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.

Genomic dissection of the microevolution of Australian epidemic Bordetella pertussis.

ABSTRACTWhooping cough (pertussis) is a highly contagious respiratory disease caused by the bacterium Bordetella pertussis. Despite high vaccine coverage, pertussis has re-emerged in many countries including Australia and caused two large epidemics in Australia since 2007. Here, we undertook a genomic and phylogeographic study of 385 Australian B. pertussis isolates collected from 2008 to 2017. The Australian B. pertussis population was found to be composed of mostly ptxP3 strains carrying different fim3 alleles, with ptxP3-fim3A genotype expanding far more than ptxP3-fim3B. Within the former, there were six co-circulating epidemic lineages (EL1 to EL6). The multiple ELs emerged, expanded, and then declined at different time points over the two epidemics. In population genetics terms, both hard and soft selective sweeps through vaccine selection pressures have determined the population dynamics of Australian B. pertussis. Relative risk estimation suggests that once a new B. pertussis lineage emerged, it was more likely to spread locally within the first 1.5 years. However, after 1.5 years, any new lineage was likely to expand to a wider region. Phylogenetic analysis revealed the expansion of ptxP3 strains was also associated with replacement of the type III secretion system allele bscI1 with bscI3. bscI3 is associated with decreased T3SS secretion and may allow B. pertussis to reduce immune recognition. This study advanced our understanding of the epidemic population structure and spatial and temporal dynamics of B. pertussis in a highly immunized population.

Testing for COVID-19.

Accurate diagnostic tests that provide results in a timely manner are essential for the clinical and public health management of COVID-19 disease The choice as to which test to use will depend on the clinical presentation and the stage of the illness Nucleic acid tests, using real-time reverse transcriptase-polymerase chain reaction, are the most appropriate for diagnosing acute infection. Combined deep nasal (or nasopharyngeal) and throat swabs are the preferred sample Serology can be used to diagnose previous infection, more than 14 days after the onset of symptoms Antigen tests are in development and their role is not yet defined Interpretation of results must take into account the pre-test probability of the patient having the disease. This is based on their clinical presentation and epidemiological risk

Identification and characterisation of fosfomycin resistance in Escherichia coli urinary tract infection isolates from Australia.

Of 1033 Escherichia coli urinary tract infection isolates collected from females >12 years of age in Australia in 2019, only 2 isolates were resistant to fosfomycin with a minimum inhibitory concentration (MIC) of >256 mg/L. Despite having different multilocus sequence types, the two isolates harboured an identical plasmid-encoded fosA4 gene. The fosA4 gene has previously been identified in a single clinical E. coli isolate cultured in Japan in 2014. Each fosfomycin-resistant isolate harboured two conjugative plasmids that possessed an array of genes conferring resistance to aminoglycosides, ß-lactams, macrolides, quinolones, sulfonamides and/or trimethoprim.

Antibodies to the conserved region of the M protein and a streptococcal superantigen cooperatively resolve toxic shock-like syndrome in HLA-humanized mice.

Invasive streptococcal disease (ISD) and toxic shock syndrome (STSS) result in over 160,000 deaths each year. We modelled these in HLA-transgenic mice infected with a clinically lethal isolate expressing Streptococcal pyrogenic exotoxin (Spe) C and demonstrate that both SpeC and streptococcal M protein, acting cooperatively, are required for disease. Vaccination with a conserved M protein peptide, J8, protects against STSS by causing a dramatic reduction in bacterial burden associated with the absence of SpeC and inflammatory cytokines in the blood. Furthermore, passive immunotherapy with antibodies to J8 quickly resolves established disease by clearing the infection and ablating the inflammatory activity of the M protein, which is further enhanced by addition of SpeC antibodies. Analysis of 77 recent isolates of Streptococcus pyogenes causing ISD, demonstrated that anti-J8 antibodies theoretically recognize at least 73, providing strong support for using antibodies to J8, with or without antibodies to SpeC, as a therapeutic approach.

Q fever vaccination of children in Australia: Limited experience to date.

AIM: Q fever is a zoonotic disease caused by the bacterium Coxiella burnetii and is associated with significant morbidity and mortality in both adults and children. Australia is the only country that has produced and registered a Q fever vaccine for human use, but this vaccine is licenced only for people aged over 15 years as data and experience in children are limited. This review describes the experience of Q fever vaccination of known paediatric cases in Australia to date. METHODS: Patients aged younger than 15 years who received the Q fever vaccination had data abstracted from medical records after consent was obtained from the relevant guardians. Data on risk factors for Q fever, skin testing procedure, dose of vaccination, adverse effects and follow-up assessment were obtained. RESULTS: Twelve children were identified as having received the Q fever vaccination. Vaccination was feasible, with empirical weight-based dose adjustment performed for younger children. There were no significant adverse effects. CONCLUSIONS: Q fever vaccine may be safe in children and should be considered in children who are at significant risk of Q fever infection. Safe vaccine protocols with proven efficacy will allow children of all ages to be protected. Prospective studies of vaccination in children are indicated. Expanding available Q fever registries to include children would allow outcomes to be systematically followed.

Comparison of Clostridium difficile Ribotypes Circulating in Australian Hospitals and Communities.

Clostridium difficile infection (CDI) is becoming less exclusively a health care-associated CDI (HA-CDI). The incidence of community-associated CDI (CA-CDI) has increased over the past few decades. It has been postulated that asymptomatic toxigenic C. difficile (TCD)-colonized patients may play a role in the transfer of C. difficile between the hospital setting and the community. Thus, to investigate the relatedness of C. difficile across the hospital and community settings, we compared the characteristics of symptomatic and asymptomatic host patients and the pathogens from these patients in these two settings over a 3-year period. Two studies were simultaneously conducted; the first study enrolled symptomatic CDI patients from two tertiary care hospitals and the community in two Australian states, while the second study enrolled asymptomatic TCD-colonized patients from the same tertiary care hospitals. A total of 324 patients (96 with HA-CDI, 152 with CA-CDI, and 76 colonized with TCD) were enrolled. The predominant C. difficile ribotypes isolated in the hospital setting corresponded with those isolated in the community, as it was found that for 79% of the C. difficile isolates from hospitals, an isolate with a matching ribotype was isolated in the community, suggesting that transmission between these two settings is occurring. The toxigenic C. difficile strains causing symptomatic infection were similar to those causing asymptomatic infection, and patients exposed to antimicrobials prior to admission were more likely to develop a symptomatic infection (odds ratio, 2.94; 95% confidence interval, 1.20 to 7.14). Our findings suggest that the development of CDI symptoms in a setting without establishment of hospital epidemics with binary toxin-producing C. difficile strains may be driven mainly by host susceptibility and exposure to antimicrobials, rather than by C. difficile strain characteristics.

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.

Draft Whole-Genome Sequence of Haemophilus ducreyi Strain AUSPNG1, Isolated from a Cutaneous Ulcer of a Child from Papua New Guinea.

Haemophilus ducreyi has recently emerged as a leading cause of cutaneous ulcers in the yaws-endemic areas of Papua New Guinea and other South Pacific islands. Here, we report the draft genome sequence of the H. ducreyi strain AUSPNG1, isolated from a cutaneous ulcer of a child from Papua New Guinea.

Acanthamoeba encephalitis: isolation of genotype T1 in mycobacterial liquid culture medium.

We report a case of Acanthamoeba encephalitis diagnosed from an antemortem brain biopsy specimen, where the organism was first isolated in mycobacterial liquid medium and first identified by using a sequence generated by a commercial panfungal sequencing assay. We correlate susceptibility results with clinical outcome.

A population-based spatio-temporal analysis of Clostridium difficile infection in Queensland, Australia over a 10-year period.

OBJECTIVES: To identify the spatio-temporal patterns and environmental factors associated with Clostridium difficile infection (CDI) in Queensland, Australia. METHODS: Data from patients tested for CDI were collected from 392 postcodes across Queensland between May 2003 and December 2012. A binomial logistic regression model, with CDI status as the outcome, was built in a Bayesian framework, incorporating fixed effects for sex, age, source of the sample (healthcare facility or community), elevation, rainfall, land surface temperature, seasons of the year, time in months and spatially unstructured random effects at the postcode level. RESULTS: C. difficile was identified in 13.1% of the samples, the proportion significantly increased over the study period from 5.9% in 2003 to 18.8% in 2012. CDI peaked in summer (14.6%) and was at its lowest in autumn (10.1%). Other factors significantly associated with CDI included female sex (OR: 1.08; 95%CI: 1.01-1.14), community source samples (OR: 1.12; 95%CI: 1.05-1.20), and higher rainfall (OR: 1.09; 95%CI: 1.02-1.17). There was no significant spatial variation in CDI after accounting for the fixed effects in the model. CONCLUSIONS: There was an increasing annual trend in CDI in Queensland from 2003 to 2012. Peaks of CDI were found in summer (December-February), which is at odds with the current epidemiological pattern described for northern hemisphere countries. Epidemiologically plausible explanations for this disparity require further investigation.

Rapid increase in pertactin-deficient Bordetella pertussis isolates, Australia.

Acellular vaccines against Bordetella pertussis were introduced in Australia in 1997. By 2000, these vaccines had replaced whole-cell vaccines. During 2008-2012, a large outbreak of pertussis occurred. During this period, 30% (96/320) of B. pertussis isolates did not express the vaccine antigen pertactin (Prn). Multiple mechanisms of Prn inactivation were documented, including IS481 and IS1002 disruptions, a variation within a homopolymeric tract, and deletion of the prn gene. The mechanism of lack of expression of Prn in 16 (17%) isolates could not be determined at the sequence level. These findings suggest that B. pertussis not expressing Prn arose independently multiple times since 2008, rather than by expansion of a single Prn-negative clone. All but 1 isolate had ptxA1, prn2, and ptxP3, the alleles representative of currently circulating strains in Australia. This pattern is consistent with continuing evolution of B. pertussis in response to vaccine selection pressure.

Detection of novel polyomaviruses, TSPyV, HPyV6, HPyV7, HPyV9 and MWPyV in feces, urine, blood, respiratory swabs and cerebrospinal fluid.

Eight novel human polyomaviruses have been discovered since 2007. Prevalence rates and tissue tropism for the most recent members HPyV 6, 7, 9, TSPyV and MWPyV are largely unknown. We used real-time PCR to determine the presence of HPyV 6, 7, 9, TSPyV and MWPyV in feces (n = 263), urine (n = 189), blood (n = 161), respiratory swabs (n = 1385) and cerebrospinal fluid (n = 171) from both healthy control children and children and adults undergoing diagnostic testing. Whole genome sequencing was able to be performed on 9 MWPyV positive specimens. Novel polyomaviruses were only detected in respiratory swabs and feces, with no detections of HPyV 9 in any sample type. MWPyV was found to be the most prevalent novel polyomavirus, being detected in 18 (1.5%) respiratory specimens from symptomatic patients, 16 (9.8%) respiratory sample from healthy control children, 11 (5.9%) fecal specimens from patient suffering gastrointestinal illness, and in 13 (15.3%) of feces from healthy control children. MWPyV was found only in respiratory and fecal specimens from children, the oldest being 9 years old. HPyV 6, 7, 9 and TSPyV were also detected in respiratory specimens and fecal specimens at low prevalence (<1.3%). The majority of these detections were found in immunocompromised patients. Our findings suggest that MWPyV can result in a subclinical infection, persistent or intermittent shedding, particularly in young children. The other novel polyomaviruses were also found in respiratory and fecal specimens, but at lower prevalence and most commonly in immunocompromised individuals.

The rarity of Trichomonas vaginalis in urban Australia.

OBJECTIVES: Infection with Trichomonas vaginalis has declined dramatically in urban Australia but remains endemic in some predominantly indigenous rural regions. The objective was to determine T vaginalis positivity rates in clinical specimens by PCR detection, from a large community-based private pathology laboratory servicing rural and urban Australian populations. METHODS: Retrospective analysis of data from 44 464 specimens referred for T vaginalis PCR testing over 8 years from 2004 to 2011. RESULTS: 44 464 consecutive specimens (37 137 female, 7242 male, 85 sex-unspecified) were analysed: T vaginalis was detected in 633 specimens. The overall community T vaginalis positivity rate was 1.4% (95% CI 1.3% to 1.5%). Overall rates were 2.1-fold higher in women than in men (1.5% vs 0.7%). Positivity rates were highest in the 10-14 year age group (p<0.0001). Referrals from urban areas of South-East Queensland accounted for 52% of specimens (23 121): the T vaginalis positivity rate in this urban cohort was 0.7% (95% CI 0.6% to 0.8%). Referrals identified to be from indigenous patients accounted for 48% of positive cases (304/633), and came from predominantly rural and regional areas of northern Queensland. Where follow-up testing was available 21% of patients (14/66) remained T vaginalis PCR positive when tested again within 3 months and 25% (26/101) within 6 months of the initial diagnosis. CONCLUSIONS: This study confirms that T vaginalis is rare in the urban non-indigenous Australian setting. Guidelines need to be developed to allow targeted testing. Follow-up testing 3 months after treatment should be considered.

Mycetoma caused by Nocardia yamanashiensis, Papua New Guinea.

We report the first documented case of a mycetoma caused by Nocardia yamanashiensis after the initial description of this species. The 16S-rRNA gene sequence analysis was used to identify the novel species, which showed a similarity of 99.9% to the gene sequence of the type strain. The case showed both clinical non-response and reduced susceptibility in vitro to amoxicillin plus clavulanate, and it was treated successfully with trimethoprim-sulfamethoxazole and doxycycline. Given antibiotic resistance concerns, we suggest that antimicrobial susceptibility testing should be done for the majority of Nocardia species without well-established resistance patterns.

HMS-related hemolysis after acute attacks of Plasmodium vivax malaria.

Among a cohort of 1,213 cases treated for Plasmodium vivax malaria from an isolated Papua New Guinean population, seven adults with severe and sustained hemolytic anemia after clearance of the peripheral parasitemia were prospectively investigated. All the patients fulfilled the criteria for hyper-reactive malarial splenomegaly and in 2 of 7 cases an IgG warm antibody was identified. Hereditary hemolytic anemia was excluded in 5 of 5 patients. All treated cases improved after an initial high dose of prednisone and antimalarial chemoprophylaxis. The persistence of marked anemia in a patient with splenomegaly after a P. vivax attack should raise the suspicion of hyper-reactive malarial splenomegaly.