polymorphic loci and multicopy insertion elements have been discovered in the Mycobacterium tuberculosis genome, such as the direct repeat (DR) locus, the major polymorphic tandem repeats, the polymorphic GC-rich repetitive sequence, IS6110, and IS1081. These, especially IS6110 and the DR locus, have been widely used as genetic markers to differentiate M. tuberculosis isolates and will continue to be so used, due to the conserved nature of the genome of M. tuberculosis. However, little is known about the processes involved in generating these or of their relative rates of change. Without an understanding of the biological characteristics of these genetic markers, it is difficult to use them to their full extent for understanding the population genetics and epidemiology of M. tuberculosis. To address these points, we identified a cluster of 7 isolates in a collection of 101 clinical isolates and investigated them with various polymorphic genetic markers, which indicated that they were highly related to each other. This cluster provided a model system for the study of IS6110 transposition, evolution at the DR locus, and the effects of these on the determination of evolutionary relationships among M. tuberculosis strains. Our results suggest that IS6110 restriction fragment length polymorphism patterns are useful in grouping closely related isolates together; however, they can be misleading if used for making inferences about the evolutionary relationships between closely related isolates. DNA sequence analysis of the DR loci of these isolates revealed an evolutionary scenario, which, complemented with the information from IS6110, allowed a reconstruction of the evolutionary steps and relationships among these closely related isolates. Loss of the IS6110 copy in the DR locus was noted, and the mechanisms of this loss are discussed.

Use of cisapride in treatment of constipation in children

BACKGROUND

Chronic constipation is a common problem in children. We observed the effects of cisapride in the management of idiopathic constipation in children.

METHODS

Thirty-seven children with a history of constipation (i.e., pain and difficulty or delay in defecation for > 3 months) were recruited and randomly assigned to 8 weeks of treatment with either cisapride, 0.2 mg/kg three times daily, or matching placebo after a 2-week run-in period in a double-blind, parallel-group study design. In phase 1 (2 weeks), patients had plain abdominal radiographs to assess degree of faecal load, and those with impaction were given laxatives. After satisfactory clearance of faeces, total gastrointestinal transit time and orocaecal transit time were measured. In phase 2, after 8 weeks of treatment with either cisapride or placebo (0.2 mg/kg t.d.s.), the transit studies were repeated.

RESULTS

Compared with placebo, cisapride did not improve either stool frequency or transit time in this study population.

CONCLUSION

This study did not demonstrate a clinical role for the use of cisapride in the treatment of idiopathic constipation in children.

Paraneoplastic intestinal pseudo-obstruction, mononeuritis multiplex, and sensory neuropathy/neuronopathy

A patient with diffuse intestinal pseudo-obstruction consisting of gastric paresis and impaired small and large bowel motility, mononeuropathy multiplex, and sensory neuropathy/neuronopathy was found to have small-cell carcinoma of the lung. The clinical symptoms were thought to be consistent with paraneoplastic neuropathy, and high antineuronal and anti-calcium channel antibodies led to the diagnosis of small-cell carcinoma of the lung. Identification of paraneoplastic neuropathy is important, because early treatment may halt the progression of the underlying carcinoma.

Diffuse juvenile non-adenomatous polyposis: a rare cause of severe hypoalbuminaemia in childhood

Hypoalbuminaemia is a well-recognized complication of juvenile polyposis, which is often not clinically apparent. We describe a child with diffuse colonic non-adenomatous polyposis who presented with generalized oedema and severe hypoalbuminaemia. The site of the protein loss was the polyps, and the problem resolved after colectomy. This is a case of unusually severe hypoalbuminaemia complicating juvenile polyposis.

Rhodococcus equi--an easily missed opportunistic pathogen

Over the last 10 years Rhodococcus equi has been identified as an important, albeit very rare, opportunistic pathogen. As the number of patients immunocompromised from HIV infection grows, this microorganism will likely become of increasing clinical importance. Infection with R. equi is usually insidious, causing progressive pulmonary disease that is typically pleural based at the time of microbiological diagnosis. As in the case we present, the clinical and microbiological diagnoses may be significantly delayed, either by the common pitfalls encountered in the laboratory identification of R. equi, or by the failure to recognize the pathogenic potential of the isolate. R. equi infection should be suspected in immunocompromised patients with pneumonia, when a pure or predominant growth of aerobic, non-sporeforming gram-positive bacilli is found on cultures of bronchoalveolar lavage fluid and other pulmonary pathogens have been excluded.