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Objective: To identify groups more likely to be referred for HIV testing because of symptomatic presentation rather than as part of asymptomatic screening., Design: A retrospective analysis of Australian National HIV Registry (NHR) surveillance data including sociodemographic and clinical data, as well as reasons for HIV test., Methods: Using notification records from 2017 to 2022, we summarised reasons for testing leading to an HIV diagnosis. Reasons for testing were combined with clinical status at diagnosis to derive HIV testing categories: testing while symptomatic; asymptomatic HIV screening; seroconversion; and other test reason. We stratified these categories by stage of HIV at diagnosis with late-stage HIV defined as a CD4 + cell count <350 cells/μl at time of diagnosis., Results: Among 4134 HIV notifications with at least one reason for testing recorded, STI screening was the predominant reason for test referral (38%), followed by HIV indicative symptoms (31%), and risk behaviour (13%). By testing category, people aged 50 years or older (24%), people with HIV attributed to heterosexual sex (21%), people born in sub-Saharan Africa (19%), and women (17%) had lower levels of asymptomatic screening. More late-stage HIV diagnoses resulted from testing while symptomatic (58%) compared with asymptomatic screening (25%)., Conclusions: Older people and heterosexuals may not access HIV focused healthcare where HIV screening is routinely offered. Instead, HIV testing opportunities may arise in other settings. By normalising HIV testing and offering low-cost HIV screening in a range of settings, it may be possible to facilitate earlier HIV diagnoses, better health outcomes, and reduced onward transmission., (Copyright © 2024 The Author(s). Published by Wolters Kluwer Health, Inc.)

The aminoglycoside antibiotics amikacin, gentamicin, and tobramycin are important therapeutic options for Acinetobacter iinfections. Several genes that confer resistance to one or more of these antibiotics are prevalent in the globally distributed resistant clones of Acinetobacter baumannii, but the aac ( 6 ')- Im ( aacA16 ) gene (amikacin, netilmicin, and tobramycin resistance), first reported in isolates from South Korea, has rarely been reported since. In this study, GC2 isolates (1999 to 2002) from Brisbane, Australia, carrying aac ( 6 ')- Im and belonging to the ST2:ST423:KL6:OCL1 type were identified and sequenced. The aac ( 6 ')- Im gene and surrounds have been incorporated into one end of the IS 26 -bounded AbGRI2 antibiotic resistance island and are accompanied by a characteristic 70.3-kbp deletion of adjacent chromosome. The compete genome of the 1999 isolate F46 (RBH46) includes only two copies of ISAba1 (in AbGRI1-3 and upstream of ampC ) but later isolates, which differ from one another by <10 single nucleotide differences (SND), carry two to seven additional shared copies. Several complete GC2 genomes with aac ( 6 ')- Im in an AbGRI2 island (2004 to 2017; several countries) found in GenBank and two additional Australian A. baumannii isolates (2006) carry different gene sets, KL2, KL9, KL40, or KL52, at the capsule locus. These genomes include ISAba1 copies in a different set of shared locations. The distribution of SND between F46 and AYP-A2, a 2013 ST2:ST208:KL2:OCL1 isolate from Victoria, Australia, revealed that a 640-kbp segment that includes KL2 and the AbGRI1 resistance island replaces the corresponding region in F46. Over 1,000 A. baumannii draft genomes also include aac ( 6 ')- Im , indicating that it is currently globally disseminated and significantly underreported. IMPORTANCE Aminoglycosides are important therapeutic options for treatment of Acinetobacter infections. Here, we show that a little-known aminoglycoside resistance gene, aac(6')-Im ( aacA16 ), that confers amikacin, netilmicin, and tobramycin resistance has been circulating undetected for many years in a sublineage of A. baumannii global clone 2 (GC2), generally with a second aminoglycoside resistance gene, aacC1 , which confers resistance to gentamicin. These two genes are commonly found together in GC2 complete and draft genomes and globally distributed. One isolate appears to be ancestral, as its genome contains few ISAba1 copies, providing insight into the original source of this insertion sequence (IS), which is abundant in most GC2 isolates. Tracking ISAba1 spread can provide a simple means to track the development and ongoing evolution as well as the dissemination of specific lineages and detect the formation of many sublineages. The complete ancestral genome will provide an essential base point for tracking this process., Competing Interests: The authors declare no conflict of interest.

Introduction: Australia has set the goal for the virtual elimination of HIV transmission by the end of 2022, yet accurate information is lacking on the level of HIV transmission occurring among residents. We developed a method for estimating the timing of HIV acquisition among migrants, relative to their arrival in Australia. We then applied this method to surveillance data from the Australian National HIV Registry with the aim of ascertaining the level of HIV transmission among migrants to Australia occurring before and after migration, and to inform appropriate local public health interventions., Methods: We developed an algorithm incorporating CD4 + T-cell decline back-projection and enhanced variables (clinical presentation, past HIV testing history and clinician estimate of the place of HIV acquisition) and compared it to a standard algorithm which uses CD4 + T-cell back-projection only. We applied both algorithms to all new HIV diagnoses among migrants to estimate whether HIV infection occurred before or after arrival in Australia., Results: Between 1 January 2016 and 31 December 2020, 1909 migrants were newly diagnosed with HIV in Australia, 85% were men, and the median age was 33 years. Using the enhanced algorithm, 932 (49%) were estimated to have acquired HIV after arrival in Australia, 629 (33%) before arrival (from overseas), 250 (13%) close to arrival and 98 (5%) were unable to be classified. Using the standard algorithm, 622 (33%) were estimated to have acquired HIV in Australia, 472 (25%) before arrival, 321 (17%) close to arrival and 494 (26%) were unable to be classified., Conclusions: Using our algorithm, close to half of migrants diagnosed with HIV were estimated to have acquired HIV after arrival in Australia, highlighting the need for tailored culturally appropriate testing and prevention programmes to limit HIV transmission and achieve elimination targets. Our method reduced the proportion of HIV cases unable to be classified and can be adopted in other countries with similar HIV surveillance protocols, to inform epidemiology and elimination efforts., (© 2023 The Authors. Journal of the International AIDS Society published by John Wiley & Sons Ltd on behalf of the International AIDS Society.)

Objectives: To understand the acquisition of resistance genes by a non-GC1, non-GC2 Acinetobacter baumannii strain responsible for a 4 year outbreak at a Sydney hospital., Methods: Representative isolates were screened for resistance to antibiotics. Three were subjected to WGS using Illumina HiSeq. One genome was completed with MinION long reads. Resistance regions were compared with known sequences using bioinformatics., Results: Isolates were resistant to third-generation cephalosporins, gentamicin and tobramycin, sulfamethoxazole and erythromycin. Sequenced isolates were ST49 (Institut Pasteur scheme) and ST128 (Oxford scheme) and carried KL11 at the capsule locus and OCL8 at the lipooligosaccharide outer core locus. The complete genome of isolate J9 revealed that the resistance genes were all in plasmids; pRAY* contained aadB, and a large plasmid, pJ9-3, contained sul2 and floR genes and a dif module containing the mph(E)-msr(E) macrolide resistance genes. Transposon Tn6168, consisting of a second copy of the chromosomal ampC gene region flanked by ISAba1s, confers resistance to third-generation cephalosporins. Tn6168 is located inside the mph(E)-msr(E) dif module. pJ9-3 includes a set of four dif modules and the orientation of the pdif sites, XerC-XerD or XerD-XerC, alternates. A large transposon, Tn6175, containing tniCABDE transposition genes and genes annotated as being involved in heavy metal metabolism, uptake or export was found in the comM gene. Other ST49:ST128:KL11:OCL8 genomes found in the GenBank WGS database carried Tn6175 but neither of the plasmids carrying the resistance genes., Conclusions: An early carbapenem-susceptible A. baumannii outbreak recorded in Australia was caused by an unusual clone that had acquired plasmids carrying antibiotic resistance genes., (© The Author(s) 2021. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Introduction: The human immunodeficiency virus 1 (HIV-1) pandemic is characterized by numerous distinct sub-epidemics (clusters) that continually fuel local transmission. The aims of this study were to identify active growing clusters, to understand which factors most influence the transmission dynamics, how these vary between different subtypes and how this information might contribute to effective public health responses., Methods: We used HIV-1 genomic sequence data linked to demographic factors that accounted for approximately 70% of all new HIV-1 notifications in New South Wales (NSW). We assessed differences in transmission cluster dynamics between subtype B and circulating recombinant form 01&#95;AE (CRF01&#95;AE). Separate phylogenetic trees were estimated using 2919 subtype B and 473 CRF01&#95;AE sequences sampled between 2004 and 2018 in combination with global sequence data and NSW-specific clades were classified as clusters, pairs or singletons. Significant differences in demographics between subtypes were assessed with Chi-Square statistics., Results: We identified 104 subtype B and 11 CRF01&#95;AE growing clusters containing a maximum of 29 and 11 sequences for subtype B and CRF01&#95;AE respectively. We observed a > 2-fold increase in the number of NSW-specific CRF01&#95;AE clades over time. Subtype B clusters were associated with individuals reporting men who have sex with men (MSM) as their transmission risk factor, being born in Australia, and being diagnosed during the early stage of infection (p < 0.01). CRF01&#95;AE infections clusters were associated with infections among individuals diagnosed during the early stage of infection (p < 0.05) and CRF01&#95;AE singletons were more likely to be from infections among individuals reporting heterosexual transmission (p < 0.05). We found six subtype B clusters with an above-average growth rate (>1.5 sequences / 6-months) and which consisted of a majority of infections among MSM. We also found four active growing CRF01&#95;AE clusters containing only infections among MSM. Finally, we found 47 subtype B and seven CRF01&#95;AE clusters that contained a large gap in time (>1 year) between infections and may be indicative of intermediate transmissions via undiagnosed individuals., Conclusions: The large number of active and growing clusters among MSM are the driving force of the ongoing epidemic in NSW for subtype B and CRF01&#95;AE., (© 2021 The Authors. Journal of the International AIDS Society published by John Wiley & Sons Ltd on behalf of the International AIDS Society.)

Objectives: The objective of this study was to examine the evolution of carbapenem-resistant global clone 2 (GC2) Acinetobacter baumannii in Australia focusing on the complement of aminoglycoside resistance genes and their location in resistance islands and plasmids., Methods: Sixty-two carbapenem-resistant GC2 A. baumannii isolates with various aminoglycoside resistance profiles and resistance gene content that were recovered over the period 1999-2010 from hospitals on the east coast of Australia were examined. PCR was used to link relevant contigs retrieved from whole genomes sequenced using Illumina HiSeq and assembled de novo using Velvet. Resistance phenotypes were extended to include additional antibiotics using a disc diffusion assay., Results: Sixty-one isolates were ST208 (formerly ST92; Oxford scheme) and one was ST425. All isolates included the oxa23 carbapenem resistance gene in Tn2006 located in the same position in AbGRI1-2, along with the ISAba1-sul2-CR2Δ-tetA(B)-tetA(R)-CR2-strB-strA configuration. All isolates harboured either AbGRI2-1 carrying the aacC1 (gentamicin resistance) cassette or a variant derived from it via loss of some of the island content. When aacC1 was lost, aminoglycoside resistance was sometimes regained via acquisition of aadB (gentamicin, kanamycin and tobramycin resistance) in pRAY*-v1 or TnaphA6 (amikacin, kanamycin and neomycin resistance) in a repAci6 plasmid. A small cryptic plasmid or a deletion variant of this plasmid was always present and a large cryptic plasmid was also variably present., Conclusions: The extensively antibiotic-resistant GC2 isolates from Sydney, Brisbane and Canberra appear to have arisen from a single import that was introduced into Australia in, or prior to, 1999 that then evolved and spread., (© The Author 2016. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)

Objectives: To determine the context and location of antibiotic resistance genes in carbapenem- and aminoglycoside-resistant Acinetobacter baumannii global clone 2 (GC2) isolates carrying a class 1 integron., Methods: Isolates were from Sydney hospitals. Resistance to antibiotics was determined by disc diffusion. BLAST searches identified relevant DNA fragments in a draft genome sequence. PCR was used to assemble fragments and map equivalent regions., Results: In two isolates belonging to GC2, WM99c and A91, the bla(TEM) gene, the class 1 integron carrying the aacC1-orfP-orfP-orfQ-aadA1 cassette array and sul1 gene, and the aphA1b gene in Tn6020 were each in segments flanked by IS26. These, together with a fourth IS26-flanked segment, formed a 19.5 kb genomic resistance island (GRI), designated AbGRI2-1, containing five copies of IS26. Part of this island was identical to part of the multiple antibiotic resistance region of AbaR-type islands found in global clone 1 (GC1). AbGRI2-1 has replaced a 40.9 kb segment found in the AB0057 genome. Related GRIs were identified in the same location in published GC2 genomes and appear to have arisen from AbGRI2-1 via IS26-mediated deletions. Like A91, WM99c carries ISAba1 upstream of ampC and Tn6167, an AbGRI1-type island in the chromosomal comM gene containing sul2, tet(B), strA and strB genes and bla(OXA-23) in Tn2006. In WM99c, the chromosomal gene encoding OXA-Ab is interrupted by ISAba17., Conclusions: AbGRI2-1 is the largest so far of a new type of GRI designated AbGRI2 to distinguish them from the islands in comM in GC1 isolates (AbaR type) and in GC2 isolates (AbGRI1 type).

Objectives: To determine the cause of resistance to the aminoglycosides gentamicin and tobramycin in Acinetobacter isolates and the location of the resistance genes., Methods: Australian Acinetobacter baumannii isolates were screened for resistance to aminoglycosides. PCR followed by restriction digestion of amplicons was used to detect genes and plasmids. Plasmids were isolated and examined by restriction digestion. Plasmid DNA sequences were determined and bioinformatic analysis was used to identify features. The sequence of the bla(OXA-Ab) gene and multilocus sequence typing were used to determine strain types., Results: Isolates that exhibited resistance to gentamicin, kanamycin and tobramycin were of diverse strain types. These isolates all carried the aadB gene cassette, and in all but one the cassette was in a 6 kb plasmid similar to pRAY. The three plasmid sequences determined revealed multiple frame-shift differences in the available pRAY sequence that altered the reading frames. In pRAY*, mobA and mobC mobilization genes were identified, but no potential replication initiation protein was found. pRAY*-v1 differed from pRAY* by 66 single-base differences, and pRAY*-v2 included two insertion sequences, ISAba22, located upstream of the aadB gene cassette, and IS18-like, within ISAba22., Conclusions: The plasmid pRAY* and variants are widely distributed in Acinetobacter spp. and are the most common cause of resistance to gentamicin and tobramycin. Mobilization genes should assist in the dissemination of pRAY* and its variants.

Objectives: To determine the context and location of the bla(OXA-23) carbapenem-resistance gene and the structure of the resistance island in the chromosomal comM gene in a representative Australian global clone 2 (GC2) Acinetobacter baumannii isolate., Methods: Long-range PCR was used to link genes and determine the organization of the resistance island. PCR amplicons were sequenced, and bioinformatic analysis identified features. Multilocus sequence typing (MLST) was performed., Results: The GC2 isolate A91 is sequence type (ST) ST92 (Oxford MLST scheme). It includes a 37 kb genomic resistance island, Tn6167, in the comM gene. At one end, Tn6167 carries Tn6022Δ1 interrupted by a novel insertion sequence, ISAba17. The sul2 (sulphonamide resistance) and strA-strB (streptomycin resistance) genes and tet(B) tetracycline resistance determinant are at the other end in the configuration ISAba1-sul2-CR2Δ-tetA(B)-tetR(B)-CR2-strB-strA with part of the tni end of a Tn6022-related transposon preceding them and an orf4 end following them. Transposon Tn2006 carrying bla(OXA-23) was found in an 11 kb region located between Tn6022Δ1 and the other resistance genes. The 17.6 kb Tn6166 from the GC2 reference strain A320/RUH134 can be derived from Tn6167 via a single deletion arising adjacent to Tn6022Δ1 and causing loss of a large central segment., Conclusions: The transposons found in comM in the GC2 isolates A91 and A320 differ substantially from AbaR3-type islands, found predominantly in global clone 1 (GC1) isolates, in both resistance gene content and organization. However, the A. baumannii GC1 and GC2 clones have both acquired antibiotic resistance genes via their association with transposons that target comM.

Objectives: To examine the distribution and context of aminoglycoside resistance genes in multiply antibiotic-resistant Acinetobacter baumannii isolates from Australia that are members of the global clone 2 and carry the bla(OXA-23) gene conferring resistance to carbapenems., Methods: Sixty-one multiply antibiotic-resistant A. baumannii strains isolated between 2000 and 2010 at six Australian hospitals that belonged to global clone 2 and carried the bla(OXA-23) gene were studied. Various molecular techniques were used to determine their relatedness and to detect antibiotic resistance genes and insertion sequences. Structures surrounding the aminoglycoside resistance genes were sequenced., Results: The isolates all shared several antibiotic resistance genes, including the sul2 sulphonamide resistance gene, but varied in their pattern of resistance to aminoglycosides. The aminoglycoside resistance profiles of isolates were accounted for by four resistance genes-aadB, aacC1, aphA1b and aphA6-in various combinations. The aadB gene cassette was located at a secondary site on a 6 kb plasmid similar to pRAY. The aphA6 gene was in a transposon, TnaphA6, bounded by directly oriented copies of ISAba125. The aacC1 gene cassette in a class 1 integron and Tn6020 carrying aphA1b were always present together, but were not linked., Conclusions: Imipenem-resistant global clone 2 A. baumannii isolates containing bla(OXA-23) have been present in Australian hospitals for at least 10 years. Variation in this global clone 2 type has occurred with the introduction of various aminoglycoside resistance genes carried on a small plasmid or within transposons.