Antimicrobial resistance in Enterobacterales, Acinetobacter spp. and Pseudomonas aeruginosa isolates from bloodstream infections in Australian children, 2013-2021.

BACKGROUND: Gram-negative bloodstream infections are associated with significant morbidity and mortality in children. Increasing antimicrobial resistance (AMR) is reported globally, yet efforts to track pediatric AMR at a national level over time are lacking. METHODS: The Australian Group on Antimicrobial Resistance (AGAR) surveillance program captures clinical and microbiological data of isolates detected in blood cultures across Australia. EUCAST 2022 was used for MIC interpretation and the AMR package in R for data analysis. RESULTS: Over a nine-year period, there were 3,145 bloodstream infections with 3,266 gram-negative isolates reported in hospitalized children aged <18 years; 21.0% were from neonates. The median length of stay was 9 days, and 30-day all-cause mortality was 5.2%. A greater odds of death was observed in those with a multi-drug resistant organism (aOR: 2.1, 95%CI: 1.3, 3.3, p: 0.001). Escherichia coli (44.5%) and Klebsiella pneumoniae complex (12.6%) were the two most frequently reported organisms. Overall resistance in Enterobacterales to gentamicin/tobramycin was 11.6%, to ceftazidime/ceftriaxone was 12.9%, and 13.2% to ciprofloxacin. Resistance increased over time.Of 201 Pseudomonas aeruginosa isolates reported, 19.7% were resistant to piperacillin-tazobactam, 13.1% resistant to cefepime/ceftazidime and 9.8% to ciprofloxacin. Of 108 Acinetobacter spp. isolates, one was resistant to meropenem, and two were resistant to ciprofloxacin. Resistance did not increase over time. CONCLUSION: AMR in gram-negative organisms causing bloodstream infections in Australian children is increasing which should be considered when updating guidelines and empiric treatment regimens. Ongoing pediatric-specific national surveillance with pediatric reporting must remain a priority to strengthen antimicrobial stewardship and infection control programs.

Antimicrobial resistance in Staphylococcus aureus and Enterococci spp. isolates from bloodstream infections in Australian children, 2013 - 2021.

BACKGROUND: Rising proportions of antimicrobial resistance (AMR) have been observed in both Staphylococcus aureus and Enterococcus spp. isolates. METHODS: The Australian Group on Antimicrobial Resistance (AGAR) surveillance program captures clinical and microbiological data of isolates detected in blood cultures across Australia. EUCAST 2022 was used for MIC interpretation and the AMR package in R for data analysis. RESULTS: There were 2,091 BSIs with S. aureus and 534 enterococcal BSI episodes over the nine years. Three-quarters of S. aureus BSI episodes were community-onset (78.3%) whilst more than half of enterococcal BSIs were hospital-onset (56.9%). The median age for S. aureus BSIs was 6 years, whilst >50% enterococcal BSIs were in children <12 months old.Fifteen percent of S. aureus isolates were methicillin-resistant (MRSA). Overall, 85.3% of S. aureus were resistant to penicillin, 12.5% resistant to erythromycin, 10.3% to clindamycin, and 4.7% to ciprofloxacin. Resistance to penicillin decreased over time whilst clindamycin resistance increased.Resistance in Enterococcus spp. was almost entirely observed in E. faecium; only one E. faecalis isolate was ampicillin resistant, and no E. faecalis isolates were vancomycin or teicoplanin resistant. Seventy-three percent of E. faecium were resistant to ampicillin, 25.5% to vancomycin (VREfm) and 8.8% to teicoplanin. CONCLUSION: Significant shifts in the epidemiology and resistance profiles of S. aureus and Enterococcus spp. BSIs in Australian children were observed, making clear the importance of age-stratified reporting in antimicrobial resistance data.

Australian Group on Antimicrobial Resistance (AGAR) Australian Gram-negative Surveillance Outcome Program (GnSOP) Bloodstream Infection Annual Report 2022.

The Australian Group on Antimicrobial Resistance (AGAR) performs regular period-prevalence studies to monitor changes in antimicrobial resistance in selected enteric gram-negative pathogens. The 2022 survey was the tenth year to focus on blood stream infections caused by Enterobacterales, and the eighth year where Pseudomonas aeruginosa and Acinetobacter species were included. Fifty-five hospitals Australia-wide participated in 2022. The 2022 survey tested 9,739 isolates, comprising Enterobacterales (8,773; 90.1%), P. aeruginosa (840; 8.6%) and Acinetobacter species (126; 1.3%), using commercial automated methods. The results were analysed using Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints (January 2023). Key resistances included resistance to the third-generation cephalosporin ceftriaxone in 12.7%/12.7% (CLSI/EUCAST criteria) of Escherichia coli and in 6.6%/6.6% of Klebsiella pneumoniae complex. Resistance rates to ciprofloxacin were 13.7%/13.7% for E. coli; 7.8%/7.8% for K. pneumoniae complex; 5.3%/5.3% for Enterobacter cloacae complex; and 4.3%/10.0% for P. aeruginosa. Resistance rates to piperacillin-tazobactam were 2.8%/5.9%; 2.9%/8.7%; 18.3%/27.2%; and 6.1%/14.7% for the same four species, respectively. Twenty-nine Enterobacterales isolates from 28 patients were shown to harbour a carbapenemase gene: 18 blaIMP-4; four blaNDM-5; three blaNDM-1; one blaOXA-181; one blaOXA-244; one blaNDM-1 + blaOXA-181; and one blaNDM-5 + blaOXA-181. Transmissible carbapenemase genes were also detected among two Acinetobacter baumannii complex isolates (blaOXA-23) and one P. aeruginosa (blaNDM-1) in the 2022 survey.

Australian Group on Antimicrobial Resistance (AGAR) Australian Gram-negative Surveillance Outcome Program (GnSOP).

Abstract: The Australian Group on Antimicrobial Resistance (AGAR) performs regular period-prevalence studies to monitor changes in antimicrobial resistance in selected enteric gram-negative pathogens. The 2021 survey was the ninth year to focus on bloodstream infections caused by Enterobacterales, and the seventh year where Pseudomonas aeruginosa and Acinetobacter species were included. The 2021 survey tested 8,947 isolates, comprising Enterobacterales (8,104; 90.6%), P. aeruginosa (745; 8.3%) and Acinetobacter species (98; 1.1%), using commercial automated methods. The results were analysed using Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints (January 2022). Of the key resistances, resistance to the third-generation cephalosporin ceftriaxone was found in 12.5%/12.5% (CLSI/EUCAST criteria) of Escherichia coli and in 6.1%/6.1% of Klebsiella pneumoniae. Resistance rates to ciprofloxacin were 12.3%/12.3% for E. coli; 7.2%/7.2% for K. pneumoniae; 5.4%/5.4% for Enterobacter cloacae complex; and 3.7%/8.0% for P. aeruginosa. Resistance rates to piperacillin-tazobactam were 2.8%/6.5%; 2.9%/9.9%; 18.4%/28.1%; and 6.9%/12.8% for the same four species, respectively. Seventeen Enterobacterales isolates from 17 patients were shown to harbour a carbapenemase gene: 12 blaIMP-4; two blaNDM-7; one blaNDM-1; one blaOXA-181; and one blaKPC-2. No transmissible carbapenemase genes were detected among P. aeruginosa or Acinetobacter isolates in the 2021 survey.

Australian Group on Antimicrobial Resistance (AGAR) Australian Gram-negative Sepsis Outcome Programme (GnSOP) Annual Report 2020.

Abstract: The Australian Group on Antimicrobial Resistance (AGAR) performs regular period-prevalence studies to monitor changes in antimicrobial resistance in selected enteric gram-negative pathogens. The 2020 survey was the eighth year to focus on bloodstream infections caused by Enterobacterales, and the sixth year in which Pseudomonas aeruginosa and Acinetobacter species were included. Eight thousand seven hundred and fifty-two isolates, comprising Enterobacterales (7,871, 89.9%), P. aeruginosa (771, 8.8%) and Acinetobacter species (110, 1.3%), were tested using commercial automated methods. The results were analysed using Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints (January 2021). Of the key resistances, resistance to the third-generation cephalosporin ceftriaxone was found in 13.5%/13.5% (CLSI/EUCAST criteria) of Escherichia coli and 8.7%/8.7% of Klebsiella pneumoniae. Resistance rates to ciprofloxacin were 16.1%/16.1% for E. coli; 9.9%/9.9% for K. pneumoniae; 5.8%/5.8% for Enterobacter cloacae complex; and 4.5%/8.1% for P. aeruginosa. Resistance rates to piperacillin-tazobactam were 2.5%/6.6%; 3.9%/12.5%; 16.9%/26.3%; and 5.5%/14.4% for the same four species respectively. Thirty-two isolates from 32 patients were shown to harbour at least one carbapenemase gene: 19 blaIMP-4, three blaGES-5, two blaNDM-1, two blaNDM-5, two blaOXA-48, two blaOXA-181, one blaIMI-1, and one blaOXA-23+NDM-1.

Worldwide distribution and environmental origin of the Adelaide imipenemase (AIM-1), a potent carbapenemase in Pseudomonas aeruginosa.

Carbapenems are potent broad-spectrum ß-lactam antibiotics reserved for the treatment of serious infections caused by multidrug-resistant bacteria such as Pseudomonas aeruginosa. The surge in P. aeruginosa resistant to carbapenems is an urgent threat, as very few treatment options remain. Resistance to carbapenems is predominantly due to the presence of carbapenemase enzymes. The assessment of 147 P. aeruginosa isolates revealed that 32 isolates were carbapenem non-wild-type. These isolates were screened for carbapenem resistance genes using PCR. One isolate from wastewater contained the Adelaide imipenemase gene (blaAIM-1) and was compared phenotypically with a highly carbapenem-resistant clinical isolate containing the blaAIM-1 gene. A further investigation of wastewater samples from various local healthcare and non-healthcare sources as well as river water, using probe-based qPCR, revealed the presence of the blaAIM-1 gene in all the samples analysed. The widespread occurrence of blaAIM-1 throughout Adelaide hinted at the possibility of more generally extensive spread of this gene than originally thought. A blast search revealed the presence of the blaAIM-1 gene in Asia, North America and Europe. To elucidate the identity of the organism(s) carrying the blaAIM-1 gene, shotgun metagenomic sequencing was conducted on three wastewater samples from different locations. Comparison of these nucleotide sequences with a whole-genome sequence of a P. aeruginosa isolate revealed that, unlike the genetic environment and arrangement in P. aeruginosa, the blaAIM-1 gene was not carried as part of any mobile genetic elements. A phylogenetic tree constructed with the deduced amino acid sequences of AIM-1 suggested that the potential origin of the blaAIM-1 gene in P. aeruginosa might be the non-pathogenic environmental organism, Pseudoxanthomonas mexicana.

Inactivation, removal, and regrowth potential of opportunistic pathogens and antimicrobial resistance genes in recycled water systems.

With two thirds of the global population living in areas affected by water scarcity, wastewater reuse is actively being implemented or explored by many nations. There is a need to better understand the efficacy of recycled water treatment plants (RWTPs) for removal of human opportunistic pathogens and antimicrobial resistant microorganisms. Here, we used a suite of probe-based multiplex and SYBR green real-time PCR assays to monitor enteric opportunistic pathogens (EOPs; Acinetobacter baumannii, Arcobacter butzlieri, Escherichia coli, Enterococcus faecalis, Klebsiella pneumoniae, Legionella spp., Listeria monocytogenes, Pseudomonas aeruginosa, Salmonella Enteritidis, Streptococcus spp.) and antimicrobial resistance genes (ARGs; qnrS, blaSHV, blaTEM, blaGES, blaKPC, blaIMI, blaSME, blaNDM, blaVIM, blaIMP, blaOXA-48-like, mcr-1 and mcr-3) of key concern from an antimicrobial resistance (AMR), waterborne and foodborne disease perspective. The class 1 integron-integrase gene (intl1) was quantified as a proxy for multi-drug resistance. EOPs, intl1 and ARGs absolute abundance (DNA and RNA) and metabolic activity (RNA) was assessed through three RWTPs with differing treatment trains. Our results indicate that RWTPs produced high quality recycled water for non-potable reuse by removing >95% of EOPs and ARGs, however, subpopulations of EOPs and ARGs survived disinfection and demonstrated potential to become actively growing members of the recycled water and distribution system microbiomes. The persistence of functional intl1 suggests that significant genetic recombination capacity remains in the recycled water, along with the likely presence of multi-drug resistant bacteria. Results provide new insights into the persistence and growth of EOPs, and prevalence and removal of ARGs in recycled water systems. These data will contribute towards the emerging evidence base of AMR risks in recycled water to inform quantitative risk-based policy development regarding water recycling schemes.

Australian Group on Antimicrobial Resistance (AGAR) Australian Gram-negative Sepsis Outcome Programme (GNSOP) Annual Report 2018.

The Australian Group on Antimicrobial Resistance (AGAR) performs regular period-prevalence studies to monitor changes in antimicrobial resistance in selected enteric gram-negative pathogens. The 2018 survey was the sixth year to focus on bloodstream infections, and included Enterobacterales, Pseudomonas aeruginosa and Acinetobacter species. Eight thousand three hundred and fifty isolates, comprising Enterobacterales (7,512, 90.0%), P. aeruginosa (743, 8.9%) and Acinetobacter species (95, 1.1%), were tested using commercial automated methods. The results were analysed using Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints (January 2019). Of the key resistances, resistance to the third-generation cephalosporin, ceftriaxone, was found in 13.4%/13.4% of Escherichia coli (CLSI/EUCAST criteria), and 9.4%/9.4% of Klebsiella pneumoniae. Resistance rates to ciprofloxacin were 15.2%/15.2% for E. coli, 11.3%/11.3% for K. pneumoniae, 7.4%/7.4% for Enterobacter cloacae complex, and 3.6%/7.7% for P. aeruginosa. Resistance rates to piperacillin-tazobactam were 3.0%/6.0%, 4.3%/7.9%, 18.2%/22.0%, and 5.1%/11.1% for the same four species respectively. Thirty-one isolates from 27 patients were shown to harbour a carbapenemase gene: 14 blaIMP-4 (11 patients), including one with blaIMP-4+blaOXA-23, four blaKPC (three patients), three blaOXA-48, three blaNDM, three blaGES, two blaOXA-181, and two blaOXA-23.

Australian Group on Antimicrobial Resistance (AGAR) Australian Gram-negative Sepsis Outcome Programme (GNSOP) Annual Report 2019.

The Australian Group on Antimicrobial Resistance (AGAR) performs regular period-prevalence studies to monitor changes in antimicrobial resistance in selected enteric gram-negative pathogens. The 2018 survey was the sixth year to focus on bloodstream infections, and included Enterobacterales, Pseudomonas aeruginosa and Acinetobacter species. Eight thousand eight hundred and fifty-seven isolates, comprising Enterobacterales (7,983; 90.1%), P. aeruginosa (764; 8.6%) and Acinetobacter species (110; 1.2%), were tested using commercial automated methods. The results were analysed using Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints (January 2020). Of the key resistances, resistance to the third-generation cephalosporin ceftriaxone was found in 13.3%/13.3% (CLSI/EUCAST criteria) of Escherichia coli and 8.4%/8.4% of Klebsiella pneumoniae. Resistance rates to ciprofloxacin were 16.0%/16.0% for E. coli, 10.2%/10.2% for K. pneumoniae complex, 5.9%/5.9% for Enterobacter cloacae complex, and 4.1%/9.3% for P. aeruginosa. Resistance rates to piperacillin-tazobactam were 3.2%/5.7%, 4.7%/8.5%, 14.8%/21.4%, and 6.9%/12.5% for the same four species/complex respectively. Twenty-nine isolates from 29 patients were shown to harbour a carbapenemase gene: 15 blaIMP-4, five blaOXA-181, four blaOXA-23 (one with blaOXA-58 also), three blaNDM-4/5, one blaGES-5, and one blaIMP-1.

Progress towards a coordinated, national paediatric antimicrobial resistance surveillance programme: Staphylococcus aureus, enterococcal and Gram-negative bacteraemia in Australia.

BACKGROUND: There is increasing knowledge of antimicrobial usage in children yet limited availability of nationally representative paediatric-specific data on antimicrobial resistance. OBJECTIVES: Paediatric data from this national surveillance programme are presented to explore differences between childhood and adult bloodstream infections and antimicrobial resistance surveillance. METHODS: Using information collected from a prospective coordinated antimicrobial resistance surveillance programme, children ≤18 years and adults >18 years with a positive blood culture for Staphylococcus aureus, Enterococcus spp. or Gram-negative spp. presenting to one of 34 Australian hospitals during 2013-16 were evaluated. Consistent methodologies for key sepsis pathogens were employed and a comparative analysis between children and adults was conducted. RESULTS: There are stark contrasts between children and adults in this national antimicrobial resistance (AMR) data set. Notable differences include lower rates of AMR, different clinical and molecular phenotypes and lower mortality amongst children. The burden of Gram-negative resistance is disproportionately experienced in children, with higher odds of death with an ESBL versus non-ESBL bacteraemia in comparison with adults. CONCLUSIONS: These data support that children are not just 'little adults' in the AMR era, and analyses by age group are important to detect differences in antibiotic susceptibility, clinical phenotype and genetic virulence factors. Antimicrobial surveillance incorporated into routine laboratory practice is vital to inform an array of wider applications including antimicrobial guidelines, stewardship and direction for prioritization of novel antimicrobial development.

Australian Group on Antimicrobial Resistance (AGAR) Australian Gram-negative Sepsis Outcome Programme (GNSOP) Annual Report 2017.

The Australian Group on Antimicrobial Resistance (AGAR) performs regular period-prevalence studies to monitor changes in antimicrobial resistance in selected enteric Gram-negative pathogens. The 2017 survey was the fifth year to focus on blood stream infections, and included Enterobacterales, Pseudomonas aeruginosa and Acinetobacter species. Seven thousand nine hundred and ten isolates, comprising Enterobacterales (7,100, 89.8%), P. aeruginosa (697, 8.8%) and Acinetobacter species (113, 1.4%), were tested using commercial automated methods. The results were analysed using Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints (January 2018). Of the key resistances, non-susceptibility to the third-generation cephalosporin, ceftriaxone, was found in 11.3%/11.3% of Escherichia coli (CLSI/EUCAST criteria), 8.8%/8.8% of Klebsiella pneumoniae, and 5.7%/5.7% of K. oxytoca. Non-susceptibility rates to ciprofloxacin were 12.1%/18.0% for E. coli, 4.4%/11.2% for K. pneumoniae, 1.3%/3.5% for K. oxytoca, 3.0%/8.5% for Enterobacter cloacae complex, and 5.1%/9.8% for P. aeruginosa. Resistance rates to piperacillin-tazobactam were 2.8%/5.9%, 3.7%/7.3%, 9.6%/11.0%, 22.5%/27.6%, and 6.4%/13.2% for the same five species respectively. Twenty-seven isolates from 25 patients were shown to harbour a carbapenemase gene: 12 blaIMP (11 patients), five blaOXA-181 (four patients), three blaOXA-23, two blaNDM, two blaKPC, two blaVIM, and one blaGES.

Antimicrobial Susceptibility of Escherichia coli and Salmonella spp. Isolates From Healthy Pigs in Australia: Results of a Pilot National Survey.

This study investigated the frequency of antimicrobial non-susceptibility (defined as the frequency of isolates with minimum inhibitory concentrations above the CLSI susceptible clinical breakpoint) among E. coli and Salmonella spp. isolated from healthy Australian finisher pigs. E. coli (n = 201) and Salmonella spp. (n = 69) were isolated from cecal contents of slaughter-age pigs, originating from 19 farms distributed throughout Australia during July-December 2015. Isolates underwent minimum inhibitory concentration (MIC) susceptibility testing to 11 antimicrobials. The highest frequencies of non-susceptibility among respective isolates of E. coli and Salmonella spp. were to ampicillin (60.2 and 20.3%), tetracycline (68.2 and 26.1%), chloramphenicol (47.8 and 7.3%), and trimethoprim/sulfamethoxazole (33.8 and 11.6%). Four E. coli isolates had MICs above the wild-type epidemiological cut-off value for ciprofloxacin, with two isolates from the same farm classified as clinically resistant (MICs of > 4 µg/ml), a noteworthy finding given that fluoroquinolones (FQs) are not legally available for use in Australian food-producing animals. Three of these four E. coli isolates belonged to the sequence type (ST) 10, which has been isolated from both humans and production animals, whilst one isolate belonged to a new ST (7573) and possessed qnrS1. This study shows that non-susceptibility to first line antimicrobials is common among E. coli and Salmonella spp. isolates from healthy slaughter age pigs in Australia. However, very low levels of non-susceptibility to critically important antimicrobials (CIAs), namely third generation cephalosporins and fluoroquinolones were observed. Nevertheless, the isolation of two ciprofloxacin-resistant E. coli isolates from Australian pigs demonstrates that even in the absence of local antimicrobial selection pressure, fluoroquinolone-resistant E. coli clonal lineages may enter livestock production facilities despite strict biosecurity.

Superbugs in the supermarket? Assessing the rate of contamination with third-generation cephalosporin-resistant gram-negative bacteria in fresh Australian pork and chicken.

Background: Antibiotic misuse in food-producing animals is potentially associated with human acquisition of multidrug-resistant (MDR; resistance to ≥ 3 drug classes) bacteria via the food chain. We aimed to determine if MDR Gram-negative (GNB) organisms are present in fresh Australian chicken and pork products. Methods: We sampled raw, chicken drumsticks (CD) and pork ribs (PR) from 30 local supermarkets/butchers across Melbourne on two occasions. Specimens were sub-cultured onto selective media for third-generation cephalosporin-resistant (3GCR) GNBs, with species identification and antibiotic susceptibility determined for all unique colonies. Isolates were assessed by PCR for SHV, TEM, CTX-M, AmpC and carbapenemase genes (encoding IMP, VIM, KPC, OXA-48, NDM). Results: From 120 specimens (60 CD, 60 PR), 112 (93%) grew a 3GCR-GNB (n = 164 isolates; 86 CD, 78 PR); common species were Acinetobacter baumannii (37%), Pseudomonas aeruginosa (13%) and Serratia fonticola (12%), but only one E. coli isolate. Fifty-nine (36%) had evidence of 3GCR alone, 93/163 (57%) displayed 3GCR plus resistance to one additional antibiotic class, and 9/163 (6%) were 3GCR plus resistance to two additional classes. Of 158 DNA specimens, all were negative for ESBL/carbapenemase genes, except 23 (15%) which were positive for AmpC, with 22/23 considered to be inherently chromosomal, but the sole E. coli isolate contained a plasmid-mediated CMY-2 AmpC. Conclusions: We found low rates of MDR-GNBs in Australian chicken and pork meat, but potential 3GCR-GNBs are common (93% specimens). Testing programs that only assess for E. coli are likely to severely underestimate the diversity of 3GCR organisms in fresh meat.

Australian Group on Antimicrobial Resistance (AGAR) Australian Gram-negative Sepsis Outcome Programme (GNSOP) Annual Report 2016.

The Australian Group on Antimicrobial Resistance (AGAR) performs regular period-prevalence studies to monitor changes in antimicrobial resistance in selected enteric Gram-negative pathogens. The 2016 survey was the fourth year to focus on blood stream infections, and included Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter species. Seven thousand five hundred and sixty-five species, comprising Enterobacteriaceae (6,750, 89.2%), P. aeruginosa (723, 9.6%) and Acinetobacter species (92, 1.2%), were tested using commercial automated methods (Vitek 2, BioMérieux; Phoenix, BD) and results were analysed using Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints (January 2017). Of the key resistances, non-susceptibility to the third-generation cephalosporin, ceftriaxone, was found in 11.8%/11.8% of Escherichia coli (CLSI/EUCAST criteria) and 7.7%/7.7% of Klebsiella pneumoniae, and 11.1%/11.1% K. oxytoca. Non-susceptibility rates to ciprofloxacin were 12.8%/16.3% for E.coli, 3.8%/10.0% for K. pneumoniae, 0.8%/2.1% for K. oxytoca, 1.8%/5.6% for Enterobacter cloacae complex, and 5.5%/9.4% for Pseudomonas aeruginosa. Resistance rates to piperacillin-tazobactam were 3.1%/6.5%, 3.6%/7.1%, 14.1%/14.9%, 19.9%/22.3%, and 5.2%/11.8% for the same 4 species respectively. Twenty-eight isolates were shown to harbour a carbapenemase gene, 14 blaIMP, five blaOXA-23, two blaOXA-48-like, two blaNDM, one blaKPC, one blaGES, three blaIMP+OXA-23.

Australian Group on Antimicrobial Resistance (AGAR) Australian Enterococcal Sepsis Outcome Programme(AESOP) Annual Report 2015.

From 1st January to 31st December 2015, 31 Australian institutions participated in the Australian Enterococcal Sepsis Outcome Programme (AESOP). The aim of AESOP 2015 was to determine the proportion of enterococcal bacteraemia isolates in Australia that were antimicrobial resistant, and to characterise the molecular epidemiology of the Enterococcus faecium isolates. Of the 1,009 unique episodes of bacteraemia investigated, 95.4% were caused by either E. faecalis (55.7%) or E. faecium (39.6%). Ampicillin resistance was detected in 0.2% of E. faecalis and in 86.0% of E. faecium. Vancomycin non-susceptibility was reported in 0.4% and 50.1% of E. faecalis and E. faecium respectively. Overall 56.2% of E. faecium harboured vanA or vanB genes. For the vanA/B positive E. faecium isolates, 61.0% harboured vanB genes and 36.8% vanA genes. The percentage of E. faecium bacteraemia isolates resistant to vancomycin in Australia is significantly higher than that seen in most European countries. E. faecium consisted of 49 multilocus sequence types (STs) of which 85.6% of isolates were classified into 11 major STs containing five or more isolates. All major STs belong to clonal cluster 17, a major hospital-adapted polyclonal E. faecium cluster. Four of the five predominant STs (ST796, ST555, ST203, and ST80) were found across most regions of Australia. The second most predominant clone was non-typable by multilocus sequence typing and found only in NSW and the ACT. Overall 73.9% of isolates belonging to the five predominant STs harboured vanA or vanB genes. In conclusion, the AESOP 2015 has shown enterococcal bacteraemias in Australia are frequently caused by polyclonal ampicillin-resistant high-level gentamicin resistant vanA or vanB E. faecium which have limited treatment options.

Australian Group on Antimicrobial Resistance (AGAR) Australian Gram-negative Sepsis Outcome Programme(GNSOP) Annual Report 2015.

The Australian Group on Antimicrobial Resistance (AGAR) performs regular period-prevalence studies to monitor changes in antimicrobial resistance in selected enteric Gram-negative pathogens. The 2015 survey was the third year to focus on blood stream infections, and included Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter species. Seven thousand three hundred and thirty species, comprising Enterobacteriaceae (6,567, 89.6%), P. aeruginosa (660, 9.0%) and Acinetobacter species (103, 1.4%), were tested using commercial automated methods (Vitek® 2, BioMérieux; Phoenix™, BD) and results were analysed using Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints (January 2016). Of the key resistances, non-susceptibility to the third-generation cephalosporin, ceftriaxone, was found in 10.6%/10.6% of E. coli (CLSI/EUCAST criteria) and 5.9%/5.9% of Klebsiella pneumoniae, and 8.4%/8.4% K. oxytoca. Non-susceptibility rates to ciprofloxacin were 12.6%/13.6% for E. coli, 3.9%/7.2% for K. pneumoniae, 0.4%/0.4% for K. oxytoca, 3.4%/4.0% for Enterobacter cloacae, and 6.3%/6.5% for Pseudomonas aeruginosa. Resistance rates to piperacillin-tazobactam were 2.8%/6.3%, 3.5%/6.4%, 8.9%/10.2%, 15.9%/20.6%, and 7.1%/13.9% for the same four species respectively. Twenty-two isolates were shown to harbour a carbapenemase gene, 14 blaIMP, four blaOXA-48, one blaKPC, one blaGES, one blaNDM+OXA-48, and one blaIMP+VIM.

Australian Group on Antimicrobial Resistance (AGAR) Australian Staphylococcus aureus Sepsis Outcome Programme (ASSOP) Annual Report 2015.

The Australian Group on Antimicrobial Resistance (AGAR) performs regular period-prevalence studies to monitor changes in antimicrobial resistance in selected enteric Gram-negative pathogens. The 2015 survey was the third year to focus on blood stream infections, and included Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter species. Seven thousand three hundred and thirty species, comprising Enterobacteriaceae (6,567, 89.6%), P. aeruginosa (660, 9.0%) and Acinetobacter species (103, 1.4%), were tested using commercial automated methods (Vitek® 2, BioMérieux; Phoenix™, BD) and results were analysed using Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints (January 2016). Of the key resistances, non-susceptibility to the third-generation cephalosporin, ceftriaxone, was found in 10.6%/10.6% of E. coli (CLSI/EUCAST criteria) and 5.9%/5.9% of Klebsiella pneumoniae, and 8.4%/8.4% K. oxytoca. Non-susceptibility rates to ciprofloxacin were 12.6%/13.6% for E. coli, 3.9%/7.2% for K. pneumoniae, 0.4%/0.4% for K. oxytoca, 3.4%/4.0% for Enterobacter cloacae, and 6.3%/6.5% for Pseudomonas aeruginosa. Resistance rates to piperacillin-tazobactam were 2.8%/6.3%, 3.5%/6.4%, 8.9%/10.2%, 15.9%/20.6%, and 7.1%/13.9% for the same four species respectively. Twenty-two isolates were shown to harbour a carbapenemase gene, 14 blaIMP, four blaOXA-48, one blaKPC, one blaGES, one blaNDM+OXA-48, and one blaIMP+VIM.

Phylogenetic diversity, antimicrobial susceptibility and virulence characteristics of phylogroup F Escherichia coli in Australia.

Unlike Escherichia coli strains belonging to phylogroup B2, the clinical significance of strains belonging to phylogroup F is not well understood. Here we report on a collection of phylogroup F strains recovered in Australia from faeces and extra-intestinal sites from humans, companion animals and native animals, as well as from poultry meat and water samples. The distribution of sequence types was clearly non-random with respect to isolate source. The antimicrobial resistance and virulence trait profiles also varied with the sequence type of the isolate. Phylogroup F strains tended to lack the virulence traits typically associated with phylogroup B2 strains responsible for extra-intestinal infection in humans. Resistance to fluoroquinolones and/or expanded-spectrum cephalosporins was common within ST648, ST354 and ST3711. Although ST354 and ST3711 are part of the same clonal complex, the ST3711 isolates were only recovered from native birds being cared for in a single wildlife rehabilitation centre, whereas the ST354 isolates were from faeces and extra-intestinal sites of dogs and humans, as well as from poultry meat. Although ST354 isolates from chicken meat in Western Australia were distinct from all other ST354 isolates, those from poultry meat samples collected in eastern Australia shared many similarities with other ST354 isolates from humans and companion animals.

Australian Group on Antimicrobial Resistance Australian Enterobacteriaceae Sepsis Outcome Programme annual report, 2014.

The Australian Group on Antimicrobial Resistance performs regular period-prevalence studies to monitor changes in antimicrobial resistance in selected enteric Gram-negative pathogens. The 2014 survey was the second year to focus on blood stream infections. During 2014, 5,798 Enterobacteriaceae species isolates were tested using commercial automated methods (Vitek 2, BioMérieux; Phoenix, BD) and results were analysed using the Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints (January 2015). Of the key resistances, non-susceptibility to the third-generation cephalosporin, ceftriaxone, was found in 9.0%/9.0% of Escherichia coli (CLSI/EUCAST criteria) and 7.8%/7.8% of Klebsiella pneumoniae, and 8.0%/8.0% K. oxytoca. Non-susceptibility rates to ciprofloxacin were 10.4%/11.6% for E. coli, 5.0%/7.7% for K. pneumoniae, 0.4%/0.4% for K. oxytoca, and 3.5%/6.5% in Enterobacter cloacae. Resistance rates to piperacillin-tazobactam were 3.2%/6.8%, 4.8%/7.2%, 11.1%/11.5%, and 19.0%/24.7% for the same 4 species respectively. Fourteen isolates were shown to harbour a carbapenemase gene, 7 blaIMP-4, 3 blaKPC-2, 3 blaVIM-1, 1 blaNDM-4, and 1 blaOXA-181-lke.

Australian Group on Antimicrobial Resistance Australian Enterococcal Sepsis Outcome Programme annual report, 2014.

From 1 January to 31 December 2014, 27 institutions around Australia participated in the Australian Enterococcal Sepsis Outcome Programme (AESOP). The aim of AESOP 2014 was to determine the proportion of enterococcal bacteraemia isolates in Australia that were antimicrobial resistant, and to characterise the molecular epidemiology of the Enterococcus faecium isolates. Of the 952 unique episodes of bacteraemia investigated, 94.4% were caused by either E. faecalis (54.9%) or E. faecium (39.9%). Ampicillin resistance was detected in 0.6% of E. faecalis and in 89.4% of E. faecium. Vancomycin non-susceptibility was reported in 0.2% and 46.1% of E. faecalis and E. faecium respectively. Overall 51.1% of E. faecium harboured vanA or vanB genes. For the vanA/B positive E. faecium isolates, 81.5% harboured vanB genes and 18.5% vanA genes. The percentage of E. faecium bacteraemia isolates resistant to vancomycin in Australia is significantly higher than that seen in most European countries. E. faecium consisted of 113 pulsed-field gel electrophoresis pulsotypes of which 68.9% of isolates were classified into 14 major pulsotypes containing 5 or more isolates. Multilocus sequence typing grouped the 14 major pulsotypes into clonal cluster 17, a major hospital-adapted polyclonal E. faecium cluster. The geographical distribution of the 4 predominant sequence types (ST203, ST796, ST555 and ST17) varied with only ST203 identified across most regions of Australia. Overall 74.7% of isolates belonging to the four predominant STs harboured vanA or vanB genes. In conclusion, the AESOP 2014 has shown enterococcal bacteraemias in Australia are frequently caused by polyclonal ampicillin-resistant high-level gentamicin resistant vanA or vanB E. faecium, which have limited treatment options.