Dr Lyn-li Lim joined VICNISS in early 2019. She is an infectious diseases physician with post-graduate training in epidemiology, public health and medical administration, and holds a co-appointment as a physician and antimicrobial stewardship lead at a public health service in Melbourne.
See below for her latest literature review:
(*NB: This information was up to date and current at the time of publication however as this is a rapidly changing situation please refer to the links mentioned in the review for any further updates as information becomes available)
On December 30th 2019, a cluster of cases of pneumonia of unknown origin was identified by authorities in Wuhan, China. On January 7th 2020, novel coronavirus (2019-nCoV) was isolated. As of February 2nd 2020, health authorities in China have reported more than 12,000 cases and 259 deaths. Confirmed cases have been identified in mainland China, as well as 26 other countries including Hong Kong, Macau, Taiwan, Thailand, Japan, Malaysia, South Korea, Vietnam, Cambodia, Sri Lanka, Singapore, Nepal, France, Italy, Germany, USA, Canada and Australia. The World Health Organisation declared on January 30th 2020 that the outbreak of 2019-nCoV constitutes a Public Health Emergency of International Concern.
The situation is evolving rapidly as we find out more about this new virus.
DHHS alert: update 2/2/20
As of 1 February 2020, the case definition for a person suspected to have contracted novel coronavirus (2019-nCoV) has been expanded to any person who has an acute respiratory infection and has been in mainland China or had close contact with a confirmed case of novel coronavirus in the 14 days prior to onset of illness.
People who have been in mainland China (excluding Hong Kong SAR, Macau and Taiwan) are advised to self-isolate if they were in mainland China on or after 1 February 2020.
The requirement to self-isolate continues to apply to people who have been in Hubei Province, China, for 14 days after they left Hubei Province.
Anyone who has been in close contact with a confirmed case of 2019-nCoV should also stay at home and avoid public settings until 14 days after their last contact.
The department has confirmed four cases of novel coronavirus in Victoria.
Be alert for patients who meet the updated case definition, ensure they wear a surgical mask and place them in a negative pressure or single room.
Take a travel history in patients with respiratory symptoms. Note the updated case definition to inform testing.
Notify the Department of Health and Human Services on 1300 651 160.
Links to resources on 2019-nCoV
For Victorian Department of Health and Human Services regular updates and guidance on case definitions, testing and resources including signage and consumer information
The Commonwealth Department of Health has updates on the national response to this health threat and provides resources to health professionals and consumers, including Coronavirus Health Information Line.
For information and guidance updated daily from WHO regarding the current outbreak of novel coronavirus (2019-nCoV)
To assist HCW and researchers, The Lancet has created a Coronavirus Resource Centre to bring together content across Lancet journals as it is published.
To assist HCW and researchers, New England Journal of Medicine has curated a collection of articles and other resources on 2019-nCoV
Carbapenemase-Producing Enterobacterales (CPE) are multi-drug resistant organisms that can a pose a potential public health threat; carbapenems are the most broad–spectrum β-lactam antibiotics active against gram-negative organisms where effectiveness is challenged by the global emergence of CPE. Furthermore, the production of carbapenemase enzymes on mobile genetic elements increases the transmission potential of CPE.
There have been multiple recently published systematic review and meta-analyses examining the health outcomes attributable to CPE infections. Soontaros et al (Am J Inf C 2019; 47(10):1200-12) performed a systematic review of published studies assessing the association between CPE and death from 2012 to 2017, identifying 21 studies included in the meta-analysis. CPE increased the risk of death by 273% (pooled OR 3.73, 95% CI 2.03-6.88); when adjusted for confounders such as age increased risk of death remained (OR 2.85, 95% CI 1.88-4.30).
Budhram et al (Inf C & Hosp Epi 2020; 41:37-43) performed a systematic review to identify studies from 2008 to 2018 that included a control group of patients with CPE infections. 17 studies met inclusion criteria; most were from Europe (68%). Mortality was the most commonly reported outcome (60%), followed by sequelae (including relapse, secondary BSI), antibiotic therapy (e.g. duration, appropriateness), and length of stay. None reported health-related quality of life outcomes. Of studies that reported mortality outcomes, mortality rates ranged from 11.1 to 82.4%, with 76.3% of all deaths reported as in-patient including ICU deaths. A meta-analysis (n=5 studies) identified the risk of in-hospital death related to secondary bloodstream infection is increased four-fold in patients with CPE compared to those with a carbapenem-susceptible infection (ARD 0.25 [95% CI 0.17-0.32]).
Both these studies suggest that the risk of death is significant amongst patients with infection or colonised with CPE infection and warrants strict infection control procedures. Victoria has established guidelines on detection, reporting, identification and management of CPE colonised and infected patients in hospitals and residents in aged care facilities. https://www2.health.vic.gov.au/about/publications/policiesandguidelines/carbapenemase-producing-enterobacteriaceae-guidelines. The DHHS also provides CPE reports, updated in 2020 to a new format, that are uploaded each quarter. https://www2.health.vic.gov.au/public-health/infectious-diseases/infectious-diseases-surveillance/interactive-infectious-disease-reports/cpe-surveillance-report
Candida auris (C. auris) is an emerging fungal pathogen: it is considered a potential public health threat to Victorian health services based on overseas experience where it has been associated with healthcare outbreaks. In contrast to other Candida species, C.auris can spread easily in healthcare settings causing nosocomial outbreaks and persist, both on the human host and on inanimate surfaces. It is a multidrug resistant organism, intrinsically resistant to fluconazole and with variable susceptibility to other important anti-fungal drug classes including amphotericin B and echinocandins.
Since 2009, it has been identified in over 30 countries and every continent except Antarctica however; it is thought to have been misidentified as C. haemulonii complex in the past. The first Australian detection of C. auris (South Africa clade) was in 2015 in WA with further detection since mid-2018 in Victoria, NSW and WA. The Victorian guideline on Candida auris for health services1 was released in August 2019 (www2.health.vic.gov.au/infection-control) and the Australian Society for Infectious Diseases (ASID) has also published a position statement.2
The ASID statement2 reviews evidence regarding diagnosis, treatment and prevention and provides consensus recommendations for clinicians and microbiologists in Australia and New Zealand, which are summarised.
Based on recent European data, bloodstream infections are the most frequently reported infections (18%), with infection at other sites (7%) and colonisations (75%). Candidaemia is associated with high mortality rates (up to 30-60%). Most patients have had extensive healthcare exposure, with a median of 19 days from hospitalisation to acquisition. Other identified risk factors include chronic illness, immunocompromised and presence of indwelling devices. Colonisation of skin and mucosal surfaces often occurs in outbreaks and can reappear after apparent clearance. Current Victorian recommendations1 advise that once a person is identified as a case of C. auris, they are considered potentially infectious indefinitely.
Patients should be screened using swabs of groin and axilla. 1,2 Additional sites can also be considered for screening to enhance yield (e.g. line exit sites, wounds).1,2 Data from colonised patients show that a single negative screen does not reliably exclude carriage. Victorian guidelines1 advise one set of screening specimens is sufficient for patients screened based on overseas hospital stay in last 12-months or ward contacts of C. auris patient, whilst two sets separated by at least 24 hours is required for patients screened based on direct transfer from overseas hospital or room contact.
Culture-based (phenotypic) approaches are the mainstay of laboratory diagnosis of C. auris. All yeast isolates should be identified to species level (e.g. “Candida albicans” not just “Candida spp.”) if from a sterile site or from a non-sterile site if screening based on risk (e.g. patient with overnight hospitalisation overseas). Delays to results can occur as culture-based methods can require up to 10 days incubation to call a negative result; as well C. auris can be misidentified by conventional culture-based methods and require further work-up.
MALDI-TOF MS used by some hospital laboratories can provide reliable identification using the appropriate database containing C. auris spectra representing all clades. In an outbreak setting, molecular techniques including whole genome sequencing is used for genotyping strains.
Use of an echinocandin is the current first-line recommendation for suspected/proven C. auris infections in adults. Antifungal susceptibilities for C. auris including MIC values should be interpreted with caution2 and formal Infectious Diseases consultation recommended1. Antifungal treatment of C. auris colonisation is generally not recommended.
Infection control precautions
Isolation with standard and contact precautions. HCW caring for patients with C. auris should use ABHR when hands are not visibly soiled. If soiled, washing with soap and water recommended.2 Detergents and sporicidal disinfectants (e.g. ≥1000ppm bleach, peracetic acid, accelerated hydrogen peroxide) for environmental decontamination. Further information is provided in Victorian Guideline1 (Section 5 “Management and control of C. auris”).
Victorian health service response including local incident response and supporting roles of DHHS, VIDRL, MDU and VICNISS are outlined in detail in the Victorian guideline.1
O’Connor et al. (J Hosp Infect 2019: 103; 106-111) describe their experience of an eight-week Candida auris outbreak on a vascular ward. Key learnings form their experience include the importance of early activation of a local incident management team supported by public health in screening and contact tracing. Of significance, isolates from two of the four cases demonstrated reduced susceptibility to echinocandins (first-line treatment for C. auris). As well, one bay contact with negative initial screening was positive when re-screened three-weeks later after transfer to another hospital.
Since its discovery in 2009, C. auris has been identified in more than 30 countries including Australia. In contrast to other Candida species, C. auris spreads easily in healthcare settings and has been associated with nosocomial outbreaks. The ability to persist in human hosts and inanimate surfaces, as well as the fact that this yeast is resistant to antifungal agents (resistance to fluconazole, variable susceptibility to other azoles, amphotericin and echinocandins), highlights the significance of this organism as a new nosocomial threat requiring enhanced infection control measures.
A proposed strategy to reduce transmission of multi-drug resistant organisms is to accommodate patients in single rooms to reduce chance of transmission from other patients and improve compliance with infection control measures. Evidence to date linking hospital architectural design and prevention of healthcare-associated infection (HAI) is conflicting. McDonald et al. (JAMA Int Med August 2019) report a reduction in infections (VRE) and colonisations (VRE and MRSA) when a Canadian hospital moved to a new 350-bed facility in which all patients had single rooms. However, no differences were observed in Clostridioides difficile infections (CDI) or MRSA infections.
In this time-series analysis, the move was associated with immediate and sustained reductions over 3-years in the incidence of nosocomial VRE colonisation (from 766 to 209 colonisations, incident rate ratio 0.25; 95% CI 0.19-0.34). There was also a fall in MRSA colonisation (from 129 to 112 colonisations, IRR 0.57; 95% CI 0.33-0.96) and VRE infection (from 55 to 14 infections, IRR 0.30; 95% CI 0.12-0.75). However, no change in nosocomial CDI (236 to 223 infections, IRR 1.00; 95% CI 0.98-1.02) or MRSA infections (27 to 37 infections; IRR 1.02, 95% CI 0.97-1.07) was observed. The IRR estimates adjusted rates pre- and post-hospital move. For VRE colonisation (IRR = 0.25), the colonisation rate reduced by 75% post-move. For MRSA colonisation (IRR 0.57), colonisation rate reduced by 43% post-move.
Limitations of the study include being unable to control for other contemporaneous interventions in infection control and antimicrobial stewardship and no data on MDR Gram-negative organisms. As well, MRSA colonisation may have been acquired pre-admission. While reasons for no change in CDI rate were not clear, it is possible that CDI disease burden may be associated with additional factors, including antibiotic prescribing patterns prior to hospitalisation.
This study adds observational evidence to support recommendations for single-room design in healthcare facility construction, in order to decrease risks of transmission of specific multidrug resistant organisms and healthcare–associated infections. However, there is on-going need to also optimise practices around use of antimicrobials, hand hygiene and facility cleaning.
Russo and colleagues (Antimic Res & Inf Control 2019:8;114) undertook a point prevalence study in a sample of large acute care hospitals. The primary objectives were (1) to estimate the total prevalence of HAIs among adult inpatients in public acute care hospitals in Australia and (2) to describe the HAIs by site, patient factors, medical specialty and geographical location.
Hospitals were recruited by seeking an expression of interest. To maximise representation of large acute care public facilities, inclusion criteria included being in the AIHW Principal Referral or Group A hospitals peer grouping (i.e. hospitals with 24-hour emergency departments, ICU and specialised units including, but not limited to, oncology and coronary care). Exclusions included specialist and private hospitals. Patients were systemically sampled according to random allocation of each ward to odd or even bed numbers. Patients were excluded if <18 years, in emergency or admitted for same-day procedure. European Centre for Disease Prevention and Control HAI definitions were used.
2,767 patients from 19 hospitals were included. The median age of patients was 67 years, and 52.9% of the sample were male. Presence of multi-drug resistant organisms was documented for 10.3% of the patients. There were 363 HAIs present in 273 patients. The prevalence of patients with a HAI was 9.9% (95%CI: 8.8–11.0) with individual hospital prevalence rates ranging from 5.7% (95%CI:2.9–11.0) to 17.0% (95%CI:10.7–26.1). The most common HAIs were surgical site infection, pneumonia and urinary tract infection, comprising 64% of all HAIs identified. A peripheral intravascular device was present in 55.2% and an IDC in 20.7%. Of 38 patients with a BSI, 35 (92.1%) had a vascular device in-situ. The most common organisms isolated were S. aureus (18.9%), E.coli or Klebsiella (24.3%), Enterococcus spp (13.5%), Candida spp (10.8%). Of 66 of patients with a UTI, 33 (50%) an IDC in-situ. Risk adjustment was not undertaken and severity of illness was not reported. The authors note selection bias in this study to ensure jurisdictional representation and inclusion limited to large public hospitals.
Russo et al have undertaken the first HAI point prevalence survey to be conducted in Australia in 34 years concluding that regular, large-scale HAI surveys should be undertaken to generate national HAI data to inform and drive national interventions. These study results complement state-level and regional healthcare-associated infection surveillance program activities which incorporate continuous surveillance, point-prevalence surveys and periodic monitoring to provide hospitals with ward-level data, risk adjustment, measures of severity of illness to assist with immediate responses and tailoring of prevention strategies.
Bundles improve staff compliance with best practice by simplifying guidelines into a short point-of-care reminders. CVAD insertion and maintenance bundles have been widely implemented and are recognised to reduce infection rates. The success of the CVAD bundle in ICU patients can be attributed to standardisation of the bundle components and consistency in their application. Ray-Barruel and colleagues (Inf, Dis & Health 2019: 24; 152e168) have undertaken the first systematic review to examine the effects of bundles on PIVC insertion and maintenance on PIVC complications (pain, infiltration, extravasation, blockage, premature dislodgement, thrombosis, phlebitis) and PIVC-related BSI.
13 studies were included in this review where an insertion or maintenance bundle was defined a priori as including at least two evidence-based practices for insertion respectively. All included studies reported implementing a PIVC care bundle for insertion (n= 9) or maintenance (n =10), or both (n =8) in an acute care hospital inpatient setting. Twenty-one different insertion bundle components were detailed in 10 studies. Each insertion bundle comprised two to seven items: the most often reported items were 2% chlorhexidine gluconate (CHG) skin prep, hand hygiene, vessel assessment/ site selection, aseptic technique, integrated closed catheter, and transparent film dressing. Twenty-two different maintenance bundle components were identified in 11 studies. Each maintenance bundle comprised two to seven items: the most common maintenance bundle items included daily review of need for PIVC (n=7) and poster reminders of the bundle intervention (n=7).
There are fewer published RCTs in PIVCs than CVADs, and while CVAD bundles are generally based on components supported by RCT evidence, this is not the case for PIVC bundles. The effect of PIVC care bundles on PIVC-related bloodstream infection rates appears promising but further research is needed to identify which bundle components are effective to support standardisation of bundle components.
Healthcare-associated, hospital-onset (HO) Clostridioides difficile infection is associated with both antibiotics and prolonged hospital stays. C. difficile spores can survive on surfaces for up to five months, suggesting that hospital environments may play an important role in the spread of HO-CDI. There is little data on the role of intra-hospital transfers on transmission dynamics of HO-CDI.
McHaney-Lindstorm (Jour Hosp Infect 2019; 102 (2): 168-169) and colleagues examined whether a higher number of intra-hospital patient transfers increases the risk of HO-CDI infection. This was a case-control study where the control group was selected by performing a 1:3 match based antibiotic use during hospitalization and age.
In all, 386 cases of HO-CDI were identified during the 2-year study period. The case and control groups were well balanced for age, antibiotic usage and Charlson Comorbidity Index scores. Multivariate logistic regression analysis suggested a significant relationship between CDI risk and the number of transfers, where for each additional transfer, the odds of HO-CDI infection increased by ∼7% (OR: 1.07; 95% CI: 1.02–1.13).
These results suggest that intra-hospital transfers expose patients to more environments that may harbour the C. difficile spores, putting patients who experience more intra-hospital transfers at greater risk of CDI. This supports the practice of reducing unnecessary patient movement within hospitals.
Infection control in endoscopy presents increasingly complex challenges. Since 2010, there have been several overseas outbreaks of CPE linked to the use of flexible endoscopes. The Gastroenterological Society of Australia (GESA) and Gastroenterological Nurses College of Australia (GENCA) published the Infection Control in Endoscopy Guidelines (3rd edition, 2010) which are being updated this year. In 2017, GESA, GENCA, ACIPC and Australasian Society of Infectious Diseases (ASID) developed consensus statements addressing this issue (J of Gastro and Hepatol 2019: 34:650-658).
In this recent report (CID 2019: 68 (8); 1327–1334), transmission of mobile colistin resistance gene (mcr-1) was identified in two patients with highly-related K. pneumoniae clinical isolates. An extensive field investigation, including screening targeted high-risk groups, evaluation of the duodenoscope, and genome sequencing of isolated organism, identified that a duodenoscope was the only common epidemiological link. There were no identifiable breaches in reprocessing or infection control practices however evaluation of the scope identified intrusion of biomaterial under the sealed distal cap which was recalled.
Polymyxins such as colistin are used as a last-line antimicrobial treatment option for multi-drug resistant gram-negative infections. The spread of plasmid-mediated, mobile colistin resistance genes into carbapenamese-producing Enterobacteriacae raises the concern of potentially untreatable infections with significant transmission risks. Instruments with complex tips (e.g. duodenoscopes and linear echoendoscopes) may transmit multidrug-resistant organisms persist despite recent initiatives to improve device safety.
ACIPC 2018 delegates had the opportunity to hear investigators present interim findings from the REACH study which has now been published in Lancet Infectious Diseases (Mitchell B et al. Lancet Inf Dis 2019; epub 8/3/19). This is the first randomised controlled trial to investigate the effectiveness of a systematic bundle of interventions to improve environmental hygiene, targeting routine daily cleaning and terminal cleaning and disinfection in reducing health-care associated infections (HCAI) in hospitals.
The study was a stepped-wedge randomised controlled design, performed in 11 Australian hospitals between May 2016 and 2017. The intervention involved a review of the environmental hygiene approach in each hospital, and a structured, tailored set of recommendations to improve product choice, technique, audit, training, and communication of performance. The primary outcomes were incidences of health-care-associated S.aureus bacteraemia (SAB), C. difficile infection (CDI), and VRE infection. The secondary outcome was the thoroughness of cleaning of frequent touch points, assessed by a fluorescent marking gel. A unique aspect of the intervention was to raise the profile and importance of cleaning, support a culture shift in the perception and profile of environmental hygiene staff, and to encourage daily contact between environmental hygiene staff and ward leaders or managers. This is separately published (Mitchell B et al. Am J Inf Control 2018; 46(9):980-985).
Overall, there was a 37% reduction in VRE infections (from 0.35 to 0.22 per 10,000 occupied bed days (RR 0.63, 95% CI 0.41–0.97, p=0.0340), but no significant changes in the incidence of S. aureus bacteraemia (0.97 to 0.80/10,000 occupied bed days; RR 0.82, 95% CI 0.60–1.12, p=0.2180) or C. difficle infection (2.34 to 2.52/10,000 occupied bed days; RR 1.07, 95% CI 0.88–1.30, p=0.4655). The intervention increased the percentage of frequent touch points cleaned in bathrooms from 55% to 76% (odds ratio 2·07, 1·83–2·34, p<0·0001) and bedrooms from 64% to 86% (1·87, 1·68–2·09, p<0·0001). There were no noticeable changes in hand hygiene compliance or antimicrobial use during the study period.
This study underlines both the importance of environmental hygiene in preventing HCAI and also highlights our knowledge gaps around how what an effective environmental hygiene intervention looks like. The intervention was a mixture of training, education, organisational policy changes as required to increase the status of environmental hygiene and environmental hygiene staff. Any or all of these changes could have resulted in the reduction of VRE. It is unclear why there were no significant reductions in SAB and CDI: this could be further explored in the future by evaluating acquisition of colonisation rather than infection and looking also at the impact of appropriate use of a sporicidal disinfectant for C.difficile.
Clostridium difficile is a leading cause of health-care associated infections, rivalling MRSA, accounting for $3.2 billion in excess costs annually globally. A recently updated ASID/ACIPC position statement on infection control for patients with CDI in Australian healthcare facilities was published (IDH 2019:24:32-43). Infection control recommendations for hospitals focus on preventing transmission from symptomatic CDI patients. Kong et al (CID 2019; 68 (1):204-209) undertook to investigate the relative roles of carrier and cases as a source of transmission to patients with CDI.
Investigators analysed patient movement data and performed whole genome sequencing (WGS) on 554 C. difficile isolates originally obtained during a NAP1 strain outbreak. Samples were collected from 353 colonised patients and 201 CDI cases for genetic testing.
Of CDI cases, 105 (52%) were genetically linked with 81 (77%) also having a plausible ward link. Of those with a likely source, 34/81 (42%) of linked cases were associated exclusively with a previous CDI case and 19/81 (23%) associated exclusively with an asymptomatic carrier.
This is the largest study to date investigating the roles of carriers and cases as sources of transmission. The use of WGS is currently considered the most discriminating typing/fingerprinting method and being increasingly adopted over other techniques such as pulsed-field gel electrophoresis (PFGE) or PCR ribotyping. This study confirms that colonised patients may be a source of onward transmission to incident CDI cases, but that spread from infected donors with diarrhoea is likely more frequent.