Nocardia species distribution and antimicrobial susceptibility within Australia.

BACKGROUND: Nocardia is a ubiquitous saprophyte capable of causing human disease. Disease is primarily respiratory or cutaneous, usually acquired via inhalation or inoculation. Under the influence of environmental and host factors, Nocardia incidence and species distribution demonstrate geographical variation. AIMS: To examine for differences in Nocardia incidence within Western Australia (WA) and analyse species distribution in the context of prior published studies. To analyse antibiogram data from a nationwide passive antimicrobial resistance surveillance program. METHODS: Retrospective extraction of laboratory data for Western Australian Nocardia isolates over a 21-year period. Analysis of Nocardia antimicrobial susceptibility testing data submitted to the Australian Passive Antimicrobial Resistance Surveillance (APAS) program between 2005 and 2022. RESULTS: Nine hundred sixty WA isolates were identified, giving an annual incidence of 3.03 per 100 000 population with apparent latitudinal variation. The four most common species identified within WA and amongst APAS isolates were N. nova, N. cyriacigeorgica, N. brasiliensis and N. farcinica. APAS data demonstrated that all species exhibited high rates of susceptibility to linezolid (100%) and trimethoprim-sulfamethoxazole (98%). Amikacin (>90% susceptibility for all species except N. transvalensis) was the next most active parenteral agent, superior to both carbapenems and third-generation cephalosporins. Susceptibility to oral antimicrobials (other than linezolid) demonstrated significant interspecies variation. CONCLUSIONS: We demonstrate geographical variation in the distribution of Nocardia incidence. Four species predominate in the Australian setting, and nationwide data confirm a high in vitro susceptibility to trimethoprim-sulphamethoxazole and linezolid, justifying their ongoing role as part of first-line empiric therapy.

Human Neural Larva Migrans Caused by Ophidascaris robertsi Ascarid.

We describe a case in Australia of human neural larva migrans caused by the ascarid Ophidascaris robertsi, for which Australian carpet pythons are definitive hosts. We made the diagnosis after a live nematode was removed from the brain of a 64-year-old woman who was immunosuppressed for a hypereosinophilic syndrome diagnosed 12 months earlier.

Current Epidemiology and Clinical Features of Cryptococcus Infection in Patients Without Human Immunodeficiency Virus: A Multicenter Study in 46 Hospitals in Australia and New Zealand.

BACKGROUND: Patients without human immunodeficiency virus (HIV) are increasingly recognized as being at risk for cryptococcosis. Knowledge of characteristics of cryptococcosis in these patients remains incomplete. METHODS: We conducted a retrospective study of cryptococcosis in 46 Australian and New Zealand hospitals to compare its frequency in patients with and without HIV and describe its characteristics in patients without HIV. Patients with cryptococcosis between January 2015 and December 2019 were included. RESULTS: Of 475 patients with cryptococcosis, 90% were without HIV (426 of 475) with marked predominance in both Cryptococcus neoformans (88.7%) and Cryptococcus gattii cases (94.3%). Most patients without HIV (60.8%) had a known immunocompromising condition: cancer (n = 91), organ transplantation (n = 81), or other immunocompromising condition (n = 97). Cryptococcosis presented as incidental imaging findings in 16.4% of patients (70 of 426). The serum cryptococcal antigen test was positive in 85.1% of tested patients (319 of 375); high titers independently predicted risk of central nervous system involvement. Lumbar puncture was performed in 167 patients to screen for asymptomatic meningitis, with a positivity rate of 13.2% where meningitis could have been predicted by a high serum cryptococcal antigen titer and/or fungemia in 95% of evaluable cases. One-year all-cause mortality was 20.9% in patients without HIV and 21.7% in patients with HIV (P = .89). CONCLUSIONS: Ninety percent of cryptococcosis cases occurred in patients without HIV (89% and 94% for C. neoformans and C. gattii, respectively). Emerging patient risk groups were evident. A high level of awareness is warranted to diagnose cryptococcosis in patients without HIV.

Public health interventions successfully mitigated multiple incursions of SARS-CoV-2 Delta variant in the Australian Capital Territory.

The COVID-19 pandemic has presented a unique opportunity to understand how real-time pathogen genomics can be used for large-scale outbreak investigations. On 12 August 2021, the Australian Capital Territory (ACT) detected an incursion of the SARS-CoV-2 Delta (B.1.617.2) variant. Prior to this date, SARS-CoV-2 had been eliminated locally since 7 July 2020. Several public health interventions were rapidly implemented in response to the incursion, including a territory-wide lockdown and comprehensive contact tracing. The ACT has not previously used pathogen genomics at a population level in an outbreak response; therefore, this incursion also presented an opportunity to investigate the utility of genomic sequencing to support contact tracing efforts in the ACT. Sequencing of >75% of the 1793 laboratory-confirmed cases during the 3 months following the initial notification identified at least 13 independent incursions with onwards spread in the community. Stratification of cases by genomic cluster revealed that distinct cohorts were affected by the different incursions. Two incursions resulted in most of the community transmission during the study period, with persistent transmission in vulnerable sections of the community. Ultimately, both major incursions were successfully mitigated through public health interventions, including COVID-19 vaccines. The high rates of SARS-CoV-2 sequencing in the ACT and the relatively small population size facilitated detailed investigations of the patterns of virus transmission, revealing insights beyond those gathered from traditional contact tracing alone. Genomic sequencing was critical to disentangling complex transmission chains to target interventions appropriately.

Off-season RSV epidemics in Australia after easing of COVID-19 restrictions.

Human respiratory syncytial virus (RSV) is an important cause of acute respiratory infection with the most severe disease in the young and elderly. Non-pharmaceutical interventions and travel restrictions for controlling COVID-19 have impacted the circulation of most respiratory viruses including RSV globally, particularly in Australia, where during 2020 the normal winter epidemics were notably absent. However, in late 2020, unprecedented widespread RSV outbreaks occurred, beginning in spring, and extending into summer across two widely separated regions of the Australian continent, New South Wales (NSW) and Australian Capital Territory (ACT) in the east, and Western Australia. Through genomic sequencing we reveal a major reduction in RSV genetic diversity following COVID-19 emergence with two genetically distinct RSV-A clades circulating cryptically, likely localised for several months prior to an epidemic surge in cases upon relaxation of COVID-19 control measures. The NSW/ACT clade subsequently spread to the neighbouring state of Victoria and to cause extensive outbreaks and hospitalisations in early 2021. These findings highlight the need for continued surveillance and sequencing of RSV and other respiratory viruses during and after the COVID-19 pandemic, as mitigation measures may disrupt seasonal patterns, causing larger or more severe outbreaks.

Consensus guidelines for the diagnosis and management of invasive fungal disease due to moulds other than Aspergillus in the haematology/oncology setting, 2021.

Invasive fungal disease (IFD) due to moulds other than Aspergillus is a significant cause of mortality in patients with malignancies or post haemopoietic stem cell transplantation. The current guidelines focus on the diagnosis and management of the common non-Aspergillus moulds (NAM), such as Mucorales, Scedosporium species (spp.), Lomentospora prolificans and Fusarium spp. Rare but emerging NAM including Paecilomyces variotii, Purpureocillium lilacinum and Scopulariopsis spp. are also reviewed. Culture and histological examination of tissue biopsy specimens remain the mainstay of diagnosis, but molecular methods are increasingly being used. As NAM frequently disseminate, blood cultures and skin examination with biopsy of any suspicious lesions are critically important. Treatment requires a multidisciplinary approach with surgical debridement as a central component. Other management strategies include control of the underlying disease/predisposing factors, augmentation of the host response and the reduction of immunosuppression. Carefully selected antifungal therapy, guided by susceptibility testing, is critical to cure. We also outline novel antifungal agents still in clinical trial which offer substantial potential for improved outcomes in the future. Paediatric recommendations follow those of adults. Ongoing epidemiological research, improvement in diagnostics and the development of new antifungal agents will continue to improve the poor outcomes that have been traditionally associated with IFD due to NAM.

Bacteraemia, antimicrobial susceptibility and treatment among Campylobacter-associated hospitalisations in the Australian Capital Territory: a review.

BACKGROUND: Campylobacter spp. cause mostly self-limiting enterocolitis, although a significant proportion of cases require hospitalisation highlighting potential for severe disease. Among people admitted, blood culture specimens are frequently collected and antibiotic treatment is initiated. We sought to understand clinical and host factors associated with bacteraemia, antibiotic treatment and isolate non-susceptibility among Campylobacter-associated hospitalisations. METHODS: Using linked hospital microbiology and administrative data we identified and reviewed Campylobacter-associated hospitalisations between 2004 and 2013. We calculated population-level incidence for Campylobacter bacteraemia and used logistic regression to examine factors associated with bacteraemia, antibiotic treatment and isolate non-susceptibility among Campylobacter-associated hospitalisations. RESULTS: Among 685 Campylobacter-associated hospitalisations, we identified 25 admissions for bacteraemia, an estimated incidence of 0.71 cases per 100,000 population per year. Around half of hospitalisations (333/685) had blood culturing performed. Factors associated with bacteraemia included underlying liver disease (aOR 48.89, 95% CI 7.03-340.22, p < 0.001), Haematology unit admission (aOR 14.67, 95% CI 2.99-72.07, p = 0.001) and age 70-79 years (aOR 4.93, 95% CI 1.57-15.49). Approximately one-third (219/685) of admissions received antibiotics with treatment rates increasing significantly over time (p < 0.05). Factors associated with antibiotic treatment included Gastroenterology unit admission (aOR 3.75, 95% CI 1.95-7.20, p < 0.001), having blood cultures taken (aOR 2.76, 95% CI 1.79-4.26, p < 0.001) and age 40-49 years (aOR 2.34, 95% CI 1.14-4.79, p = 0.02). Non-susceptibility of isolates to standard antimicrobials increased significantly over time (p = 0.01) and was associated with overseas travel (aOR 11.80 95% CI 3.18-43.83, p < 0.001) and negatively associated with tachycardia (aOR 0.48, 95%CI 0.26-0.88, p = 0.02), suggesting a healthy traveller effect. CONCLUSIONS: Campylobacter infections result in considerable hospital burden. Among those admitted to hospital, an interplay of factors involving clinical presentation, presence of underlying comorbidities, complications and increasing age influence how a case is investigated and managed.

Campylobacter-associated hospitalisations in an Australian provincial setting.

BACKGROUND: Campylobacter spp. infections are a globally important cause of enterocolitis, causing substantial morbidity. Capturing accurate information on hospitalisations is challenging and limited population-level data exist to describe the clinico-epidemiological characteristics of hospitalised cases. METHODS: Hospital administrative and laboratory datasets were linked to identify Campylobacter-associated hospitalisations between 2004 and 2013. Accuracy of morbidity coding was assessed using laboratory diagnosis as a gold standard, with health department surveillance data used to calculate population-based rates. Additional patient-level data were collected via review of medical records. Descriptive statistics were used to assess changes in rates and proportions and to assess relationships between key variables including age, length of stay, comorbidity and complications. RESULTS: In total 685 Campylobacter-associated hospital admissions were identified, with the sensitivity of morbidity coding 52.8% (95% CI 48.9-56.7%). The mean annual rate of hospitalisation was 13.6%. Hospitalisation rates were higher for females across most age-groups, while for both genders marked increases were observed for those aged ≥60 years. Median admission age was 39.5 years, with an average length of stay of 3.5 days. Comorbidities were present in 34.5% (237/685) of admissions, with these patients more likely to develop electrolyte disturbances, hypotension, renal impairment or acute confusion (all p < 0.001). Bacteraemia and acute kidney injury were observed in 4.1% (28/685) and 3.6% (23/685) of admissions, respectively. Inpatient mortality was low (0.15%). CONCLUSION: Under reporting of Campylobacter-associated hospitalisations is substantial but can be improved through data linkage. We observed demographic differences among those hospitalised but further work is needed to determine risk factors and predictors for hospitalisation.

Risk factors for candidaemia: A prospective multi-centre case-control study.

OBJECTIVES: Candidaemia carries a mortality of up to 40% and may be related to increasing complexity of medical care. Here, we determined risk factors for the development of candidaemia. METHODS: We conducted a prospective, multi-centre, case-control study over 12 months. Cases were aged ≥18 years with at least one blood culture positive for Candida spp. Each case was matched with two controls, by age within 10 years, admission within 6 months, admitting unit, and admission duration at least as long as the time between admission and onset of candidaemia. RESULTS: A total of 118 incident cases and 236 matched controls were compared. By multivariate analysis, risk factors for candidaemia included neutropenia, solid organ transplant, significant liver, respiratory or cardiovascular disease, recent gastrointestinal, biliary or urological surgery, central venous access device, intravenous drug use, urinary catheter and carbapenem receipt. CONCLUSIONS: Risk factors for candidaemia derive from the infection source, carbapenem use, host immune function and organ-based co-morbidities. Preventive strategies should target iatrogenic disruption of mucocutaneous barriers and intravenous drug use.

Two carbapenemase-producing Enterobacteriaceae outbreaks detected retrospectively by whole-genome sequencing at an Australian tertiary hospital.

In 2014, two genetically-linked cases of carbapenemase-producing Enterobacteriaceae (CPE) were detected at the Canberra Hospital (TCH), prompting an investigation and response that appeared to contain transmission. We report a 2017 retrospective investigation into cases of CPE in the Australian Capital Territory (ACT) that aimed to identify clusters and transmission mechanisms. Cases detected between 2012 and 2016 were identified from the hospital laboratory information system. Whole-genome sequencing (WGS) was performed retrospectively on stored isolates. Seventy-two cases were identified, with nearly 90% of isolates containing blaIMP genes. Using multilocus sequence type (ST) data, we identified two small outbreaks of CPE containing blaIMP-4 (Enterobacter cloacae complex ST24, n = 7; Citrobacter freundii ST8, n = 10), each spanning over three years. Epidemiological and environmental evidence implicate environmental reservoirs and carriers undetected by routine infection prevention and control investigations.

Corrigendum: Whole Genome Sequencing of Australian Candida glabrata Isolates Reveals Genetic Diversity and Novel Sequence Types.

[This corrects the article DOI: 10.3389/fmicb.2018.02946.].

Short-read fastA files dataset from complexity-reduced genotyping by sequencing data of bacterial isolates from a public hospital in Australia.

This data article contains short-read sequences (length 30-69 bp) obtained from complexity-reduced genotyping by sequencing (GBS) of 165 samples bacterial isolates from hospital patients in the Australian Capital Territory, between 2013 and 2015. These samples represented 14 bacterial species. Data format is shown as filtered fastA files obtained from an Illumina HiSeq2500 sequencer. The experimental factors of this research used three complexity reduction methods with three combinations of restriction enzymes: PstI with MseI, PstI with HpaII and MseI with HpaII.

Vancomycin-resistant Enterococcus (VRE) outbreak in a neonatal intensive care unit and special care nursery at a tertiary-care hospital in Australia-A retrospective case-control study.

OBJECTIVE: We investigated the risk factors and origins of the first known occurrence of VRE colonization in the neonatal intensive care unit (NICU) at the Canberra Hospital. DESIGN: A retrospective case-control study. SETTING: A 21-bed neonatal intensive care unit (NICU) and a 15-bed special care nursey (SCN) in a tertiary-care adult and pediatric hospital in Australia. PATIENTS: All patients admitted to the NICU and SCN over the outbreak period: January-May 2017. Of these, 14 were colonized with vancomycin-resistant Enterococcus (VRE) and 77 were noncolonized. METHODS: Demographic and clinical variables of cases and controls were compared to evaluate potential risk factors for VRE colonization. Whole-genome sequencing of the VRE isolates was used to determine the origin of the outbreak strain. RESULTS: Swift implementation of wide-ranging infection control measures brought the outbreak under control. Multivariate logistic regression revealed a strong association between early gestational age and VRE colonization (odds ratio [OR], 3.68; 95% confidence interval [CI], 1.94-7.00). Whole-genome sequencing showed the isolates to be highly clonal Enterococcus faecium ST1421 harboring a vanA gene and to be closely related to other ST1421 previously sequenced from the Canberra Hospital and the Australian Capital Territory. CONCLUSION: The colonization of NICU patients was with a highly successful clone endemic to the Canberra Hospital likely introduced into the NICU environment from other wards, with subsequent cross-contamination spreading among the neonate patients. Use of routine surveillance screening may have identified colonization at an earlier stage and have now been implemented on a 6-monthly schedule.

Identification of bacterial isolates from a public hospital in Australia using complexity-reduced genotyping.

Bacterial identification methods used in routine identification of pathogens in medical microbiology include a combination approach of biochemical tests, mass spectrometry or molecular biology techniques. Extensive publicly-available databases of DNA sequence data from pathogenic bacteria have been amassed in recent years; this provides an opportunity for using bacterial genome sequencing for identification purposes. Whole genome sequencing is increasing in popularity, although at present it remains a relatively expensive approach to bacterial identification and typing. Complexity-reduced bacterial genome sequencing provides an alternative. We evaluate genomic complexity-reduction using restriction enzymes and sequencing to identify bacterial isolates. A total of 165 bacterial isolates from hospital patients in the Australian Capital Territory, between 2013 and 2015 were used in this study. They were identified and typed by the Microbiology Department of Canberra Public Hospital, and represented 14 bacterial species. DNA extractions from these samples were processed using a combination of the restriction enzymes PstI with MseI, PstI with HpaII and MseI with HpaII. The resulting sequences (length 30-69 bp) were aligned against publicly available bacterial genome and plasmid sequences. Results of the alignment were processed using a bioinformatics pipeline developed for this project, Currito3.1 DNA Fragment Analysis Software. All 165 samples were correctly identified to genus and species by each of the three combinations of restriction enzymes. A further 35 samples typed to the level of strain identified and compared for consistency with MLST typing data and in silico MLST data derived from the nearest sequenced candidate reference. The high level of agreement between bacterial identification using complexity-reduced genome sequencing and standard hospital identifications indicating that this new approach is a viable alternative for identification of bacterial isolates derived from pathology specimens. The effectiveness of species identification and in particular, strain typing, depends on access to a comprehensive and taxonomically accurate bacterial genome sequence database containing relevant bacterial species and strains.

Whole Genome Sequencing of Australian Candida glabrata Isolates Reveals Genetic Diversity and Novel Sequence Types.

Candida glabrata is a pathogen with reduced susceptibility to azoles and echinocandins. Analysis by traditional multilocus sequence typing (MLST) has recognized an increasing number of sequence types (STs), which vary with geography. Little is known about STs of C. glabrata in Australia. Here, we utilized whole genome sequencing (WGS) to study the genetic diversity of 51 Australian C. glabrata isolates and sought associations between STs over two time periods (2002-2004, 2010-2017), and with susceptibility to fluconazole by principal component analysis (PCA). Antifungal susceptibility was determined using Sensititre YeastOneTM Y010 methodology and WGS performed on the NextSeq 500 platform (Illumina) with in silico MLST STs inferred by WGS data. Single nucleotide polymorphisms (SNPs) in genes linked to echinocandin, azole and 5-fluorocytosine resistance were analyzed. Of 51 isolates, WGS identified 18 distinct STs including four novel STs (ST123, ST124, ST126, and ST127). Four STs accounted for 49% of isolates (ST3, 15.7%; ST83, 13.7%; ST7, 9.8%; ST26, 9.8%). Split-tree network analysis resolved isolates to terminal branches; many of these comprised multiple isolates from disparate geographic settings but four branches contained Australian isolates only. ST3 isolates were common in Europe, United States and now Australia, whilst ST8 and ST19, relatively frequent in the United States, were rare/absent amongst our isolates. There was no association between ST distribution (genomic similarity) and the two time periods or with fluconazole susceptibility. WGS identified mutations in the FKS1 (S629P) and FKS2 (S663P) genes in three, and one, echinocandin-resistant isolate(s), respectively. Both mutations confer phenotypic drug resistance. Twenty-five percent (13/51) of isolates were fluconazole-resistant (MIC ≥ 64 µg/ml) of which 9 (18%) had non wild-type MICs to voriconazole and posaconazole. Multiple SNPs were present in genes linked to azole resistance such as CgPDR1 and CgCDR1, as well as several in MSH2; however, SNPs occurred in both azole-susceptible and azole-resistant isolates. Although no particular SNP in these genes was definitively associated with resistance, azole-resistant/non-wild type isolates had a propensity to harbor SNPs resulting in amino acid substitutions in Pdr1 beyond the first 250 amino acid positions. The presence of SNPs may be markers of STs. Our study shows the value of WGS for high-resolution sequence typing of C. glabrata, discovery of novel STs and potential to monitor trends in genetic diversity. WGS assessment for echinocandin resistance augments phenotypic susceptibility testing.

Chlorhexidine washing in intensive care does not reduce bloodstream infections, blood culture contamination and drug-resistant microorganism acquisition: an interrupted time series analysis.

BACKGROUND: Health care-associated infections are a major cause of morbidity and mortality in intensive care patients. The effect of daily washing with chlorhexidine on these infections is controversial. METHODS: Single-centre, retrospective, open-label, sequential period, interrupted time series (ITS) analysis in a 31-bed tertiary referral mixed intensive care unit (ICU), comparing daily washing with water and soap (from January 2011 to August 2013) with chlorhexidine washing (from November 2013 to December 2015), after the introduction of a unit-level policy of chlorhexidine washing. All patients in the ICU were included in the study, except: if they were under 18 years of age, if their ICU stay was less than 24 hours (to ensure that all studied patients had at least one exposure to the daily wash intervention), or if patients had a known allergy to chlorhexidine. Outcome measures included: clinically significant positive blood cultures attributable to the ICU stay; contaminated blood cultures; newly acquired multidrug-resistant microorganisms (MDRO) such as methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococcus (VRE) or multidrug-resistant gram-negative (MRGN) isolates attributable to ICU from clinical and screening cultures; and newly acquired Clostridium difficile infections (CDIs). Incidence rates of these outcomes were calculated per 1000 patient days. MDRO acquisition rates were corrected for background hospital period prevalence rates of MDRO. RESULTS: A total of 6634 patients were included in the study. ITS analysis showed no significant level or slope changes in any of the outcome measures after implementation of chlorhexidine washing. The incidence rate of clinically significant positive blood cultures during the chlorhexidine period compared with the water and soap period was 3.6 v 4.7 (P =0.37); blood culture contamination rates were 11.8 v 9.5 (P =0.56); incidence rates of new ICU-associated MDRO acquisitions were 3.22 v 3.69 (P =0.27); incidence rates of new CDI were 2.01 v 0.79 (P =0.16). Outcomes after adjustment for known and potential confounders were similar. CONCLUSIONS: In this real-world, long term ICU study, implementation of a unit-level policy of daily washing with chlorhexidine impregnated cloths was not associated with a reduction in the rates of ICU-associated clinically significant positive blood cultures, blood culture contamination, newly acquired MDRO isolates, and CDIs.

Epidemiology of non-typhoid Salmonella infection in the Australian Capital Territory over a 10-year period.

AIM: To describe the epidemiology of non-typhoid Salmonella (NTS) infection in the Australian Capital Territory (ACT), including factors associated with hospitalisation. METHODS: This was a retrospective descriptive and observational study of culture-confirmed NTS infections using data collected from ACT public health, public pathology and hospital services in the period 2003-2012. Outcome measures include incidence and NTS serotype for total reported and hospitalised cases and focus of infection, complications and antibiotic susceptibility for hospitalised cases. RESULTS: In total, 1469 cases of NTS infection were reported, with the crude annual incidence increasing from 24.4 to 61.3 cases per 100 000 population; 14% were hospitalised, representing an incidence of 5.9 hospitalisations per 100 000 population, without significant change over time. Hospitalisation incidence peaked at the extremes of age. Comorbid disease and age ≥ 80 years were associated with complications during hospitalisation. Salmonella serotype Typhimurium was the most common serotype, accounting for 64% of NTS. Independent risk factors for invasive disease included non-S. Typhimurium serotype (aRR 5.46, 95%CI 1.69-17.65 P = 0.005), ischaemic heart disease (aRR 4.18, 95%CI 1.20-14.60 P = 0.025) and haematological malignancy (aRR 6.93, 95%CI 2.54-18.94 P < 0.001). Among hospitalised patients, resistance to ampicillin, ceftriaxone, trimethoprim-sulfamethoxazole and quinolones was 9.9%, 0%, 4.4% and 2.5% respectively. CONCLUSIONS: NTS notifications in the ACT have increased over time, with outbreaks of food-borne disease contributing to this increase. Crude age-specific incidence is highest in the very young, while rates of hospitalisation are highest in the elderly. Comorbid disease and infection with a non-S. Typhimurium serotype were associated with complicated NTS disease course. Antimicrobial resistance in NTS is low and has not increased over time.

Factors affecting the presence, genetic diversity and antimicrobial sensitivity of Escherichia coli in poultry meat samples collected from Canberra, Australia.

To investigate the factors determining the clonal composition of Escherichia coli in poultry meat samples, 306 samples were collected from 16 shops, representing three supermarket chains and an independent butchery located in each of the four town centers of Canberra, Australia, during the summer, autumn and winter. A total of 3415 E. coli isolates were recovered and assigned to a phylogenetic group using the Clermont quadruplex PCR method, fingerprinted using repetitive element palindromic (REP) PCR and screened for their antimicrobial susceptibility profiles. The probability of detecting E. coli and the number of fingerprint types detected per sample, as well as the phylogroup membership of the isolates and their antimicrobial sensitivity profiles varied, with one or more of retailer, store, meat type, season and husbandry. The results of this study demonstrate that poultry meat products are likely to be contaminated with a genetically diverse community of E. coli and suggest that factors relating to the nature of the meat product and distribution chain are determinants of the observed diversity.

Fine-Scale Structure Analysis Shows Epidemic Patterns of Clonal Complex 95, a Cosmopolitan Escherichia coli Lineage Responsible for Extraintestinal Infection.

The Escherichia coli lineage known as clonal complex 95 (CC95) is a cosmopolitan human-associated lineage responsible for a significant fraction of extraintestinal infections of humans. Whole-genome sequence data of 200 CC95 strains from various origins enabled determination of the CC95 pangenome. The pangenome analysis revealed that strains of the complex could be assigned to one of five subgroups that vary in their serotype, extraintestinal virulence, virulence gene content, and antibiotic resistance gene profile. A total of 511 CC95 strains isolated from humans living in France, Australia, and the United States were screened for their subgroup membership using a PCR-based method. The CC95 subgroups are nonrandomly distributed with respect to their geographic origin. The relative frequency of the subgroups was shown to change through time, although the nature of the changes varies with continent. Strains of the subgroups are also nonrandomly distributed with respect to source of isolation (blood, urine, or feces) and host sex. Collectively, the evidence indicates that although strains belonging to CC95 may be cosmopolitan, human movement patterns have been insufficient to homogenize the distribution of the CC95 subgroups. Rather, the manner in which CC95 strains evolve appears to vary both spatially and temporally. Although CC95 strains appeared globally as pandemic, fine-scale structure analysis shows epidemic patterns of the CC95 subgroups. Furthermore, the observation that the relative frequency of CC95 subgroups at a single locality has changed over time indicates that the relative fitness of the subgroups has changed. IMPORTANCEEscherichia coli clonal complex 95 represents a cosmopolitan, genetically diverse lineage, and the extensive substructure observed in this lineage is epidemiologically and clinically relevant. The frequency with which CC95 strains are responsible for extraintestinal infection appears to have been stable over the past 15 years. However, the different subgroups identified within this lineage have an epidemic structure depending on the host, sample, continent, and time. Thus, the evolution and spread of strains belonging to CC95 are very different from those of another cosmopolitan human-associated clonal complex, CC131, which has increased significantly in frequency as a cause of extraintestinal infection over the past 15 years due to the evolution and spread of two very closely related, nearly monomorphic lineages.