RESUMO
Background: Healthcare-associated wastewater and asymptomatic patient reservoirs colonized by carbapenemase-producing Enterobacterales (CPE) contribute to nosocomial CPE dissemination, but the characteristics and dynamics of this remain unclear. Methods: We systematically sampled wastewater sites (nâ=â4488 samples; 349 sites) and patients (nâ=â1247) across six wards over 6-12â months to understand blaKPC-associated CPE (KPC-E) diversity within these reservoirs and transmission in a healthcare setting. Up to five KPC-E-positive isolates per sample were sequenced (Illumina). Recombination-adjusted phylogenies were used to define genetically related strains; assembly and mapping-based approaches were used to characterize antimicrobial resistance genes, insertion sequences (ISs) and Tn4401 types/target site sequences. The accessory genome was evaluated in some of the largest clusters, and those crossing reservoirs. Results: Wastewater site KPC-E-positivity was substantial [101/349 sites (28.9%); 228/5601 (4.1%) patients cultured]. Thirteen KPC-E species and 109 strains were identified using genomics, and 24% of wastewater and 26% of patient KPC-E-positive samples harboured one or more strains. Most diversity was explained by the individual niche, suggesting localized factors are important in selection and spread. Tn4401 + flanking target site sequence diversity was greater in wastewater sites (Pâ<â0.001), which might favour Tn4401-associated transposition/evolution. Shower/bath- and sluice/mop-associated sites were more likely to be KPC-E-positive (adjusted ORâ=â2.69; 95% CI: 1.44-5.01; Pâ=â0.0019; and adjusted ORâ=â2.60; 95% CI: 1.04-6.52; Pâ=â0.0410, respectively). Different strains had different blaKPC dissemination dynamics. Conclusions: We identified substantial and diverse KPC-E colonization of wastewater sites and patients in this hospital setting. Reservoir and niche-specific factors (e.g. microbial interactions, selection pressures), and different strains and mobile genetic elements likely affect transmission dynamics. This should be considered in surveillance and control strategies.
RESUMO
INTRODUCTION: Wounds are invariably dressed postoperatively but the evidence for the timing of dressing changes is limited. This meta-analysis evaluated whether the relative risk of wound infection varies depending on when dressings are changed. METHODS: A frequentist random-effects network meta-analysis was conducted on the results of a systematic review of the MEDLINE®, Ovid®, Scopus®, Web of Science™ and PubMed® databases and the Cochrane Central Register of Controlled Trials performed in May 2023. Evidence quality was graded using the Confidence In Network Meta-Analysis tool. RESULTS: A total of 4 studies were included with 878 patients. A significant increase in the relative risk of wound infection was found when dressings were left in situ for more than 4.5 days when compared with 48 hours (3.18, 95% confidence interval: 1.22-8.33). There were no significant differences in the relative risk of infection between the other groups. Model heterogeneity and inconsistency were insignificant (Cochran's Q: 0.44, p=0.51). The quality of the evidence was graded as generally very low and risk of bias evaluations showed it to be of high concern for bias. CONCLUSIONS: Late dressing changes significantly increase the risks of wound infection and changes at 48 hours minimise these risks. There was no advantage demonstrated for earlier dressing changes. Ensuring that dressings are changed appropriately can minimise patient harm and health service costs.
RESUMO
BACKGROUND: Perianal abscesses are common presentations and reasons for emergency general surgery admissions. Management involves incision and drainage of the abscess and packing the cavity with internal wound dressings. This meta-analysis aimed to assess in adults if packing an abscess or leaving it unpacked leads to a significant difference in the outcomes of pain on wound dressing, time to healing, rate of fistulation and abscess recurrence. METHODS: Randomised controlled trials (RCTs) with participants aged 18 years or older that compared packing of perianal abscess cavities with no packing between 2002 and 2022 were searched for in December 2022 on OVID Medline and Embase, the CENTRAL register of trials, PubMed and Google Scholar. Risk of bias was assessed using the Cochrane Risk of Bias tool. Random effects meta-analysis was conducted on the data extracted. RESULTS: Three RCTs involving 490 patients were analysed for the outcomes of abscess recurrence and postoperative fistula formation; the data were not adequate to assess pain on dressing and time to healing. For unpacked versus packed, the pooled relative risk of abscess recurrence was 1.57 (95% confidence interval (CI) 0.764, 3.29, p=0.219) and for fistula formation 0.686 (95% CI 0.430, 1.09, p=0.114). These results suggest there is no significant benefit to packing abscess cavities. CONCLUSIONS: Analysis of the outcomes suggests there is no significant difference with regards to rates of abscess recurrence or fistula formation between the packed and unpacked groups; however, appropriately powered RCTs are required in this area to provide more primary evidence to inform best practice and clinical management.
RESUMO
Current prospective reports suggest a pandemic-related increase in adolescent mental health problems. We examine whether age-related change over 11-14 years accounts for this increase. Mothers and adolescents in a UK-based birth cohort (Wirral Child Health and Development Study; WCHADS; N = 737) reported on adolescent depression and behavioural problems pre-pandemic (December 2019-March 2020), mid-pandemic (June 2020-March 2021) and late pandemic (July 2021-March 2022). Analysis used repeated measures models for over-dispersed Poisson counts with an adolescent-specific intercept with age as a time-varying covariate. Maturational curves for girls, but not for boys, showed a significant increase in self-reported depression symptoms over ages 11-14 years. Behavioural problems decreased for both. After adjusting for age-related change, girls' depression increased by only 13% at mid-pandemic and returned to near pre-pandemic level at late pandemic (mid versus late - 12%), whereas boys' depression increased by 31% and remained elevated (mid versus late 1%). Age-adjusted behavioural problems increased for both (girls 40%, boys 41%) and worsened from mid- to late pandemic (girls 33%, boys 18%). Initial reports of a pandemic-related increase in depression in young adolescent girls could be explained by a natural maturational rise. In contrast, maturational decreases in boys' depression and both boys' and girls' behavioural problems may mask an effect of the pandemic.
Assuntos
COVID-19 , Depressão , Saúde Mental , Humanos , Adolescente , COVID-19/epidemiologia , COVID-19/psicologia , Feminino , Masculino , Criança , Reino Unido/epidemiologia , Depressão/epidemiologia , Depressão/psicologia , Comportamento Problema/psicologia , Fatores SexuaisRESUMO
Wastewater-based epidemiology (WBE) for population-level surveillance of antimicrobial resistance (AMR) is gaining significant traction, but the impact of wastewater sampling methods on results is unclear. In this study, we characterized taxonomic and resistome differences between single-timepoint-grab and 24 h composites of wastewater influent from a large UK-based wastewater treatment work [WWTW (population equivalent: 223â435)]. We autosampled hourly influent grab samples (n=72) over three consecutive weekdays, and prepared additional 24 h composites (n=3) from respective grabs. For taxonomic profiling, metagenomic DNA was extracted from all samples and 16S rRNA gene sequencing was performed. One composite and six grabs from day 1 underwent metagenomic sequencing for metagenomic dissimilarity estimation and resistome profiling. Taxonomic abundances of phyla varied significantly across hourly grab samples but followed a repeating diurnal pattern for all 3 days. Hierarchical clustering grouped grab samples into four time periods dissimilar in both 16S rRNA gene-based profiles and metagenomic distances. 24H-composites resembled mean daily phyla abundances and showed low variability of taxonomic profiles. Of the 122 AMR gene families (AGFs) identified across all day 1 samples, single grab samples identified a median of six (IQR: 5-8) AGFs not seen in the composite. However, 36/36 of these hits were at lateral coverage <0.5 (median: 0.19; interquartile range: 0.16-0.22) and potential false positives. Conversely, the 24H-composite identified three AGFs not seen in any grab with higher lateral coverage (0.82; 0.55-0.84). Additionally, several clinically significant human AGFs (bla VIM, bla IMP, bla KPC) were intermittently or completely missed by grab sampling but captured by the 24 h composite. Wastewater influent undergoes significant taxonomic and resistome changes on short timescales potentially affecting interpretation of results based on sampling strategy. Grab samples are more convenient and potentially capture low-prevalence/transient targets but are less comprehensive and temporally variable. Therefore, we recommend 24H-composite sampling where feasible. Further validation and optimization of WBE methods is vital for its development into a robust AMR surveillance approach.
Assuntos
Metagenoma , Águas Residuárias , Humanos , RNA Ribossômico 16S/genéticaRESUMO
OBJECTIVES: We systematically reviewed studies using wastewater for AMR surveillance in human populations, to determine: (i) evidence of concordance between wastewater-human AMR prevalence estimates, and (ii) methodological approaches which optimised identifying such an association, and which could be recommended as standard. We used Lin's concordance correlation coefficient (CCC) to quantify concordance between AMR prevalence estimates in wastewater and human compartments (where CCC = 1 reflects perfect concordance), and logistic regression to identify study features (e.g. sampling methods) associated with high agreement studies (defined as >70% of within-study wastewater-human AMR prevalence comparisons within ±10%). RESULTS: Of 8,867 records and 441 full-text methods reviewed, 33 studies were included. AMR prevalence data was extractable from 24 studies conducting phenotypic-only (n = 7), genotypic-only (n = 1) or combined (n = 16) AMR detection. Overall concordance of wastewater-human AMR prevalence estimates was reasonably high for both phenotypic (CCC = 0.85 [95% CI 0.8-0.89]) and genotypic approaches (CCC = 0.88 (95% CI 0.84-0.9)) despite diverse study designs, bacterial species investigated and phenotypic/genotypic targets. No significant relationships between methodological approaches and high agreement studies were identified using logistic regression; however, this was limited by inconsistent reporting of study features, significant heterogeneity in approaches and limited sample size. Based on a secondary, descriptive synthesis, studies conducting composite sampling of wastewater influent, longitudinal sampling >12 months, and time-/location-matched sampling of wastewater and human compartments generally had higher agreement. CONCLUSION: Wastewater-based surveillance of AMR appears promising, with high overall concordance between wastewater and human AMR prevalence estimates in studies irrespective of heterogenous approaches. However, our review suggests future work would benefit from: time-/location-matched sampling of wastewater and human populations, composite sampling of influent, and sampling >12 months for longitudinal studies. Further research and clear and consistent reporting of study methods is required to identify optimal practice.
Assuntos
Farmacorresistência Bacteriana , Águas Residuárias , Antibacterianos/farmacologia , Bactérias/genética , Humanos , Vigilância Epidemiológica Baseada em Águas ResiduáriasRESUMO
OBJECTIVES: This study determined associations between respiratory viruses and subsequent illness course in primary care adult patients presenting with acute cough and/or suspected lower respiratory tract infection. METHODS: A prospective European primary care study recruited adults with symptoms of lower respiratory tract infection between November 2007 and April 2010. Real-time in-house polymerase chain reaction (PCR) was performed to test for six common respiratory viruses. In this secondary analysis, symptom severity (scored 1 = no problem, 2 = mild, 3 = moderate, 4 = severe) and symptom duration were compared between groups with different viral aetiologies using regression and Cox proportional hazard models, respectively. Additionally, associations between baseline viral load (cycle threshold (Ct) value) and illness course were assessed. RESULTS: The PCR tested positive for a common respiratory virus in 1354 of the 2957 (45.8%) included patients. The overall mean symptom score at presentation was 2.09 (95% confidence interval (CI) 2.07-2.11) and the median duration until resolution of moderately bad or severe symptoms was 8.70 days (interquartile range 4.50-11.00). Patients with influenza virus, human metapneumovirus (hMPV), respiratory syncytial virus (RSV), coronavirus (CoV) or rhinovirus had a significantly higher symptom score than patients with no virus isolated (0.07-0.25 points or 2.3-8.3% higher symptom score). Time to symptom resolution was longer in RSV infections (adjusted hazard ratio (AHR) 0.80, 95% CI 0.65-0.96) and hMPV infections (AHR 0.77, 95% CI 0.62-0.94) than in infections with no virus isolated. Overall, baseline viral load was associated with symptom severity (difference 0.11, 95% CI 0.06-0.16 per 10 cycles decrease in Ct value), but not with symptom duration. CONCLUSIONS: In healthy, working adults from the general community presenting at the general practitioner with acute cough and/or suspected lower respiratory tract infection other than influenza impose an illness burden comparable to influenza. Hence, the public health focus for viral respiratory tract infections should be broadened.
Assuntos
Atenção Primária à Saúde/estatística & dados numéricos , Infecções Respiratórias/epidemiologia , Infecções Respiratórias/fisiopatologia , Viroses/epidemiologia , Viroses/fisiopatologia , Adulto , Bélgica/epidemiologia , Convalescença , Coronavirus/crescimento & desenvolvimento , Coronavirus/patogenicidade , Feminino , Humanos , Masculino , Metapneumovirus/crescimento & desenvolvimento , Metapneumovirus/patogenicidade , Países Baixos/epidemiologia , Orthomyxoviridae/crescimento & desenvolvimento , Orthomyxoviridae/patogenicidade , Modelos de Riscos Proporcionais , Estudos Prospectivos , Vírus Sincicial Respiratório Humano/crescimento & desenvolvimento , Vírus Sincicial Respiratório Humano/patogenicidade , Infecções Respiratórias/classificação , Infecções Respiratórias/diagnóstico , Rhinovirus/crescimento & desenvolvimento , Rhinovirus/patogenicidade , Índice de Gravidade de Doença , Carga Viral , Viroses/classificação , Viroses/diagnósticoRESUMO
INTRODUCTION: Risk factors for carbapenemase-producing Enterobacterales (CPE) acquisition/infection and associated clinical outcomes have been evaluated in the context of clonal, species-specific outbreaks. Equivalent analyses for complex, multi-species outbreaks, which are increasingly common, are lacking. METHODS: Between December 2010 and January 2017, a case-control study of Klebsiella pneumoniae carbapenemase (KPC)-producing organism (KPCO) acquisition was undertaken using electronic health records from inpatients in a US academic medical centre and long-term acute care hospital (LTACH) with ongoing multi-species KPCO transmission despite a robust CPE screening programme. Cases had a first KPCO-positive culture >48 h after admission, and included colonizations and infections (defined by clinical records). Controls had at least two negative perirectal screens and no positive cultures. Risk factors for KPCO acquisition, first infection following acquisition, and 14-day mortality following each episode of infection were identified using multi-variable logistic regression. RESULTS: In 303 cases (89 with at least one infection) and 5929 controls, risk factors for KPCO acquisition included: longer inpatient stay, transfusion, complex thoracic pathology, mechanical ventilation, dialysis, and exposure to carbapenems and ß-lactam/ß-lactamase inhibitors. Exposure to other KPCO-colonized patients was only a risk factor for acquisition in a single unit, suggesting that direct patient-to-patient transmission did not play a major role. There were 15 species of KPCO; 61 (20%) cases were colonized/infected with more than one species. Fourteen-day mortality following non-urinary KPCO infection was 20% (20/97 episodes) and was associated with failure to achieve source control. CONCLUSIONS: Healthcare exposures, antimicrobials and invasive procedures increased the risk of KPCO colonization/infection, suggesting potential targets for infection control interventions in multi-species outbreaks. Evidence for patient-to-patient transmission was limited.
Assuntos
Infecção Hospitalar/epidemiologia , Infecção Hospitalar/microbiologia , Infecções por Klebsiella/epidemiologia , Centros Médicos Acadêmicos , Adulto , Idoso , Idoso de 80 Anos ou mais , Proteínas de Bactérias , Carbapenêmicos/uso terapêutico , Estudos de Casos e Controles , Infecção Hospitalar/tratamento farmacológico , Feminino , Humanos , Infecções por Klebsiella/tratamento farmacológico , Infecções por Klebsiella/genética , Infecções por Klebsiella/microbiologia , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/isolamento & purificação , Masculino , Pessoa de Meia-Idade , Fatores de Risco , Ubiquitina-Proteína Ligases/isolamento & purificação , Virginia/epidemiologia , beta-LactamasesRESUMO
BACKGROUND: Hospital outbreaks of carbapenemase-producing organisms, such as blaIMP-4-containing organisms, are an increasing threat to patient safety. OBJECTIVES: To investigate the genomic dynamics of a 10 year (2006-15) outbreak of blaIMP-4-containing organisms in a burns unit in a hospital in Sydney, Australia. METHODS: All carbapenem-non-susceptible or MDR clinical isolates (2006-15) and a random selection of equivalent or ESBL-producing environmental isolates (2012-15) were sequenced [short-read (Illumina), long-read (Oxford Nanopore Technology)]. Sequence data were used to assess genetic relatedness of isolates (Mash; mapping and recombination-adjusted phylogenies), perform in silico typing (MLST, resistance genes and plasmid replicons) and reconstruct a subset of blaIMP plasmids for comparative plasmid genomics. RESULTS: A total of 46/58 clinical and 67/96 environmental isolates contained blaIMP-4. All blaIMP-4-positive organisms contained five or more other resistance genes. Enterobacter cloacae was the predominant organism, with 12 other species mainly found in either the environment or patients, some persisting despite several cleaning methods. On phylogenetic analysis there were three genetic clusters of E. cloacae containing both clinical and environmental isolates, and an additional four clusters restricted to either reservoir. blaIMP-4 was mostly found as part of a cassette array (blaIMP-4-qacG2-aacA4-catB3) in a class 1 integron within a previously described IncM2 plasmid (pEl1573), with almost complete conservation of this cassette across the species over the 10 years. Several other plasmids were also implicated, including an IncF plasmid backbone not previously widely described in association with blaIMP-4. CONCLUSIONS: Genetic backgrounds disseminating blaIMP-4 can persist, diversify and evolve amongst both human and environmental reservoirs during a prolonged outbreak despite intensive prevention efforts.
Assuntos
Proteínas de Bactérias , beta-Lactamases , Antibacterianos/farmacologia , Austrália/epidemiologia , Proteínas de Bactérias/genética , Surtos de Doenças , Genômica , Hospitais , Humanos , Integrons , Testes de Sensibilidade Microbiana , Tipagem de Sequências Multilocus , Filogenia , Plasmídeos/genética , beta-Lactamases/genética , beta-Lactamases/metabolismoRESUMO
BACKGROUND: Carbapenemase-producing Enterobacteriaceae (CPE) pose a major global health risk. Mobile genetic elements account for much of the increasing CPE burden. OBJECTIVES: To investigate CPE colonization and the impact of antibiotic exposure on subsequent resistance gene dissemination within the gut microbiota using a model to simulate the human colon. METHODS: Gut models seeded with CPE-negative human faeces [screened with BioMérieux chromID® CARBA-SMART (Carba-Smart), Cepheid Xpert® Carba-R assay (XCR)] were inoculated with distinct carbapenemase-producing Klebsiella pneumoniae strains (KPC, NDM) and challenged with imipenem or piperacillin/tazobactam then meropenem. Resistant populations were enumerated daily on selective agars (Carba-Smart); CPE genes were confirmed by PCR (XCR, Check-Direct CPE Screen for BD MAX™). CPE gene dissemination was tracked using PacBio long-read sequencing. RESULTS: CPE populations increased during inoculation, plateauing at â¼105 log10 cfu/mL in both models and persisting throughout the experiments (>65 days), with no evidence of CPE 'washout'. After antibiotic administration, there was evidence of interspecies plasmid transfer of blaKPC-2 (111742 bp IncFII/IncR plasmid, 99% identity to pKpQIL-D2) and blaNDM-1 (â¼170 kb IncFIB/IncFII plasmid), and CPE populations rose from <0.01% to >45% of the total lactose-fermenting populations in the KPC model. Isolation of a blaNDM-1K. pneumoniae with one chromosomal single-nucleotide variant compared with the inoculated strain indicated clonal expansion within the model. Antibiotic administration exposed a previously undetected K. pneumoniae encoding blaOXA-232 (KPC model). CONCLUSIONS: CPE exposure can lead to colonization, clonal expansion and resistance gene transfer within intact human colonic microbiota. Furthermore, under antibiotic selective pressure, new resistant populations emerge, emphasizing the need to control exposure to antimicrobials.
Assuntos
Proteínas de Bactérias/genética , Enterobacteriáceas Resistentes a Carbapenêmicos/enzimologia , Enterobacteriáceas Resistentes a Carbapenêmicos/genética , Colo/microbiologia , Microbioma Gastrointestinal , Transferência Genética Horizontal , Microbiota , beta-Lactamases/genética , Enterobacteriáceas Resistentes a Carbapenêmicos/crescimento & desenvolvimento , Voluntários Saudáveis , Humanos , Modelos BiológicosRESUMO
The modification of river flow regimes poses a significant threat to the world's freshwater ecosystems. Northern Australia's freshwater resources, particularly dry season river flows, are being increasingly modified to support human development, potentially threatening aquatic ecosystems and biodiversity, including fish. More information is urgently needed on the ecology of fishes in this region, including their habitat requirements, to support water policy and management to ensure future sustainable development. This study used electrofishing and habitat survey methods to quantify the dry season habitat use of 20 common freshwater fish taxa in the Daly River in Australia's wet-dry tropics. Of twenty measured habitat variables, water depth and velocity were the two most important factors discriminating fish habitat use for the majority of taxa. Four distinct fish habitat guilds were identified, largely classified according to depth, velocity and structural complexity. Ontogenetic shifts in habitat use were also observed in three species. This study highlights the need to maintain dry season river flows that support a diversity of riverine mesohabitats for freshwater fishes. In particular, shallow fast-flowing areas provided critical nursery and refuge habitats for some species, but are vulnerable to water level reductions due to water extraction. By highlighting the importance of a diversity of habitats for fishes, this study assists water managers in future decision making on the ecological risks of water extractions from tropical rivers, and especially the need to maintain dry season low flows to protect the habitats of native fish.
Assuntos
Peixes/fisiologia , Animais , Austrália , Biodiversidade , Conservação dos Recursos Naturais/métodos , Ecologia , Ecossistema , Água Doce , Rios , Alimentos Marinhos , Estações do Ano , ÁguaRESUMO
BACKGROUND: Extended-spectrum cephalosporin resistance (ESC-R) in Escherichia coli and Klebsiella pneumoniae is a healthcare threat; high gastrointestinal carriage rates are reported from South-east Asia. Colonisation prevalence data in Cambodia are lacking. The aim of this study was to determine gastrointestinal colonisation prevalence of ESC-resistant E. coli (ESC-R-EC) and K. pneumoniae (ESC-R-KP) in Cambodian children/adolescents and associated socio-demographic risk factors; and to characterise relevant resistance genes, their genetic contexts, and the genetic relatedness of ESC-R strains using whole genome sequencing (WGS). RESULTS: Faeces and questionnaire data were obtained from individuals < 16 years in north-western Cambodia, 2012. WGS of cultured ESC-R-EC/KP was performed (Illumina). Maximum likelihood phylogenies were used to characterise relatedness of isolates; ESC-R-associated resistance genes and their genetic contexts were identified from de novo assemblies using BLASTn and automated/manual annotation. 82/148 (55%) of children/adolescents were ESC-R-EC/KP colonised; 12/148 (8%) were co-colonised with both species. Independent risk factors for colonisation were hospitalisation (OR: 3.12, 95% CI [1.52-6.38]) and intestinal parasites (OR: 3.11 [1.29-7.51]); school attendance conferred decreased risk (OR: 0.44 [0.21-0.92]. ESC-R strains were diverse; the commonest ESC-R mechanisms were blaCTX-M 1 and 9 sub-family variants. Structures flanking these genes were highly variable, and for blaCTX-M-15, - 55 and - 27 frequently involved IS26. Chromosomal blaCTX-M integration was common in E. coli. CONCLUSIONS: Gastrointestinal ESC-R-EC/KP colonisation is widespread in Cambodian children/adolescents; hospital admission and intestinal parasites are independent risk factors. The genetic contexts of blaCTX-M are highly mosaic, consistent with rapid horizontal exchange. Chromosomal integration of blaCTX-M may result in stable propagation in these community-associated pathogens.
Assuntos
Portador Sadio/epidemiologia , Cefalosporinas/farmacologia , Farmacorresistência Bacteriana , Infecções por Escherichia coli/epidemiologia , Trato Gastrointestinal/microbiologia , Infecções por Klebsiella/epidemiologia , Adolescente , Antibacterianos/farmacologia , Camboja/epidemiologia , Portador Sadio/microbiologia , Criança , Pré-Escolar , Escherichia coli/efeitos dos fármacos , Escherichia coli/genética , Escherichia coli/patogenicidade , Feminino , Trato Gastrointestinal/parasitologia , Hospitalização , Humanos , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/patogenicidade , Masculino , Doenças Parasitárias/epidemiologia , Doenças Parasitárias/microbiologia , Prevalência , Fatores de Risco , Inquéritos e Questionários , Sequenciamento Completo do GenomaRESUMO
BACKGROUND/OBJECTIVES: Carbapenemase-producing Enterobacteriaceae (CPE) are a public health threat, and have been found in humans, animals and the environment. Carbapenems are not authorized for use in EU or UK companion animals, and the prevalence of carbapenem-resistant Gram-negative bacilli (CRGNB) in this population is unknown. METHODS: We investigated CRGNB isolated from animal specimens received by one diagnostic laboratory from 34 UK veterinary practices (September 2015-December 2016). Any Gram-negative isolates from clinical specimens showing reduced susceptibility to fluoroquinolones and/or aminoglycosides and/or cephalosporins were investigated phenotypically and genotypically for carbapenemases. A complete genome assembly (Illumina/Nanopore) was generated for the single isolate identified to investigate the genetic context for carbapenem resistance. RESULTS: One ST410 Escherichia coli isolate [(CARB35); 1/191, 0.5%], cultured from a wound in a springer spaniel, harboured a known carbapenem resistance gene (blaNDM-5). The gene was located in the chromosome on an integrated 100 kb IncF plasmid, also harbouring other drug resistance genes (mrx, sul1, ant1 and dfrA). The isolate also contained blaCMY-42 and blaTEM-190 on two separate plasmids (IncI1 and IncFII, respectively) that showed homology with other publicly available plasmid sequences from Italy and Myanmar. CONCLUSIONS: Even though the use of carbapenems in companion animals is restricted, the concurrent presence of blaCMY-42 and other antimicrobial resistance genes could lead to co-selection of carbapenemase genes in this population. Further studies investigating the selection and flow of plasmids carrying important resistance genes amongst humans and companion animals are needed.
Assuntos
Doenças do Cão/microbiologia , Infecções por Escherichia coli/veterinária , Escherichia coli/genética , beta-Lactamases/genética , Doenças dos Animais/epidemiologia , Doenças dos Animais/microbiologia , Animais , Doenças do Cão/epidemiologia , Cães , Genoma Bacteriano , Genômica/métodos , Reino Unido/epidemiologia , Sequenciamento Completo do GenomaRESUMO
Carbapenem-resistant Enterobacteriaceae (CRE) represent a health threat, but effective control interventions remain unclear. Hospital wastewater sites are increasingly being highlighted as important potential reservoirs. We investigated a large Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli outbreak and wider CRE incidence trends in the Central Manchester University Hospital NHS Foundation Trust (CMFT) (United Kingdom) over 8 years, to determine the impact of infection prevention and control measures. Bacteriology and patient administration data (2009 to 2017) were linked, and a subset of CMFT or regional hospital KPC-producing E. coli isolates (n = 268) were sequenced. Control interventions followed international guidelines and included cohorting, rectal screening (n = 184,539 screens), environmental sampling, enhanced cleaning, and ward closure and plumbing replacement. Segmented regression of time trends for CRE detections was used to evaluate the impact of interventions on CRE incidence. Genomic analysis (n = 268 isolates) identified the spread of a KPC-producing E. coli outbreak clone (strain A, sequence type 216 [ST216]; n = 125) among patients and in the environment, particularly on 2 cardiac wards (wards 3 and 4), despite control measures. ST216 strain A had caused an antecedent outbreak and shared its KPC plasmids with other E. coli lineages and Enterobacteriaceae species. CRE acquisition incidence declined after closure of wards 3 and 4 and plumbing replacement, suggesting an environmental contribution. However, ward 3/ward 4 wastewater sites were rapidly recolonized with CRE and patient CRE acquisitions recurred, albeit at lower rates. Patient relocation and plumbing replacement were associated with control of a clonal KPC-producing E. coli outbreak; however, environmental contamination with CRE and patient CRE acquisitions recurred rapidly following this intervention. The large numbers of cases and the persistence of blaKPC in E. coli, including pathogenic lineages, are of concern.
Assuntos
Infecção Hospitalar/epidemiologia , Surtos de Doenças , Infecções por Escherichia coli/epidemiologia , Escherichia coli/genética , Klebsiella pneumoniae/genética , beta-Lactamases/genética , Infecção Hospitalar/tratamento farmacológico , Infecção Hospitalar/microbiologia , Infecção Hospitalar/transmissão , DNA Bacteriano/genética , Reservatórios de Doenças/microbiologia , Escherichia coli/efeitos dos fármacos , Escherichia coli/isolamento & purificação , Escherichia coli/patogenicidade , Infecções por Escherichia coli/tratamento farmacológico , Infecções por Escherichia coli/microbiologia , Infecções por Escherichia coli/transmissão , Expressão Gênica , Transferência Genética Horizontal , Genótipo , Hospitais Universitários , Humanos , Controle de Infecções/métodos , Klebsiella pneumoniae/patogenicidade , Resíduos de Serviços de Saúde , Filogenia , Prevalência , Reino Unido/epidemiologia , Águas Residuárias/microbiologiaRESUMO
OBJECTIVES: To describe the role of bacteria (including bacterial resistance), viruses (including those recently described) and mixed bacterial-viral infections in adults presenting to primary care with lower respiratory tract infection (LRTI). METHODS: In all, 3104 adults with LRTI were enrolled, of whom 141 (4.5%) had community-acquired pneumonia (CAP), and 2985 matched controls in a prospective study in 16 primary care networks in Europe, and followed patients up at 28-35 days. We detected Streptococcus pneumoniae and Haemophilus influenzae and assessed susceptibility, atypical bacteria and viruses. RESULTS: A potential pathogen was detected in 1844 (59%) (in 350 (11%) bacterial pathogens only, in 1190 (38%) viral pathogens only, and in 304 (10%) both bacterial and viral pathogens). The most common bacterial pathogens isolated were S. pneumoniae (5.5% overall, 9.2% in CAP patients) and H. influenzae (5.4% overall, 14.2% in CAP patients). Less than 1% of S. pneumoniae were highly resistant to penicillin and 12.6% of H. influenzae were ß-lactamase positive. The most common viral pathogens detected were human rhinovirus (20.1%), influenza viruses (9.9%), and human coronavirus (7.4%). Influenza virus, human parainfluenza viruses and human respiratory syncytial virus as well as human rhinovirus, human coronavirus and human metapneumovirus were detected significantly more frequently in LRTI patients than in controls. CONCLUSIONS: A bacterial pathogen is identified in approximately one in five adult patients with LRTI in primary care, and a viral pathogen in just under half, with mixed infections in one in ten. Penicillin-resistant pneumococci and ß-lactamase-producing H. influenzae are uncommon. These new findings support a restrictive approach to antibiotic prescribing for LRTI and the use of first-line, narrow-spectrum agents in primary care.
Assuntos
Bactérias/isolamento & purificação , Infecções Comunitárias Adquiridas/microbiologia , Pneumonia/microbiologia , Pneumonia/virologia , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Bactérias/efeitos dos fármacos , Infecções Comunitárias Adquiridas/epidemiologia , Europa (Continente)/epidemiologia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Pneumonia/epidemiologia , Estudos Prospectivos , Vírus/isolamento & purificação , Adulto JovemRESUMO
The development of effective strategies to restore the biological functioning of aquatic ecosystems with altered flow regimes requires a detailed understanding of flow-ecology requirements, which is unfortunately lacking in many cases. By understanding the flow conditions required to initiate critical life history events such as migration and spawning, it is possible to mitigate the threats posed by regulated river flow by providing targeted environmental flow releases from impoundments. In this study, we examined the influence of hydrological variables (e.g., flow magnitude), temporal variables (e.g., day of year) and spatial variables (e.g., longitudinal position of fish) on two key life history events (migration to spawning grounds and spawning activity) for a threatened diadromous fish (Australian grayling Prototroctes maraena) using data collected from 2008 to 2015 in the Bunyip-Tarago river system in Victoria. Our analyses revealed that flow changes act as a cue to downstream migration, but movement responses differed spatially: fish in the upper catchment showed a more specific requirement for rising discharge to initiate migration than fish in the lower catchment. Egg concentrations peaked in May when weekly flows increased relative to the median flow during a given spawning period. This information has recently been incorporated into the development of targeted environmental flows to facilitate migration and spawning by Australian grayling in the Bunyip-Tarago river system and other coastal systems in Victoria.
Assuntos
Migração Animal , Conservação dos Recursos Naturais/métodos , Rios , Salmonidae , Comportamento Sexual Animal , Movimentos da Água , Animais , Austrália , Ecossistema , Monitoramento Ambiental/métodos , HidrologiaRESUMO
Background and Objectives: Serratia marcescens is an emerging nosocomial pathogen, and the carbapenemase blaNDM has been reported in several surveys in Romania. We aimed to investigate the molecular epidemiology of S. marcescens in two Romanian hospitals over 2010-15, including a neonatal NDM-1 S. marcescens outbreak. Methods: Isolates were sequenced using Illumina technology together with carbapenem-non-susceptible NDM-1-positive and NDM-1-negative Klebsiella pneumoniae and Enterobacter cloacae to provide genomic context. A subset was sequenced with MinION to fully resolve NDM-1 plasmid structures. Resistance genes, plasmid replicons and ISs were identified in silico for all isolates; an annotated phylogeny was reconstructed for S. marcescens. Fully resolved study NDM-1 plasmid sequences were compared with the most closely related publicly available NDM-1 plasmid reference. Results: 44/45 isolates were successfully sequenced (S. marcescens, n = 33; K. pneumoniae, n = 7; E. cloacae, n = 4); 10 with MinION. The S. marcescens phylogeny demonstrated several discrete clusters of NDM-1-positive and -negative isolates. All NDM-1-positive isolates across species harboured a pKOX_NDM1-like plasmid; more detailed comparisons of the plasmid structures demonstrated a number of differences, but highlighted the largely conserved plasmid backbones across species and hospital sites. Conclusions: The molecular epidemiology is most consistent with the importation of a pKOX_NDM1-like plasmid into Romania and its dissemination amongst K. pneumoniae/E. cloacae and subsequently S. marcescens across hospitals. The data suggested multiple acquisitions of this plasmid by S. marcescens in the two hospitals studied; transmission events within centres, including a large outbreak on the Targu Mures neonatal unit; and sharing of the pKOX_NDM1-like plasmid between species within outbreaks.
Assuntos
Genoma Bacteriano , Infecções por Serratia/epidemiologia , Serratia marcescens/genética , beta-Lactamases/genética , DNA Bacteriano/genética , Surtos de Doenças , Enterobacteriaceae/genética , Infecções por Enterobacteriaceae/epidemiologia , Fezes/microbiologia , Transferência Genética Horizontal , Hospitais , Humanos , Infecções por Klebsiella/epidemiologia , Klebsiella pneumoniae/genética , Plasmídeos/genética , Romênia/epidemiologia , Análise de Sequência de DNA , Serratia marcescens/enzimologia , Sequenciamento Completo do Genoma/métodos , beta-Lactamases/biossínteseRESUMO
The bacterium Edwardsiella ictaluri is considered to be one of the most significant pathogens of farmed catfish in the United States of America and has also caused mortalities in farmed and wild fishes in many other parts of the world. E. ictaluri is not believed to be present in wild fish populations in Australia, although it has previously been detected in imported ornamental fishes held in quarantine facilities. In an attempt to confirm freedom from the bacterium in Australian native fishes, we undertook a risk-based survey of wild catfishes from 15 sites across northern Australia. E. ictaluri was detected by selective culturing, followed by DNA testing, in Wet Tropics tandan (Tandanus tropicanus) from the Tully River, at a prevalence of 0.40 (95% CI 0.21-0.61). The bacterium was not found in fishes sampled from any of the other 14 sites. This is the first report of E. ictaluri in wild fishes in Australia.