Genomic characterisation of CC398 MRSA causing severe disease in Australia.

Clonal complex 398 (CC398) livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) has been reported worldwide in a variety of food-animal species. Although CC398 is synonymous with LA-MRSA, community-associated MRSA (CA-MRSA) variants have emerged, including the Panton-Valentine leukocidin (PVL)-positive ST398-V and ST398 single-locus variant ST1232-V, and the PVL-negative ST398-V clones. Using comparative genomic analysis, we determined whether ten CC398 MRSA bacteraemia episodes recently identified in Australia were due to LA-MRSA or CA-MRSA CC398. Isolates were sourced from the Australian Group on Antimicrobial Resistance S. aureus surveillance programme and episodes occurred across Australia. Whole-genome sequencing (WGS) and phylogenetic comparison of the ten CC398 bacteraemia isolates with previously published CC398 MRSA whole-genome sequences identified that the Australian CC398 isolates were closely related to the human-associated II-GOI clade and the livestock-associated IIa clade. The identified CC398 MRSA clones were: PVL-positive ST1232-V (5C2&5), PVL-negative community-associated ST398-V (5C2&5) and livestock-associated ST398-V (5C2&5). Our findings demonstrate the importance of using WGS and comparing the sequences with international sequences to distinguish between CC398 CA-MRSA and LA-MRSA and to determine the isolates' origin. Furthermore, our findings suggest that CC398 CA-MRSA has become established in the Australian community and that ST398-V (5C2&5) LA-MRSA is now widespread in Australian piggeries. Our study emphasises the need for national One Health antimicrobial resistance surveillance programmes to assist in monitoring the ongoing epidemiology of MRSA and other clinically significant antimicrobial-resistant organisms.

Outbreak of health care-associated Burkholderia cenocepacia bacteremia and infection attributed to contaminated sterile gel used for central line insertion under ultrasound guidance and other procedures.

BACKGROUND: We report an outbreak of Burkholderia cenocepacia bacteremia and infection in 11 patients predominately in intensive care units caused by contaminated ultrasound gel used in central line insertion and sterile procedures within 4 hospitals across Australia. METHODS: Burkholderia cenocepacia was first identified in the blood culture of a patient from the intensive care unit at the Gold Coast University Hospital on March 26, 2017, with 3 subsequent cases identified by April 7, 2017. The outbreak response team commenced investigative measures. RESULTS: The outbreak investigation identified the point source as contaminated gel packaged in sachets for use within the sterile ultrasound probe cover. In total, 11 patient isolates of B cenocepacia with the same multilocus sequence type were identified within 4 hospitals across Australia. This typing was the same as identified in the contaminated gel isolate with single nucleotide polymorphism-based typing, demonstrating that all linked isolates clustered together. CONCLUSION: Arresting the national point-source outbreak within multiple jurisdictions was critically reliant on a rapid, integrated, and coordinated response and the use of informal professional networks to first identify it. All institutions where the product is used should look back at Burkholderia sp blood culture isolates for speciation to ensure this outbreak is no larger than currently recognized given likely global distribution.

Protein-based profiling of the immune response to uropathogenic Escherichia coli in adult patients immediately following hospital admission for acute cystitis.

Urinary tract infections (UTIs) caused by uropathogenic Escherichia coli (UPEC) are common infections in humans. Despite the substantial healthcare cost represented by these infections, the human immune response associated with the infection immediately following the onset of symptoms in patients remains largely undefined. We performed a prospective study aimed at defining the milieu of urinary cytokines in adult inpatients in the 24-48 h period immediately following hospital admission for acute cystitis due to UPEC. Urine samples, analyzed using 27-target multiplex protein assays, were used to generate immune profiles for patients and compared to age- and gender-matched healthy controls. The levels of multiple pro-inflammatory cytokines were significantly elevated in urine as a result of infection, an observation consistent with prior findings in murine models and clinical literature. We also identified significant responses for several novel factors not previously associated with the human response to UTI, including Interleukin (IL)-4, IL-7, IL-9, IL-17A, eotaxin, Granulocyte-macrophage colony-stimulating factor (GM-CSF) and several growth factors. These data establish crucial parallels between the human immune response to UPEC and murine model UTI studies, and emphasize the complex but poorly defined nature of the human immune response to UPEC, particularly in the immediate period following the onset of symptoms for acute cystitis.

A case of IMP-4-, OXA-421-, OXA-96-, and CARB-2-producing Acinetobacter pittii sequence type 119 in Australia.

An IMP-4-producing Acinetobacter pittii strain coproducing oxacillinases was isolated from a leg wound of a 67-year-old female patient. Identification to the species level by rpoB and gyrB sequencing and multiplex-PCR-based analysis revealed that the isolate was A. pittii. Whole-genome sequencing of this A. pittii isolate determined the presence of blaOXA-96, blaCARB-2, and a novel blaOXA-421 gene. The position of this novel blaOXA-421 gene was similar to that of blaOXA-51 in A. baumannii, downstream of the phosphinothricin N-acetyltransferase gene and upstream of fxsA in the chromosome. This A. pittii isolate was found to belong to sequence type 119 (ST119). Here, we report the first isolation of IMP-4-producing A. pittii ST119 with a novel blaOXA-421 gene from a patient in Australia and characterize its draft genome.

Expansive spread of IncI1 plasmids carrying blaCMY-2 amongst Escherichia coli.

Escherichia coli is a leading cause of urinary tract infections. One of the most common antibiotic classes used to treat such infections is the ß-lactams, including cephalosporins. Resistance to the third-generation cephalosporins can be caused by production of extended-spectrum ß-lactamases (ESBLs) or plasmid-mediated AmpC ß-lactamases. The most commonly reported AmpC ß-lactamase in E. coli is CMY-2. Plasmid-mediated CMY-2 has been frequently reported in E. coli and Salmonella sp. from food-producing animals. This study aimed to elucidate the molecular characteristics of clinical E. coli isolates carrying plasmids encoding CMY-2. A total of 67 CMY-2-producing E. coli were characterised by clonal analysis and phylogenetic typing. Characterisation of the plasmids carrying blaCMY-2 included replicon typing, plasmid profiling, plasmid transferability and sequencing of the blaCMY-2 genetic environment. As a result, E. coli producing CMY-2 was found to be highly polyclonal. The majority of CMY-2-producing E. coli belonged to phylogenetic group D. IncI1 plasmids were predominant among those carrying blaCMY-2 (96%). Restriction analysis revealed a single IncI1 plasmid carrying blaCMY-2 to be predominant and present in different clones of E. coli. IS1294-ISEcp1 complex or ISEcp1 that was truncated by IS1294 was the predominant insertion sequence upstream of blaCMY-2. The homogeneous genetic environment of blaCMY-2 observed among different strains of E. coli strongly suggests horizontal transfer of this IncI1, blaCMY-2-carrying plasmid. In summary, horizontal plasmid transfer plays a major role in the spread of blaCMY-2 in E. coli.

Innate transcriptional networks activated in bladder in response to uropathogenic Escherichia coli drive diverse biological pathways and rapid synthesis of IL-10 for defense against bacterial urinary tract infection.

Early transcriptional activation events that occur in bladder immediately following bacterial urinary tract infection (UTI) are not well defined. In this study, we describe the whole bladder transcriptome of uropathogenic Escherichia coli (UPEC) cystitis in mice using genome-wide expression profiling to define the transcriptome of innate immune activation stemming from UPEC colonization of the bladder. Bladder RNA from female C57BL/6 mice, analyzed using 1.0 ST-Affymetrix microarrays, revealed extensive activation of diverse sets of innate immune response genes, including those that encode multiple IL-family members, receptors, metabolic regulators, MAPK activators, and lymphocyte signaling molecules. These were among 1564 genes differentially regulated at 2 h postinfection, highlighting a rapid and broad innate immune response to bladder colonization. Integrative systems-level analyses using InnateDB (http://www.innatedb.com) bioinformatics and ingenuity pathway analysis identified multiple distinct biological pathways in the bladder transcriptome with extensive involvement of lymphocyte signaling, cell cycle alterations, cytoskeletal, and metabolic changes. A key regulator of IL activity identified in the transcriptome was IL-10, which was analyzed functionally to reveal marked exacerbation of cystitis in IL-10-deficient mice. Studies of clinical UTI revealed significantly elevated urinary IL-10 in patients with UPEC cystitis, indicating a role for IL-10 in the innate response to human UTI. The whole bladder transcriptome presented in this work provides new insight into the diversity of innate factors that determine UTI on a genome-wide scale and will be valuable for further data mining. Identification of protective roles for other elements in the transcriptome will provide critical new insight into the complex cascade of events that underpin UTI.

Predicting influenza A and 2009 H1N1 influenza in patients admitted to hospital with acute respiratory illness.

OBJECTIVE: To create a clinical decision tool for suspected influenza A (including 2009 H1N1) to facilitate treatment and isolation decisions for patients admitted to hospital with an acute respiratory illness from the emergency department (ED) during a 2009 H1N1 pandemic. METHODS: Cross-sectional study conducted in two hospitals in Queensland, Australia. All patients admitted to hospital from the ED between 24 May and 16 August 2009 with an acute respiratory illness were included. All had nasal and throat swabs taken. Data were collected from clinical chart review regarding clinical symptoms, co-morbidities, examination findings, pathology and radiology results. Influenza A status was detected by reverse transcription-PCR assay. Univariate and multivariate regression analyses were performed to identify independent predictors of influenza A status. RESULTS: 346 consecutive patients were identified, of which 106 were positive for 2009 H1N1 influenza; an additional 11 patients were positive for other influenza A viruses. Independent clinical predictors (with points allocated using weighted scoring) for all types of influenza A in patients admitted with acute respiratory illness were: age 18-64 years (2 points); history of fever (2); cough (1); normal level of consciousness (2); C-reactive protein >5 and ≤ 100 mg/l (2) and normal leucocyte count (1). A clinical score of 5 (presence of two or three predictors) gave a sensitivity of 93% (95% CI 87% to 96%), specificity of 36% (95% CI 30% to 42%), resulting in a negative-predictive value of 91% (95% CI 83% to 95%). CONCLUSION: A clinical prediction tool was developed that may be able to assist in making appropriate isolation decisions during future 2009 H1N1 outbreaks.

Nothing to sneeze at! A study into intra-operative contamination.

PURPOSE: We performed a prospective study of sneezes from orthopaedic registrars to assess the potential for intra-operative contamination from a masked surgeon, and to determine if head position can alter the potential for contamination. TYPE OF STUDY: Prospective controlled trial. METHODS: Four orthopaedic registrars from the Gold Coast Hospital each inhaled pepper to precipitate a sneeze. Cultures were taken with and without standard Smith & Nephew surgical masks, in positions directly in front and to the sides of a masked registrar. The process was repeated three times for each registrar. A control plate was left exposed to the atmosphere. A control plate and sneeze plate was cultured on blood agar. Three masks were subsequently swabbed to exclude contamination from the masks. RESULTS: 2/24 (8.33%) of the side with mask cultures returned significant bacterial growths. Also, 1/12 (8.33%) of the front with mask cultures returned significant growths. In addition, 9/12 (75%) of the direct sneezes resulted in significant bacterial counts. The control plate failed to return any growth. Subsequent culture of the exterior of three surgical masks failed to yield significant growth. There was a statistically significant odds ratio of 0.03 comparing the front and side group with the unmasked direct group. There was no statistically significant difference comparing front and side sneeze growth. CONCLUSIONS: While the use of surgical face masks significantly reduces bacterial counts following a sneeze, it fails to eliminate the potential for surgical field contamination completely. The fact that significant bacterial counts can be returned from direct culture through a mask and to the sides of a mask suggests that head position is irrelevant and contamination is possible in any direction. It is, therefore, suggested that, if possible, a sneezing surgeon distances himself/herself as much as possible from the sterile field. We also recommend following a sneeze; surgeons should re-gown and glove, given the risk of contamination of the sterile field. LEVEL OF EVIDENCE: Level II.

Diagnosis of Streptococcus pneumoniae infections in adults with bacteremia and community-acquired pneumonia: clinical comparison of pneumococcal PCR and urinary antigen detection.

The diagnosis of severe Streptococcus pneumoniae infection relies heavily on insensitive culture techniques. To improve the usefulness of PCR assays, we developed a dual-PCR protocol (targeted at pneumolysin and autolysin) for EDTA blood samples. This was compared to the Binax NOW S. pneumoniae urine antigen test in patients with bacteremic pneumococcal infections. Patients with nonbacteremic community-acquired pneumonia also were tested by these methods to determine what proportion could be confirmed as pneumococcal infections. A direct comparison was made in a group of patients who each had both tests performed. The Binax NOW S. pneumoniae urine antigen test was positive in 51 of 58 bacteremic pneumococcal cases (sensitivity, 88%; 95% confidence interval [CI], 77 to 95%), whereas the dual PCR was positive in 31 cases (sensitivity, 53.5%; 95% CI, 40 to 67%; P < 0.0001), and all of these had detectable urinary antigens. Both tests gave positive results in 2 of 51 control patients (referred to as other-organism septicemia), giving a specificity of 96% (95% CI, 86.5 to 99.5%). In 77 patients with nonbacteremic community-acquired pneumonia, urinary antigen was detected significantly more often (in 21 patients [27%]) than a positive result by the dual-PCR protocol (6 [8%]) (P = 0.002). The development of a dual-PCR protocol enhanced the sensitivity compared to that of the individual assays, but it is still significantly less sensitive than the Binax NOW urine antigen test, as well as being more time-consuming and expensive. Urinary antigen detection is the nonculture diagnostic method of choice for patients with possible severe pneumococcal infection.

Rapid diagnosis of bacteremic pneumococcal infections in adults by using the Binax NOW Streptococcus pneumoniae urinary antigen test: a prospective, controlled clinical evaluation.

The diagnosis of severe pneumococcal infections is inadequate, relying heavily on culture of Streptococcus pneumoniae from blood or other normally sterile fluids, and is severely limited by prior administration of antibiotics. We evaluated prospectively the Binax NOW S. pneumoniae urinary antigen test, a rapid immunochromatographic assay, for the diagnosis of bacteremic pneumococcal infections in hospitalized adult patients. Antigen was detected in 88 of 107 cases overall, resulting in a test sensitivity of 82% (95% confidence interval [95% CI], 74 to 89%). Antigen detection was greater in those with pneumonia (67 of 77 [87%]) than in those without pneumonia (21 of 30 [70%]) (P = 0.04). Urinary antigen was also detected in 3 of 106 adult patients with community-acquired septicemic infections caused by other organisms, giving a test specificity of 97% (95% CI, 92 to 99%). For 45 pneumococcal bacteremia patients with a positive test on treatment day 1, urinary antigen excretion was monitored for the first week of antibiotic treatment. Antigen was still detectable in 83% (29 of 35 tested; 95% CI, 66 to 93%) on treatment day 3. Detection of urinary antigen is a valuable, sensitive, and rapid test for the early diagnosis of bacteremic pneumococcal infections in adult patients, even after antibiotic treatment has commenced.