Genome Sequencing Links Persistent Outbreak of Legionellosis in Sydney (New South Wales, Australia) to an Emerging Clone of Legionella pneumophila Sequence Type 211.

The city of Sydney, Australia, experienced a persistent outbreak of Legionella pneumophila serogroup 1 (Lp1) pneumonia in 2016. To elucidate the source and guide public health actions, the genomes of clinical and environmental Lp1 isolates recovered over 7 weeks were examined. A total of 48 isolates from human cases and cooling towers were sequenced and compared using single-nucleotide polymorphism (SNP)-based core-genome multilocus sequencing typing (MLST) and pangenome approaches. All three methods confirmed phylogenetic relatedness between isolates associated with outbreaks in the Central Business District (CBD) in March and May and those in suburb 1. These isolates were designated the "main cluster" and consisted of isolates from two patients from the CBD March outbreak, one patient and one tower isolate from suburb 1, and isolates from two cooling towers and three patients from the CBD May outbreak. All main cluster isolates were sequence type 211 (ST211), which previously has only been reported in Canada. Significantly, pangenome analysis identified mobile genetic elements containing a unique type IV A F-type secretion system (T4ASS), which was specific to the main cluster, and cocirculating clinical strains, suggesting a potential mechanism for increased fitness and persistence of the outbreak clone. Genome sequencing enabled linking of the geographically dispersed environmental sources of infection among the spatially and temporally coinciding cases of legionellosis in a highly populated urban setting. The discovery of a unique T4ASS emphasizes the role of genome recombination in the emergence of successful Lp1 clones.IMPORTANCE A new emerging clone has been responsible for a prolonged legionellosis outbreak in Sydney, Australia. The use of whole-genome sequencing linked two outbreaks thought to be unrelated and confirmed the outliers. These findings led to the resampling and subsequent identification of the source, guiding public health actions and bringing the outbreak to a close. Significantly, the outbreak clone was identified as sequence type 211 (ST211). Our study reports this ST in the Southern Hemisphere and presents a description of ST211 genomes from both clinical and environmental isolates. A unique mobile genetic element containing a type IV secretion system was identified in Lp1 ST211 isolates linked to the main cluster and Lp1 ST42 isolates that were cocirculating at the time of the outbreak.

First reported outbreak of locally acquired hepatitis E virus infection in Australia.

OBJECTIVE: To determine the source and extent of a locally acquired hepatitis E virus (HEV) infection outbreak. DESIGN, SETTING AND PARTICIPANTS: A cluster of notified cases of HEV infection linked to a single restaurant (X) was identified in May 2014. People with laboratory-confirmed HEV infection in New South Wales between January 2013 and December 2014 were interviewed about potential risk factors for HEV infection. Co-diners at restaurant X and patients with suspected but unexplained viral hepatitis were retrospectively tested. Foods eaten by the infected persons were compared with those of seronegative co-diners. HEV RNA detected in sera from infected persons was sequenced and genotyped. Implicated foods were traced back to their sources. MAIN OUTCOME MEASURES: Potential sources of infection, including overseas travel and foods eaten, and origin of implicated food products. RESULTS: In 55 serologically confirmed cases of HEV infection, 24 people had not travelled overseas during their incubation periods. Of the 24, 17 reported having eaten at restaurant X, 15 of whom could be interviewed. All reported consuming pork liver pâté, compared with only four of seven uninfected co-diners (P < 0.05). The other seven people with locally acquired infections each reported consuming a pork product during their incubation periods. HEV RNA was detected in 16 of the 24 cases; all were of genotype 3. Sequencing indicated greater than 99% homology among restaurant X isolates. HEV RNA was isolated from pork sausages from a batch implicated in one of the locally acquired infections not linked with restaurant X. The pork livers used for pâté preparation by restaurant X were traced to a single Australian farm. CONCLUSIONS: This is the first reported HEV outbreak in Australia. HEV should be considered in patients presenting with a compatible illness, even without a history of overseas travel. Pork products should be thoroughly cooked before consumption.

Preparing for Ebolavirus disease: specimen collection, packaging and transport.

Ebolavirus is classified by Standards Australia as a Risk Group 4 pathogen for handling in laboratories. Specimens known or reasonably expected to contain Ebolavirus are classified by the United Nations as Dangerous Goods Infectious Substances Category A, UN 2814, which if transported by air must comply with International Air Transport Association (IATA) Hazard Class 6.2 and Packing Instruction 620 and Civil Aviation Safety Authority (CASA) Regulations. As such high risk pathogens are rarely encountered in pathology laboratories in Australia, the possibility of an imported case of Ebolavirus disease occurring in NSW during the current ongoing outbreak which began in West Africa in 2014 prompted a review and rapid implementation of specific risk management protocols for Ebolavirus testing. Here we describe and report on the management of specimen collection, packaging and transport by public and private pathology laboratories agreed by a task force led by NSW Health Pathology and Health Protection NSW.

Pandemic clinical case definitions are non-specific: multiple respiratory viruses circulating in the early phases of the 2009 influenza pandemic in New South Wales, Australia.

BACKGROUND: During the early phases of the 2009 pandemic, subjects with influenza-like illness only had laboratory testing specific for the new A(H1N1)pdm09 virus. FINDINGS: Between 25th May and 7th June 2009, during the pandemic CONTAIN phase, A(H1N1)pdm09 virus was detected using nucleic acid tests in only 56 of 1466 (3.8%) samples meeting the clinical case definition required for A(H1N1)pdm09 testing. Two hundred and fifty-five randomly selected A(H1N1)pdm09 virus-negative samples were tested for other respiratory viruses using a real-time multiplex PCR assay. Of the 255 samples tested, 113 (44.3%) had other respiratory viruses detected: rhinoviruses 63.7%, seasonal influenza A 17.6%, respiratory syncytial virus 7.9%, human metapneumovirus 5.3%, parainfluenzaviruses 4.4%, influenza B virus 4.4%, and enteroviruses 0.8%. Viral co-infections were present in 4.3% of samples. CONCLUSIONS: In the very early stages of a new pandemic, limiting testing to only the novel virus will miss other clinically important co-circulating respiratory pathogens.

One Health in NSW: coordination of human and animal health sector management of zoonoses of public health significance.

Zoonoses of public health significance may occur in wildlife, livestock or companion animals, and may be detected by the human or animal health sectors. Of particular public health interest are foodborne, arboviral and emerging zoonoses (known/unknown, endemic/exotic). A coordinated One Health approach to the management of zoonoses in NSW uses measures including: mutually agreed intersectoral procedures for detection and response; surveillance and notification systems for defined endemic and exotic diseases; joint meetings and exercises to ensure currency of response plans; and intersectoral communication during a response. This One Health approach is effective and ensures the interests of both the human health and animal health sectors are addressed.

Lessons from the NSW laboratory response to pandemic (H1N1) 2009 influenza.

Procedures undertaken by NSW Health in the laboratory response to pandemic (H1N1) 2009 influenza were reviewed to assist planning for a future infectious disease emergency. Laboratory plans developed prior to the pandemic sought rapid detection of pandemic virus in the early phases of the pandemic response until demonstration of widespread community transmission, followed then by limited testing when indicated clinically. As planned, the laboratory response was based on the Pandemic Influenza Management System with a web-based outbreak management tool, NetEpi, as the single public health database used for cases and test results. This was found to be effective for tracking specimens and results, and enhanced the public health response. The sustained large volume of community testing during this mild pandemic had an adverse effect on the timely delivery of priority results.