RESUMO
BACKGROUND: Patients with prolonged hospitalisation have a significant risk of carriage of and subsequent infection with extended spectrum ß-lactamase (ESBL)-producing and carbapenemase-producing Klebsiella pneumoniae. However, the distinctive roles of the community and hospital environments in the transmission of ESBL-producing or carbapenemase-producing K pneumoniae remain elusive. We aimed to investigate the prevalence and transmission of K pneumoniae within and between the two tertiary hospitals in Hanoi, Viet Nam, using whole-genome sequencing. METHODS: We did a prospective cohort study of 69 patients in intensive care units (ICUs) from two hospitals in Hanoi, Viet Nam. Patients were included if they were aged 18 years or older, admitted for longer than the mean length of stay in their ICU, and cultured K pneumoniae from their clinical samples. Longitudinally collected samples from patients (collected weekly) and the ICU environment (collected monthly) were cultured on selective media, and whole-genome sequences from K pneumoniae colonies analysed. We did phylogenetic analyses and correlated phenotypic antimicrobial susceptibility testing with genotypic features of K pneumoniae isolates. We constructed transmission networks of patient samples, relating ICU admission times and locations with genetic similarity of infecting K pneumoniae. FINDINGS: Between June 1, 2017, and Jan 31, 2018, 69 patients were in the ICUs and eligible for inclusion, and a total of 357 K pneumoniae isolates were cultured and successfully sequenced. 228 (64%) of K pneumoniae isolates carried between two and four different ESBL-encoding and carbapenemase-encoding genes, with 164 (46%) isolates carrying genes encoding both, with high minimum inhibitory concentrations. We found a novel co-occurrence of blaKPC-2 and blaNDM-1 in 46·6% of samples from the globally successful ST15 lineage. Despite being physically and clinically separated, the two hospitals shared closely related strains carrying the same array of antimicrobial resistance genes. INTERPRETATION: These results highlight the high prevalence of ESBL-positive carbapenem-resistant K pneumoniae in ICUs in Viet Nam. Through studying K pneumoniae ST15 in detail, we showed how important resistance genes are contained within these strains that are carried broadly by patients entering the two hospitals directly or through referral. FUNDING: Medical Research Council Newton Fund, Ministry of Science and Technology, Wellcome Trust, Academy of Medical Sciences, Health Foundation, and National Institute for Health and Care Research Cambridge Biomedical Research Centre.
Assuntos
Klebsiella pneumoniae , Humanos , Klebsiella pneumoniae/genética , Vietnã/epidemiologia , Estudos Prospectivos , Filogenia , Centros de Atenção TerciáriaRESUMO
BACKGROUND: Viet Nam has high rates of antimicrobial resistance (AMR) but little capacity for genomic surveillance. This study used whole genome sequencing to examine the prevalence and transmission of three key AMR pathogens in two intensive care units (ICUs) in Hanoi, Viet Nam. METHODS: A prospective surveillance study of all adults admitted to ICUs at the National Hospital for Tropical Diseases and Bach Mai Hospital was done between June 19, 2017, and Jan 16, 2018. Clinical and environmental samples were cultured on selective media, characterised with MALDI TOF mass spectrometry, and sequenced with Illumina. Phylogenies based on the de-novo assemblies (SPAdes) were constructed with MAFFT (PARsnp), Gubbins, and RAxML. Resistance genes were detected with Abricate against the US National Center for Biotechnology Information database. FINDINGS: 3153 Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii isolates from 369 patients were analysed. Phylogenetic analysis revealed predominant lineages within A baumannii (global clone 2, sequence types ST2 and ST571) and K pneumoniae (ST15, ST16, ST656, ST11, and ST147) isolates. Isolation from stool was most common with E coli (87·0%) followed by K pneumoniae (62·5%). Of the E coli, 85·0% carried a blaCTX-M variant, while 81·8% of K pneumoniae isolates carried blaNDM (54·4%), or blaKPC (45·1%), or both. Transmission analysis with single nucleotide polymorphisms identified 167 clusters involving 251 (68%) of 369 patients, in some cases involving patients from both ICUs. There were no clear differences between the lineages or AMR genes recovered between the two ICUs. INTERPRETATION: This study represents the largest prospective surveillance study of key AMR pathogens in Vietnamese ICUs. Clusters of closely related isolates in patients across both ICUs suggests recent transmission before ICU admission in other health-care settings or in the community. FUNDING: UK Medical Research Council Newton Fund, Viet Nam Ministry of Science and Technology, Wellcome Trust, Academy of Medical Sciences, Health Foundation, and UK National Institute for Health and Care Research Cambridge Biomedical Research Centre.
Assuntos
Acinetobacter baumannii , Infecção Hospitalar , Adulto , Humanos , Klebsiella pneumoniae/genética , Acinetobacter baumannii/genética , Escherichia coli/genética , Filogenia , Estudos Prospectivos , Vietnã/epidemiologia , Testes de Sensibilidade Microbiana , Infecção Hospitalar/epidemiologia , Unidades de Terapia Intensiva , GenômicaRESUMO
The significant bottlenecks in determining bacterial species are much more time-consuming and the biology specialist's long-term experience requirements. Specifically, it takes more than half a day to cultivate a bacterium, and then a skilled microbiologist and a costly specialized machine are utilized to analyze the genes and classify the bacterium according to its nucleotide sequence. To overcome these issues as well as get higher recognition accuracy, we proposed applying convolutional neural networks (CNNs) architectures to automatically classify bacterial species based on some key characteristics of bacterial colonies. Our experiment confirmed that the classification of three bacterial colonies could be performed with the highest accuracy (97.19%) using a training set of 5000 augmented images derived from the 40 original photos taken in the Hanoi Medical University laboratory in Vietnam.
Assuntos
Aprendizado Profundo , Bactérias , Humanos , Redes Neurais de Computação , VietnãRESUMO
In Vietnam, the public health burden of rickettsial infections continues to be underestimated due to knowledge gaps in the epidemiology of these diseases. We conducted a systematic study among 27 hospitals from 26 provinces in eight ecological regions throughout Vietnam to investigate the prevalence, distribution, and clinical characteristics of rickettsial diseases. We recruited 1834 patients in the study from April 2018 to October 2019. The findings showed that rickettsial diseases were common among undifferentiated febrile patients, with 564 (30.8%) patients positive by qPCR for scrub typhus, murine typhus or spotted fever. Scrub typhus (484, 85.8%) was the most common rickettsial disease, followed by murine typhus (67, 11.9%) and spotted fever (10, 1.8%). Rickettsial diseases were widely distributed in all regions of Vietnam and presented with nonspecific clinical manifestations.
RESUMO
Scrub typhus has been documented since 1932 in Vietnam, however, the disease burden of scrub typhus remains poorly understood in the country. We conducted this study to describe the phylogenetic analysis of the 56-kDa type-specific antigen (TSA) gene of Orientia tsutsugamushi associated with PCR positive cases of scrub typhus. Of 116 positive samples, 65 type-specific antigen gene sequences were obtained and classified into 3 genogroups: Karp, Kato and Gilliam. The Karp genogroup was the most frequently detected phylogenetic cluster in the study with 30 samples (46%), followed by Kato and Gilliam with 20 (31%) and 15 (23%), respectively. All sequences showed 94-100% nucleotide similarity to reference sequences collected in the central part of Vietnam in 2017. Patients infected with Karp genogroup were more likely to have significant thrombocytopenia than the other genogroups. These results suggest that any scrub typhus vaccine considered for use in Vietnam should provide protection against each of these 3 genogroups.
Assuntos
Antígenos de Bactérias/genética , Proteínas de Bactérias/genética , Orientia tsutsugamushi/genética , Tifo por Ácaros/microbiologia , Antígenos de Bactérias/química , Antígenos de Bactérias/imunologia , Proteínas de Bactérias/química , Proteínas de Bactérias/imunologia , Genótipo , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Tipagem Molecular , Peso Molecular , Orientia tsutsugamushi/classificação , Orientia tsutsugamushi/imunologia , Filogenia , Filogeografia , Prevalência , Tifo por Ácaros/diagnóstico , Tifo por Ácaros/epidemiologia , Tifo por Ácaros/imunologia , Análise de Sequência de DNA , Índice de Gravidade de Doença , VietnãRESUMO
OBJECTIVES: We assessed the impact of MALDITOF-MS on the timeliness of optimal antimicrobial therapy through a parallel-arm randomised controlled trial in two hospitals in Vietnam. METHODS: We recruited patients with a pathogen (bacterial or fungal) cultured from a normally sterile sample. Samples were randomly assigned (1:1) to identification by MALDITOF-MS or conventional diagnostics. The primary outcome was the proportion on optimal antimicrobial therapy within 24â¯h of positive culture, determined by a blinded independent review committee. Trial registered at ClinicalTrials.gov (NCT02306330). RESULTS: Among 1005 randomised patients, pathogens were isolated from 628 (326 intervention, 302 control), with 377 excluded as likely contaminants or discharged/died before positive culture. Most isolates were cultured from blood (421/628, 67.0%). The proportion receiving optimal antimicrobial therapy within 24â¯h (the primary outcome) or 48â¯h of growth was not significantly different between MALDITOF-MS and control arms (135/326, 41.4%â¯vs 120/302, 39.7%; Adjusted Odds ration (AOR) 1.17, pâ¯=â¯0.40 and 151/326, 46.3%â¯vs 141/302, 46.7%; AOR 1.05 pâ¯=â¯0.79, respectively). CONCLUSIONS: MALDITOF-MS, in the absence of an antimicrobial stewardship programme, did not improve the proportion on optimal antimicrobial therapy at 24 or 48â¯h after first growth in a lower-middle income setting with high rates of antibiotic resistance.
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Bacteriemia/tratamento farmacológico , Bactérias/isolamento & purificação , Fungos/isolamento & purificação , Técnicas Microbiológicas , Micoses/tratamento farmacológico , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Adulto , Antibacterianos/uso terapêutico , Antifúngicos/uso terapêutico , Bacteriemia/diagnóstico , Bacteriemia/microbiologia , Bactérias/efeitos dos fármacos , Feminino , Fungos/efeitos dos fármacos , Humanos , Masculino , Pessoa de Meia-Idade , Micoses/diagnóstico , Micoses/microbiologia , Estudos Prospectivos , Fatores de Tempo , Resultado do Tratamento , VietnãRESUMO
Rickettsioses are endemic to Vietnam; however, only a limited number of clinical studies have been performed on these vectorborne bacteria. We conducted a prospective hospital-based study at 2 national referral hospitals in Hanoi to describe the clinical characteristics of scrub typhus and murine typhus in northern Vietnam and to assess the diagnostic applicability of quantitative real-time PCR assays to diagnose rickettsial diseases. We enrolled 302 patients with acute undifferentiated fever and clinically suspected rickettsiosis during March 2015-March 2017. We used a standardized case report form to collect clinical information and laboratory results at the time of admission and during treatment. We confirmed scrub typhus in 103 (34.1%) patients and murine typhus in 12 (3.3%) patients. These results highlight the need for increased emphasis on training for healthcare providers for earlier recognition, prevention, and treatment of rickettsial diseases in Vietnam.
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Tifo por Ácaros/diagnóstico , Tifo por Ácaros/fisiopatologia , Tifo Endêmico Transmitido por Pulgas/diagnóstico , Tifo Endêmico Transmitido por Pulgas/fisiopatologia , Adulto , Diagnóstico Precoce , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Patologia Molecular , Estudos Prospectivos , Tifo por Ácaros/epidemiologia , Sorotipagem , Tifo Endêmico Transmitido por Pulgas/epidemiologia , VietnãAssuntos
Dengue/prevenção & controle , Surtos de Doenças/estatística & dados numéricos , Programas de Rastreamento/instrumentação , Programas de Rastreamento/métodos , Radar , Dengue/diagnóstico , Dengue/epidemiologia , Dengue/virologia , Surtos de Doenças/prevenção & controle , Febre/diagnóstico , Recursos em Saúde , Humanos , Sepse/epidemiologia , Vietnã/epidemiologiaRESUMO
AbstractRickettsial infections are recognized as important causes of fever throughout southeast Asia. Herein, we determined the seroprevalence to rickettsioses within rural and urban populations of northern Vietnam. Prevalence of individuals with evidence of prior rickettsial infections (IgG positive) was surprisingly low, with 9.14% (83/908) testing positive to the three major rickettsial serogroups thought to circulate in the region. Prevalence of typhus group rickettsiae (TG)-specific antibodies (6.5%, 58/908) was significantly greater than scrub typhus group orientiae (STG)- or spotted fever group rickettsiae (SFG)-specific antibodies (P < 0.05). The majority of TG seropositives were observed among urban rather than rural residents (P < 0.05). In contrast, overall antibody prevalence to STG and SFG were both very low (1.1%, 10/908 for STG; 1.7%, 15/908 for SFG), with no significant differences between rural and urban residents. These results provide data on baseline population characteristics that may help inform development of Rickettsia serological testing criteria in future clinical studies.
Assuntos
Anticorpos Antibacterianos/sangue , Infecções por Rickettsia/epidemiologia , Tifo por Ácaros/epidemiologia , Tifo Epidêmico Transmitido por Piolhos/epidemiologia , Adolescente , Adulto , Criança , Pré-Escolar , Feminino , Humanos , Masculino , Orientia tsutsugamushi/classificação , Orientia tsutsugamushi/isolamento & purificação , Prevalência , Rickettsia/classificação , Rickettsia/isolamento & purificação , Infecções por Rickettsia/sangue , Infecções por Rickettsia/diagnóstico , Rickettsia prowazekii/classificação , Rickettsia prowazekii/isolamento & purificação , População Rural , Tifo por Ácaros/sangue , Tifo por Ácaros/diagnóstico , Estudos Soroepidemiológicos , Sorotipagem , Tifo Epidêmico Transmitido por Piolhos/sangue , Tifo Epidêmico Transmitido por Piolhos/diagnóstico , População Urbana , Vietnã/epidemiologiaRESUMO
BACKGROUND: Enterovirus 71 subgenogroup C4 caused the largest outbreak of Hand, Foot and Mouth Disease (HFMD) in Vietnam during 2011-2012, resulting in over 200,000 hospitalisations and 207 fatalities. METHODS: A total of 1917 samples with adequate volume for RT-PCR analysis were collected from patients hospitalised with HFMD throughout Vietnam and 637 were positive for EV71. VP1 gene (n=87) and complete genome (n=9) sequencing was performed. Maximum-likelihood phylogenetic analysis was performed to characterise the B5, C4 and C5 strains detected. RESULTS: Sequence analyses revealed that the dominant subgenogroup associated with the 2012 outbreak was C4, with B5 and C5 strains representing a small proportion of these cases. CONCLUSIONS: Numerous countries in the region including Malaysia, Taiwan and China have a large influence on strain diversity in Vietnam and understanding the transmission of EV71 throughout Southeast Asia is vital to inform preventative public health measures and vaccine development efforts.
Assuntos
Enterovirus Humano A/classificação , Enterovirus Humano A/genética , Infecções por Enterovirus/epidemiologia , Infecções por Enterovirus/virologia , Genótipo , Distribuição por Idade , Proteínas do Capsídeo/genética , Criança , Pré-Escolar , Surtos de Doenças , Infecções por Enterovirus/história , Genoma Viral , Geografia Médica , Doença de Mão, Pé e Boca/epidemiologia , Doença de Mão, Pé e Boca/virologia , História do Século XXI , Hospitalização , Humanos , Lactente , Filogenia , Estações do Ano , Vietnã/epidemiologiaRESUMO
The glucose and nitrogen starvation stimulons of Bacillus licheniformis were determined by transcriptome and proteome analyses. Under both starvation conditions, the main response of B. licheniformis was a switch to the usage of alternative nutrient sources. This was indicated by an induction of genes involved in the metabolism of C-2 substrates during glucose limitation. In addition, B. licheniformis seems to be using other organic substances like amino acids and lipids as carbon sources when subjected to glucose starvation. This observation is supported by the induction of a high number of genes coding for proteins involved in amino acid and lipid degradation. During nitrogen starvation, genes for several proteases and peptidases involved in nitrate and nitrite assimilation were induced, which enables this bacterium to recruit nitrogen from alternative sources. Both starvation conditions led to a down-regulation of transcription of most vegetative genes, which was subsequently reflected by a reduced synthesis of the corresponding proteins. A selected set of genes was induced by both starvation conditions. Among them were yvyD, citA and the putative methylcitrate shunt genes mmgD, mmgE and yqiQ. However, both starvation conditions did not induce a general SigmaB-dependent stress response.
Assuntos
Bacillus/metabolismo , Glucose/deficiência , Nitrogênio/deficiência , Proteoma/metabolismo , Glucose/metabolismo , Nitrogênio/metabolismoRESUMO
The phosphate-starvation stimulon of Bacillus licheniformis was analyzed at the transcriptional and translational level. The comparison of the transcriptome and the proteome demonstrated that this specific starvation response of B. licheniformis is partially similar to that of B. subtilis. However, it is also shown that B. licheniformis has evolved its own strategies to cope with this nutrient limitation. By means of the secretome analysis the phytase was identified as the most abundant protein under phosphate-starvation conditions. Data of this study indicate that, unlike in B. subtilis, phosphate starvation in B. licheniformis does not induce the SigmaB-dependent general stress response.