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1.
BMC Microbiol ; 21(1): 277, 2021 10 11.
Artigo em Inglês | MEDLINE | ID: mdl-34635053

RESUMO

BACKGROUND: Fusobacterium nucleatum (F. n) is an important opportunistic pathogen causing oral and gastrointestinal disease. Faecalibacterium prausnitzii (F. p) is a next-generation probiotic and could serve as a biomarker of gut eubiosis/dysbiosis to some extent. Alterations in the human oral and gut microbiomes are associated with viral respiratory infection. The aim of this study was to characterise the oral and fecal bacterial biomarker (i.e., F. n and F. p) in COVID-19 patients by qPCR and investigate the pharyngeal microbiome of COVID-19 patients through metagenomic next-generation sequencing (mNGS). RESULTS: Pharyngeal F. n was significantly increased in COVID-19 patients, and it was higher in male than female patients. Increased abundance of pharyngeal F. n was associated with a higher risk of a positive SARS-CoV-2 test (adjusted OR = 1.32, 95% CI = 1.06 ~ 1.65, P < 0.05). A classifier to distinguish COVID-19 patients from the healthy controls based on the pharyngeal F. n was constructed and achieved an area under the curve (AUC) of 0.843 (95% CI = 0.688 ~ 0.940, P < 0.001). However, the level of fecal F. n and fecal F. p remained unaltered between groups. Besides, mNGS showed that the pharyngeal swabs of COVID-19 patients were dominated by opportunistic pathogens. CONCLUSIONS: Pharyngeal but not fecal F. n was significantly increased in COVID-19 patients, clinicians should pay careful attention to potential coinfection. Pharyngeal F. n may serve as a promising candidate indicator for COVID-19.


Assuntos
COVID-19/microbiologia , Fezes/microbiologia , Infecções por Fusobacterium/microbiologia , Fusobacterium nucleatum/genética , Faringe/microbiologia , Adulto , Biomarcadores/análise , COVID-19/virologia , Portador Sadio/microbiologia , Coinfecção/microbiologia , Coinfecção/virologia , Disbiose , Feminino , Infecções por Fusobacterium/virologia , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , Metagenômica , Microbiota , Pessoa de Meia-Idade , Faringe/virologia , Fatores Sexuais
2.
Elife ; 102021 09 13.
Artigo em Inglês | MEDLINE | ID: mdl-34515028

RESUMO

Background: Understanding the dynamics of infection and carriage of typhoid in endemic settings is critical to finding solutions to prevention and control. Methods: In a 3-year case-control study, we investigated typhoid among children aged <16 years (4670 febrile cases and 8549 age matched controls) living in an informal settlement, Nairobi, Kenya. Results: 148 S. Typhi isolates from cases and 95 from controls (stool culture) were identified; a carriage frequency of 1 %. Whole-genome sequencing showed 97% of cases and 88% of controls were genotype 4.3.1 (Haplotype 58), with the majority of each (76% and 88%) being multidrug-resistant strains in three sublineages of the H58 genotype (East Africa 1 (EA1), EA2, and EA3), with sequences from cases and carriers intermingled. Conclusions: The high rate of multidrug-resistant H58 S. Typhi, and the close phylogenetic relationships between cases and controls, provides evidence for the role of carriers as a reservoir for the community spread of typhoid in this setting. Funding: National Institutes of Health (R01AI099525); Wellcome Trust (106158/Z/14/Z); European Commission (TyphiNET No 845681); National Institute for Health Research (NIHR); Bill and Melinda Gates Foundation (OPP1175797).


Assuntos
Antibacterianos/farmacologia , Portador Sadio/microbiologia , Farmacorresistência Bacteriana Múltipla , Salmonella typhi/efeitos dos fármacos , Febre Tifoide/microbiologia , Adolescente , Estudos de Casos e Controles , Criança , Pré-Escolar , Feminino , Humanos , Lactente , Quênia/epidemiologia , Masculino , Filogenia , Salmonella typhi/classificação , Salmonella typhi/genética , Salmonella typhi/isolamento & purificação , Febre Tifoide/tratamento farmacológico , Febre Tifoide/epidemiologia
3.
J Med Microbiol ; 70(8)2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34402781

RESUMO

A previous study conducted in Gabon, Central Africa, in 2010/11 found a high colonization rate with extended-spectrum ß-lactamase-producing enterobacterales (ESBL-E) among children of ~34 %. Eight years later, we aimed to reassess the ESBL-E rate and previously identified risk factors for colonization in children from Gabon. We conducted a cross-sectional cohort study in 2018 on 92 outpatients under 5 years of age with diarrhoea in Lambaréné, Gabon, in whom a rectal swab was obtained at the initial medical encounter (baseline). Fifty-eight of these provided a further rectal swab 1 week afterwards. ESBL-E colonization was assessed [following the European Committee on Antimicrobial Susceptibility Testing (EUCAST)], and in confirmed ESBL-E isolates the susceptibility to meropenem and the prevalence of the most abundant ESBL genes, bla CTX-M, bla SHV, and bla TEM, were investigated. At baseline, the ESBL-E colonization rate was 57 % (52/92; 95 % CI: 46-67). Hospitalization during the previous year, chicken consumption in the past week and young age were identified as independent risk factors for ESBL-E colonization at baseline. On day 7, the ESBL-E carriage rate was 72 % (42/58; 95 % CI: 59-83). All ESBL-E isolates (n=293) were susceptible to meropenem and bla CTX-M was the most frequently detected ß-lactamase gene. The ESBL-E colonization rate among children from Gabon is alarmingly high, with indications of further increase over recent years. While all ESBL-E strains remain currently susceptible to meropenem, in practice no adequate treatment is available locally for severe infections with such isolates. It is thus of the utmost importance to invest in improved hospital infection prevention and control measures to combat ESBL-E effectively.


Assuntos
Enterobacteriáceas Resistentes a Carbapenêmicos/fisiologia , Portador Sadio/microbiologia , Infecções por Escherichia coli/epidemiologia , Infecções por Escherichia coli/microbiologia , Criança , Estudos Transversais , Gabão/epidemiologia , Humanos , Vigilância em Saúde Pública
4.
BMC Infect Dis ; 21(1): 661, 2021 Jul 08.
Artigo em Inglês | MEDLINE | ID: mdl-34233627

RESUMO

BACKGROUND: Pneumococcal vaccine immunizations may be responsible for alterations in serotype epidemiology within a region. This study investigated the pneumococcal carriage prevalence and the impact of the 13-valent pneumococcal conjugate vaccine (PCV-13) on circulating serotypes among healthy children in Northern Ghana. METHODS: This was a cross sectional study conducted in the Kassena-Nankana districts of Northern Ghana from November to December during the dry season of 2018. Nasopharyngeal swabs collected from 193 participants were cultured per standard microbiological protocols and pneumococcal isolates were serotyped using the latex agglutination technique and the capsular Quellung reaction test. We examined for any association between the demographic characteristics of study participants and pneumococcal carriage using chi-square test and logistic regression. RESULTS: Of the 193 participants that were enrolled the mean age was 8.6 years and 54.4% were females. The carriage rate among the participants was 32.6% (63/193), and twenty different serotypes were identified. These included both vaccine serotypes (VT), 35% (7/20) and non-vaccine serotypes (NVT), 65% (13/20). The predominant serotypes (34 and 11A), both of which were NVT, accounted for a prevalence of 12.8%. PCV-13 covered only 35% of serotypes identified whiles 40% of serotypes are covered by PPV 23. CONCLUSION: Post-vaccination carriage of S. pneumoniae is high and is dominated by non-vaccine serotypes. There is therefore a need for the conduct of invasive pneumococcal disease surveillance (IPD) to find out if the high non-vaccine serotype carriage translates to disease. And in addition, a review of the currently used PCV-13 vaccine in the country would be considered relevant.


Assuntos
Portador Sadio/epidemiologia , Nasofaringe/microbiologia , Infecções Pneumocócicas/diagnóstico , Vacinas Pneumocócicas/administração & dosagem , Streptococcus pneumoniae/isolamento & purificação , Portador Sadio/microbiologia , Criança , Pré-Escolar , Estudos Transversais , Feminino , Gana/epidemiologia , Humanos , Lactente , Testes de Fixação do Látex , Masculino , Infecções Pneumocócicas/epidemiologia , Vacinas Pneumocócicas/imunologia , Prevalência , Sorogrupo , Streptococcus pneumoniae/imunologia , Vacinação
5.
PLoS One ; 16(7): e0253781, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34242263

RESUMO

BACKGROUND: Up to 15% of deaths of people living with HIV is attributable to meningeal cryptococcosis, with nearly 75% occuring in sub-Saharan Africa. Although rare in children, it is a major cause of morbidity and mortality in people living with HIV. A strong association between cryptococcal antigenemia and the development of meningeal cryptococcosis has been shown in adults. Thus, in 2018, the World Health Organization published an updated version of its guidelines for the diagnosis, prevention and management of cryptococcal infection in adults, adolescents and the HIV-infected child. GOAL: To determine the prevalence of cryptococcal antigenemia and to identify its determinants in children infected with HIV. METHODS: An analytical cross-sectional study was carried out at the approved treatment center of Laquintinie hospital in Douala over a period of 4 months. Children were recruited consecutively after informed parental consent. Cryptococcal antigenemia and CD4 assay were performed using a Cryptops® immunochromatographic rapid diagnostic test and flow cytometry, respectively. The data collected included the socio-demographic, clinical and paraclinical variables of the children, as well as their antecedents. Data analysis was performed using Epiinfo software version 3.1 and SPSS 21.0. The significance threshold was set at 5%. RESULTS: A total of 147 children were enrolled. The mean age was 9.8 ± 4.09 years. The majority were on antiretroviral therapy (142, 96.60%). Only 13 (8.80%) were in severe immunosuppression. No child showed signs of meningeal cryptococcosis. The prevalence of cryptococcal antigenemia was 6.12%. Severe immunosuppression [OR: 10.03 (1.52-65.91), p = 0.016] and contact with pigeons [OR: 9.76 (1.14-83.65), p = 0.037] were independent factors significantly associated with the carriage of the cryptococcal antigen. CONCLUSION: We recommend screening for cryptococcal antigenemia and routine treatment with fluconazole of all HIV positive children with cryptococcal antigen whether symptomatic or not.


Assuntos
Infecções Oportunistas Relacionadas com a AIDS/epidemiologia , Antígenos de Fungos/sangue , Portador Sadio/epidemiologia , Criptococose/epidemiologia , Cryptococcus/isolamento & purificação , Infecções Oportunistas Relacionadas com a AIDS/sangue , Infecções Oportunistas Relacionadas com a AIDS/imunologia , Infecções Oportunistas Relacionadas com a AIDS/microbiologia , Adolescente , Antígenos de Fungos/imunologia , Camarões/epidemiologia , Portador Sadio/sangue , Portador Sadio/imunologia , Portador Sadio/microbiologia , Criança , Pré-Escolar , Estudos Transversais , Criptococose/sangue , Criptococose/imunologia , Criptococose/microbiologia , Cryptococcus/imunologia , Feminino , Humanos , Lactente , Masculino , Prevalência
6.
PLoS One ; 16(6): e0252804, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34125848

RESUMO

Streptococcus equi subsp. equi (SEE) is a host-restricted bacterium that causes the common infectious upper respiratory disease known as strangles in horses. Perpetuation of SEE infection appears attributable to inapparent carrier horses because it neither persists long-term in the environment nor infects other host mammals or vectors, and infection results in short-lived immunity. Whether pathogen factors enable SEE to remain in horses without causing clinical signs remains poorly understood. Thus, our objective was to use next-generation sequencing technologies to characterize the genome, methylome, and transcriptome of isolates of SEE from horses with acute clinical strangles and inapparent carrier horses-including isolates recovered from individual horses sampled repeatedly-to assess pathogen-associated changes that might reflect specific adaptions of SEE to the host that contribute to inapparent carriage. The accessory genome elements and methylome of SEE isolates from Sweden and Pennsylvania revealed no significant or consistent differences between acute clinical and inapparent carrier isolates of SEE. RNA sequencing of SEE isolates from Pennsylvania demonstrated no genes that were differentially expressed between acute clinical and inapparent carrier isolates of SEE. The absence of specific, consistent changes in the accessory genomes, methylomes, and transcriptomes of acute clinical and inapparent carrier isolates of SEE indicates that adaptations of SEE to the host are unlikely to explain the carrier state of SEE. Efforts to understand the carrier state of SEE should instead focus on host factors.


Assuntos
Portador Sadio/diagnóstico , Epigenoma/genética , Genoma/genética , Doenças dos Cavalos/diagnóstico , Streptococcus/genética , Transcriptoma/genética , Animais , Portador Sadio/microbiologia , DNA Bacteriano/análise , DNA Bacteriano/genética , DNA Bacteriano/isolamento & purificação , Diagnóstico Diferencial , Surtos de Doenças , Doenças dos Cavalos/epidemiologia , Doenças dos Cavalos/microbiologia , Cavalos , Pennsylvania/epidemiologia , RNA Bacteriano/análise , RNA Bacteriano/genética , RNA Bacteriano/isolamento & purificação , RNA-Seq/métodos , Especificidade da Espécie , Streptococcus/classificação , Streptococcus/fisiologia , Suécia/epidemiologia , Sequenciamento Completo do Genoma/métodos
7.
Gut Microbes ; 13(1): 1-18, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34132169

RESUMO

Clostridioides difficile (C. difficile) infection is the most common cause of healthcare-associated infection and an important cause of morbidity and mortality among hospitalized patients. A comprehensive understanding of C. difficile infection (CDI) pathogenesis is crucial for disease diagnosis, treatment, and prevention. Here, we characterized gut microbial compositions and a broad panel of innate and adaptive immunological markers in 243 well-characterized human subjects (including 187 subjects with both microbiota and immune marker data), who were divided into four phenotype groups: CDI, Asymptomatic Carriage, Non-CDI Diarrhea, and Control. We found that the interactions between gut microbiota and host immune markers are very sensitive to the status of C. difficile colonization and infection. We demonstrated that incorporating both gut microbiome and host immune marker data into classification models can better distinguish CDI from other groups than can either type of data alone. Our classification models display robust diagnostic performance to differentiate CDI from Asymptomatic carriage (AUC~0.916), Non-CDI Diarrhea (AUC~0.917), or Non-CDI that combines all other three groups (AUC~0.929). Finally, we performed symbolic classification using selected features to derive simple mathematic formulas that explicitly quantify the interactions between the gut microbiome and host immune markers. These findings support the potential roles of gut microbiota and host immune markers in the pathogenesis of CDI. Our study provides new insights for a microbiome-immune marker-derived signature to diagnose CDI and design therapeutic strategies for CDI.


Assuntos
Clostridioides difficile/fisiologia , Infecções por Clostridium/sangue , Microbioma Gastrointestinal , Idoso , Biomarcadores/sangue , Portador Sadio/sangue , Portador Sadio/microbiologia , Clostridioides difficile/genética , Clostridioides difficile/patogenicidade , Infecções por Clostridium/microbiologia , Estudos de Coortes , Citocinas/sangue , Fezes/microbiologia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade
8.
PLoS One ; 16(6): e0253739, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34191834

RESUMO

Methicillin-resistant Staphylococcus aureus (MRSA) has long been known as a major cause of hospital-acquired (HA-MRSA) infections worldwide. For the past twenty years, an increasing number of studies have described its emergence in the community as well. In Portugal, a country with a high-prevalence of HA-MRSA, there are only limited data available on the epidemiology of MRSA in the community. We studied the prevalence of S. aureus and MRSA colonization among healthy adults in Portugal. Between February 2015 and December 2016, a longitudinal study was conducted in which 87 adults aged 25-50 years old were followed for six months. For each participant nasopharyngeal, oropharyngeal and saliva samples were obtained monthly and, in some cases, weekly. A total of 1,578 samples (n = 526 for each sampling site) were examined for the presence of S. aureus and MRSA by classical culture-based methods. Fifty-seven adults (65.5%) carried S. aureus at least once during the six months period of the study: 19.5% were persistent S. aureus carriers and 46.0% were intermittent carriers. Carriage rates per sampling site were 20.5% in nasopharynx, 18.3% in oropharynx, and 13.5% in saliva. Simultaneous screening of the three sampling sites increased detection of S. aureus, which overall occurred in 34.4% of the 526 sampling time-points. No MRSA were isolated. In conclusion, this study adds novel information about the MRSA scenario in the Portuguese community. Our results indicate that, in Portugal, MRSA does not seem to circulate among healthy adults without risk factors and therefore this age group does not constitute, at the current time, a reservoir of MRSA in the community.


Assuntos
Portador Sadio/epidemiologia , Staphylococcus aureus Resistente à Meticilina/isolamento & purificação , Infecções Estafilocócicas/epidemiologia , Adulto , Portador Sadio/diagnóstico , Portador Sadio/microbiologia , Feminino , Humanos , Estudos Longitudinais , Masculino , Pessoa de Meia-Idade , Nasofaringe/microbiologia , Orofaringe/microbiologia , Portugal/epidemiologia , Prevalência , Saliva/microbiologia , Infecções Estafilocócicas/diagnóstico , Infecções Estafilocócicas/microbiologia
9.
mBio ; 12(3)2021 05 18.
Artigo em Inglês | MEDLINE | ID: mdl-34006659

RESUMO

Carriage evaluations were conducted during 2015 to 2016 at two U.S. universities in conjunction with the response to disease outbreaks caused by Neisseria meningitidis serogroup B and at a university where outbreak and response activities had not occurred. All eligible students at the two universities received the serogroup B meningococcal factor H binding protein vaccine (MenB-FHbp); 5.2% of students (181/3,509) at one university received MenB-4C. A total of 1,514 meningococcal carriage isolates were obtained from 8,905 oropharyngeal swabs from 7,001 unique participants. Whole-genome sequencing data were analyzed to understand MenB-FHbp's impact on carriage and antigen genetic diversity and distribution. Of 1,422 isolates from carriers with known vaccination status (726 [51.0%] from MenB-FHbp-vaccinated, 42 [3.0%] from MenB-4C-vaccinated, and 654 [46.0%] from unvaccinated participants), 1,406 (98.9%) had intact fHbp alleles (716 from MenB-FHbp-vaccinated participants). Of 726 isolates from MenB-FHbp-vaccinated participants, 250 (34.4%) harbored FHbp peptides that may be covered by MenB-FHbp. Genogroup B was detected in 122/1,422 (8.6%) and 112/1,422 (7.9%) isolates from MenB-FHbp-vaccinated and unvaccinated participants, respectively. FHbp subfamily and peptide distributions between MenB-FHbp-vaccinated and unvaccinated participants were not statistically different. Eighteen of 161 MenB-FHbp-vaccinated repeat carriers (11.2%) acquired a new strain containing one or more new vaccine antigen peptides during multiple rounds of sample collection, which was not statistically different (P = 0.3176) from the unvaccinated repeat carriers (1/30; 3.3%). Our findings suggest that lack of MenB vaccine impact on carriage was not due to missing the intact fHbp gene; MenB-FHbp did not affect antigen genetic diversity and distribution during the study period.IMPORTANCE The impact of serogroup B meningococcal (MenB) vaccines on carriage is not completely understood. Using whole-genome sequencing data, we assessed the diversity and distribution of MenB vaccine antigens (particularly FHbp) among 1,514 meningococcal carriage isolates recovered from vaccinated and unvaccinated students at three U.S. universities, two of which underwent MenB-FHbp mass vaccination campaigns following meningococcal disease outbreaks. The majority of carriage isolates recovered from participants harbored intact fHbp genes, about half of which were recovered from MenB-FHbp-vaccinated participants. The distribution of vaccine antigen peptides was similar among carriage isolates recovered from vaccinated and unvaccinated participants, and almost all strains recovered from repeat carriers retained the same vaccine antigen profile, suggesting insignificant vaccine selective pressure on the carriage population in these universities.


Assuntos
Antígenos de Bactérias/genética , Proteínas de Bactérias/genética , Portador Sadio/microbiologia , Variação Genética , Infecções Meningocócicas/microbiologia , Neisseria meningitidis Sorogrupo B/genética , Estudantes/estatística & dados numéricos , Universidades , Antígenos de Bactérias/classificação , Portador Sadio/epidemiologia , Surtos de Doenças , Genótipo , Humanos , Infecções Meningocócicas/epidemiologia , Vacinas Meningocócicas/administração & dosagem , Neisseria meningitidis Sorogrupo B/isolamento & purificação , Sorogrupo , Estados Unidos/epidemiologia
10.
mBio ; 12(3)2021 05 18.
Artigo em Inglês | MEDLINE | ID: mdl-34006665

RESUMO

The polysaccharide capsule is a key virulence factor of Streptococcus pneumoniae There are numerous epidemiologically important pneumococcal capsular serotypes, and recent findings have demonstrated that several of them are commonly found among nonpathogenic commensal species. Here, we describe 9 nonpneumococcal strains carrying close homologs of pneumococcal capsular biosynthetic (cps) loci that were discovered during recent pneumococcal carriage studies of adults in the United States and Kenya. Two distinct Streptococcus infantis strains cross-reactive with pneumococcal serotype 4 and carrying cps4-like capsular biosynthetic (cps) loci were recovered. Opsonophagocytic killing assays employing rabbit antisera raised against S. infantis US67cps4 revealed serotype 4-specific killing of both pneumococcal and nonpneumococcal strains. An S. infantis strain and two Streptococcus oralis strains, all carrying cps9A-like loci, were cross-reactive with pneumococcal serogroup 9 strains in immunodiffusion assays. Antiserum raised against S. infantis US64cps9A specifically promoted killing of serotype 9A and 9V pneumococcal strains as well as S. oralis serotype 9A strains. Serotype-specific PCR of oropharyngeal specimens from a recent adult carriage study in the United States indicated that such nonpneumococcal strains were much more common in this population than serotype 4 and serogroup 9 pneumococci. We also describe S. oralis and S. infantis strains expressing serotypes identical or highly related to serotypes 2, 13, and 23A. This study has expanded the known overlap of pneumococcal capsular serotypes with related commensal species. The frequent occurrence of nonpneumococcal strains in the upper respiratory tract that share vaccine and nonvaccine capsular serotypes with pneumococci could affect population immunity to circulating pneumococcal strains.IMPORTANCE The distributions and frequencies of individual pneumococcal capsular serotypes among nonpneumococcal strains in the upper respiratory tract are unknown and potentially affect pneumococcal serotype distributions among the population and immunity to circulating pneumococcal strains. Repeated demonstration that these nonpneumococcal strains expressing so-called pneumococcal serotypes are readily recovered from current carriage specimens is likely to be relevant to pneumococcal epidemiology, niche biology, and even to potential strategies of employing commensal live vaccines. Here, we describe multiple distinct nonpneumococcal counterparts for each of the pneumococcal conjugate vaccine (PCV) serotypes 4 and 9V. Additional data from contemporary commensal isolates expressing serotypes 2, 13, and 23A further demonstrate the ubiquity of such strains. Increased focus upon this serological overlap between S. pneumoniae and its close relatives may eventually prove that most, or possibly all, pneumococcal serotypes have counterparts expressed by the common upper respiratory tract commensal species Streptococcus mitis, Streptococcus oralis, and Streptococcus infantis.


Assuntos
Cápsulas Bacterianas/classificação , Portador Sadio/microbiologia , Sorogrupo , Streptococcus/classificação , Streptococcus/genética , Idoso , Idoso de 80 Anos ou mais , Animais , Cápsulas Bacterianas/genética , Cápsulas Bacterianas/imunologia , Reações Cruzadas/imunologia , Humanos , Coelhos , Streptococcus/imunologia , Streptococcus/isolamento & purificação , Streptococcus pneumoniae/genética , Streptococcus pneumoniae/imunologia , Simbiose , Estados Unidos
11.
Int J Antimicrob Agents ; 57(6): 106340, 2021 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-33857538

RESUMO

OBJECTIVES: In patients with a history of carbapenemase-producing, carbapenem-resistant Enterobacteriaceae (CP-CRE), the need for CP-CRE targeted treatment in subsequent sepsis episodes is unclear. This study aimed to characterise the incidence of subsequent CP-CRE infective episodes in individuals with prior CP-CRE colonisation and/or infection, and identify predictors for these subsequent CP-CRE infections. METHODS: All adult inpatients with CP-CRE detected from any site between June 2012 and May 2014 at a tertiary-care hospital were prospectively followed for two years to assess for any subsequent CP-CRE infections. Potential factors to which patients were exposed during the follow-up period were collected from medical records and analysed. RESULTS: A total of 171 patients were enrolled. Of 151 patients who entered the follow-up period, 16 (10.6%) developed a subsequent CP-CRE infection. The median time to a subsequent infective episode was 24.5 days (12-105 days). The type of carbapenemase was highly conserved within index and subsequent paired episodes (16 of 17 pairs). Patients with first CP-CRE isolated from intra-abdominal or respiratory sources were ≥7 times more likely to develop a subsequent infection, while most rectal carriers remain colonised. For carriers (n = 133), Klebsiella spp. (OR 4.7) and OXA carbapenemase (OR 9.4) were significant predictors of subsequent infection. In patients with initial infection (n = 18), end-stage renal failure requiring dialysis (OR 22.0) was the only predisposing factor. CONCLUSION: The incidence of subsequent infections in patients with prior colonisation was low. Consideration for CP-CRE targeted therapy is recommended in patients on dialysis and previous CP-CRE infections involving the bloodstream and/or respiratory tract.


Assuntos
Antibacterianos/farmacologia , Enterobacteriáceas Resistentes a Carbapenêmicos/efeitos dos fármacos , Enterobacteriáceas Resistentes a Carbapenêmicos/isolamento & purificação , Infecções por Enterobacteriaceae/epidemiologia , Infecções por Enterobacteriaceae/microbiologia , Idoso , Idoso de 80 Anos ou mais , Carbapenêmicos/farmacologia , Portador Sadio/microbiologia , Farmacorresistência Bacteriana , Feminino , Seguimentos , Humanos , Incidência , Infecções Intra-Abdominais/microbiologia , Pulmão/microbiologia , Masculino , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , Estudos Prospectivos , Reto/microbiologia , Recidiva , Fatores de Risco , Singapura/epidemiologia , Pele/microbiologia , Centros de Atenção Terciária , Urina/microbiologia
12.
mBio ; 12(2)2021 04 27.
Artigo em Inglês | MEDLINE | ID: mdl-33906921

RESUMO

Shigellosis is a diarrheal disease caused mainly by Shigella flexneri and Shigella sonnei Infection is thought to be largely self-limiting, with short- to medium-term and serotype-specific immunity provided following clearance. However, cases of men who have sex with men (MSM)-associated shigellosis have been reported where Shigella of the same serotype were serially sampled from individuals between 1 and 1,862 days apart, possibly due to persistent carriage or reinfection with the same serotype. Here, we investigate the accessory genome dynamics of MSM-associated S. flexneri and S. sonnei isolates serially sampled from individual patients at various days apart to shed light on the adaptation of these important pathogens during infection. We find that pairs likely associated with persistent infection/carriage and with a smaller single nucleotide polymorphism (SNP) distance, demonstrated significantly less variation in accessory genome content than pairs likely associated with reinfection, and with a greater SNP distance. We observed antimicrobial resistance acquisition during Shigella carriage, including the gain of an extended-spectrum beta-lactamase gene during carriage. Finally, we explored large chromosomal structural variations and rearrangements in seven (five chronic and two reinfection associated) pairs of S. flexneri 3a isolates from an MSM-associated epidemic sublineage, which revealed variations at several common regions across isolate pairs, mediated by insertion sequence elements and comprising a distinct predicted functional profile. This study provides insight on the variation of accessory genome dynamics and large structural genomic changes in Shigella during persistent infection/carriage. In addition, we have also created a complete reference genome and biobanked isolate of the globally important pathogen, S. flexneri 3a.IMPORTANCE Shigella spp. are Gram-negative bacteria that are the etiological agent of shigellosis, the second most common cause of diarrheal illness among children under the age of five in low-income countries. In high-income countries, shigellosis is also a sexually transmissible disease among men who have sex with men. Within the latter setting, we have captured prolonged and/or recurrent infection with shigellae of the same serotype, challenging the belief that Shigella infection is short lived and providing an early opportunity to study the evolution of the pathogen over the course of infection. Using this recently emerged transmission scenario, we comprehensively characterize the genomic changes that occur over the course of individual infection with Shigella and uncover a distinct functional profile of variable genomic regions, findings that have relevance for other Enterobacteriaceae.


Assuntos
Cromossomos Bacterianos/química , Cromossomos Bacterianos/genética , Disenteria Bacilar/microbiologia , Genoma Bacteriano , Shigella/genética , Antibacterianos/farmacologia , Portador Sadio/microbiologia , Doenças Transmissíveis/microbiologia , Doenças Transmissíveis/transmissão , Diarreia/microbiologia , Farmacorresistência Bacteriana/genética , Disenteria Bacilar/transmissão , Humanos , Shigella/classificação , Shigella/efeitos dos fármacos , Shigella/enzimologia , beta-Lactamases/genética
13.
Clin Microbiol Infect ; 27(7): 968-980, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-33813109

RESUMO

BACKGROUND: Colonization and transmission precede invasive group B streptococcal (GBS) disease. Data on GBS colonization prevalence, detection methods and risk factors for carriage are relevant for vaccine development and to understand GBS pathogenesis. OBJECTIVES: To evaluate GBS colonization prevalence after the first week of life in the healthy non-pregnant population. DATA SOURCES: Pubmed/Medline, Embase, Latin American and Caribbean Health Sciences Literature, World Health Organization Library Information System, and Scopus. Search performed 12 January 2021 with search terms related to 'GBS' and 'colonization, epidemiology, prevalence or screening' without restrictions. STUDY ELIGIBILITY CRITERIA: All studies that reported prevalence of GBS colonization (any site) in the healthy population. PARTICIPANTS: All individuals (>6 days of age), with no indication of pregnancy, invasive disease or severe underlying immunological co-morbidities. METHODS: Logit transformation and a random effects model (DerSimonian and Laird) were used to pool colonization estimates. Subgroup analysis and meta-regression on a priori determined subgroups were performed. RESULTS: We included 98 studies with 43 112 participants. Our search identified 9309 studies of which 8831 were excluded based on title and abstract and 380 after reading the full text. Colonization rates varied considerably between studies (I2 = 97%), which could be partly explained by differences in culture methods (R2 = 27%), culture sites (R2 = 24%), continent (R2 = 10%) and participant's age (R2 = 6%). Higher prevalence was found with selective culture methods (19%, 95% CI 16%-23% versus non-selective methods 8%, 95% CI 6%-9%; p < 0.0001). Colonization rates were highest in rectum (19%, 95% CI 15%-24%), vagina (14%, 95% CI 12%-17%) and urethra (9%, 95% CI 5%-18%). In participants with negative rectal cultures, 7% (95% CI 5%-9%) had GBS cultured from another niche. Colonization prevalence was lower in children (6 months to 16 years; 3%, 95% CI 2%-5%) compared with adults (16%, 95% CI 14%-20%; p < 0.0001). Using selective culture methods in adults resulted in a prevalence of 26% (95% CI 19%-33%) rectal, 21% (95% CI 17%-25%) vaginal and 9% (95% CI 6%-14%) urethral colonization. CONCLUSION: The rectum is the most common body site colonized by GBS. The best approach to screen for any GBS colonization is to screen multiple body sites using selective culture methods.


Assuntos
Portador Sadio/epidemiologia , Portador Sadio/microbiologia , Streptococcus agalactiae/isolamento & purificação , Adolescente , Adulto , Criança , Pré-Escolar , Feminino , Humanos , Lactente , Masculino , Pessoa de Meia-Idade , Prevalência , Sorogrupo , Adulto Jovem
14.
Biomed Res Int ; 2021: 4923852, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33816612

RESUMO

Background: Haemophilus influenzae (H. influenzae) strains, which commonly reside as commensals within the human pharynx and can remain as an asymptomatic carrier, but become invasive leading to pneumonia, septic arthritis, or meningitis. The Pentavac (pentavalent vaccine, manufactured by India, SII (DTwP-HepB-Hib)) was introduced to the Iranian National Immunization Plan in November 2014. The aim of this study is to investigate H. influenzae type b (Hib) carrier rate among children under 6 years old in Tehran. Methods: This cross-sectional study was performed on 902 children including vaccinated/unvaccinated in the age of 6 months to 6 years, in Tehran. Sampling was performed from July 2019 to September 2019. Nasopharyngeal samples were taken from children by sterile swab. The PCR method was used to extract DNA. Then, all H. influenzae isolates were initially confirmed by molecular tests. BexA was used to distinguish typeable H. influenzae strains from nontypeable Haemophilus influenzae (NTHi). Results: A total of 902 children were enrolled in the study: 452 were female (51%). H. influenzae carriage rate was 267 (29%), of that 150 samples (16.6%) were typeable. The nasopharyngeal Hib carrier rate in the children was 2.6% (24/902). 262 cases did not receive Hib vaccine. Analysis in nonnursery's children aged 4 to 6 (unvaccinated) years showed that the lower educational level of father, mother, and family number correlated with increased odds of colonization of children with Hib. Conclusion: Our findings showed a significant decrease (60%) in the overall Hib nasopharyngeal carriage in healthy children under six years after 5 years after the start of Hib vaccination.


Assuntos
Portador Sadio , Vacina contra Difteria, Tétano e Coqueluche/administração & dosagem , Infecções por Haemophilus , Vacinas Anti-Haemophilus/administração & dosagem , Haemophilus influenzae tipo b/imunologia , Nasofaringe , Vacina Antipólio de Vírus Inativado/administração & dosagem , Vacinação , Portador Sadio/imunologia , Portador Sadio/microbiologia , Portador Sadio/patologia , Portador Sadio/prevenção & controle , Criança , Pré-Escolar , Estudos Transversais , Vacina contra Difteria, Tétano e Coqueluche/imunologia , Feminino , Infecções por Haemophilus/imunologia , Infecções por Haemophilus/patologia , Infecções por Haemophilus/prevenção & controle , Vacinas Anti-Haemophilus/imunologia , Humanos , Lactente , Irã (Geográfico) , Masculino , Nasofaringe/imunologia , Nasofaringe/microbiologia , Vacina Antipólio de Vírus Inativado/imunologia , Vacinas Combinadas/administração & dosagem , Vacinas Combinadas/imunologia
15.
Prev Vet Med ; 190: 105316, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33725561

RESUMO

Faecal carriage of extended-spectrum cephalosporin-resistant Escherichia coli (ESC-R E. coli) in dogs has been reported worldwide and can reduce the effectiveness of treatments against bacterial infections. However, the drivers that influence faecal carriage of ESC-R E. coli in dogs are poorly understood. The aims of this study were to estimate the prevalence of ESC-R E. coli among dogs prior to their admission to a veterinary teaching hospital and to identify risk factors associated with the faecal carriage of ESC-R E. coli. Rectal swabs (n = 130) were collected from dogs and screened for ESC-R E. coli using MacConkey agar supplemented with cefotaxime (2 µg/mL). E. coli species was confirmed by MALDI-TOF and screening of extended-spectrum beta-lactamase (ESBL) genes was conducted by multiplex PCR. Questionnaires were completed by each dog's owner to test several human and dog characteristics associated with ESC-R E. coli. The prevalence of faecal carriage of ESC-R E. coli was 9.2 % and 67 % of ESC-R E. coli isolates harboured ESBL genes including CTX-M alone or in combination with TEM. All ESC-R E. coli isolates were resistant to ceftriaxone, cefpodoxime, and cefotaxime and were susceptible to cefoxitin and carbapenems. The likelihood of carrying ESC-R E. coli was 15 times higher (OR = 14.41 [95 % CI: 1.80-38.02], p < 0.01) if the dog was treated with antibiotics 3-12 months prior to sampling and 8 times higher (OR = 7.96 [95 % CI: 2.96-92.07], p < 0.01) if the dog had direct contact with livestock, but 15 times lower (OR = 0.07 [95 % CI: 0.01-0.32], p < 0.01) if the dog was dewormed during the previous year. Our findings confirm the faecal carriage of ESC-R E. coli in subclinical dogs and call for further investigation regarding the impact of deworming on antibiotic-resistant bacteria in companion animals.


Assuntos
Doenças do Cão , Farmacorresistência Bacteriana , Infecções por Escherichia coli , Animais , Antibacterianos/farmacologia , Brasil/epidemiologia , Portador Sadio/microbiologia , Cefalosporinas/farmacologia , Doenças do Cão/tratamento farmacológico , Doenças do Cão/epidemiologia , Doenças do Cão/microbiologia , Cães , Escherichia coli/efeitos dos fármacos , Infecções por Escherichia coli/tratamento farmacológico , Infecções por Escherichia coli/epidemiologia , Infecções por Escherichia coli/veterinária , Fezes/microbiologia , Hospitais Veterinários , Hospitais de Ensino , Fatores de Risco , beta-Lactamases/genética
16.
Artigo em Inglês | MEDLINE | ID: mdl-33656137

RESUMO

Nasal carriage of Staphylococcus aureus by healthcare workers is of great clinical importance as it facilitates the contamination of medical devices and cross-transmission. However, studies regarding the epidemiology and dissemination of S. aureus and Methicillin-resistant S. aureus (MRSA) within the Primary Health Care in Brazil are scarce. The current study aimed to detect and characterize S. aureus and MRSA strains from the nasal cavities of 63 healthcare working in primary health care units in order to determine the prevalence of S. aureus and MRSA, biofilm formation and resistance profile of these isolates. PCR reactions were performed for detecting mecA, icaA and icaD genes. The phenotypic antimicrobial susceptibility was assessed by the disk diffusion method and biofilm formation by the Congo Red Agar (CRA) method. The MRSA isolates were typed for the Staphylococcal Cassette Chromosome mec (SCCmec). The prevalence of nasal carriage of S. aureus was 74.6%, of which 72.3% were MRSA carrying SCCmec type I (24.4%), III (34.1%), IV (36.6%). Two (4.9%) isolates presented a non-typeable cassette by the performed technique. The antimicrobial susceptibility evaluation evidenced penicillin resistance in 66.1% of S. aureus, erythromycin resistance in 49.2%, while 37.3% were resistant to oxacillin, 28.8% to cefoxitin, 5.1% to levofloxacin and 5.1% to clindamycin. All isolates were biofilm producers and 96.6% of the strains contained the ica biofilm-forming genes (icaA and/or icaD). We have demonstrated a high prevalence of S. aureus and MRSA carriage among health care working in Primary Health Care units, the presence of SCCmec types I, III and IV, in addition to their high ability to form biofilm, factors that possibly contribute to the dissemination and persistence of these pathogens within the primary care services. These observations highlight the importance of broadening the perspective of Health Care-Associated Infections prevention, including all health care levels, which are currently little explored. In addition, the dynamics and resistance mechanisms of S. aureus transmission still need to be further clarified to enable the implementation of more effective prevention measures.


Assuntos
Antibacterianos/farmacologia , Portador Sadio/microbiologia , Staphylococcus aureus Resistente à Meticilina/efeitos dos fármacos , Staphylococcus aureus Resistente à Meticilina/isolamento & purificação , Nariz/microbiologia , Infecções Estafilocócicas/tratamento farmacológico , Staphylococcus aureus/genética , Adulto , Biofilmes , Brasil/epidemiologia , Portador Sadio/epidemiologia , Infecção Hospitalar , Estudos Transversais , Feminino , Genes Bacterianos , Pessoal de Saúde , Humanos , Transmissão de Doença Infecciosa do Paciente para o Profissional , Transmissão de Doença Infecciosa do Profissional para o Paciente , Masculino , Staphylococcus aureus Resistente à Meticilina/genética , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , Prevalência , Atenção Primária à Saúde , Estudos Prospectivos , Infecções Estafilocócicas/epidemiologia , Infecções Estafilocócicas/microbiologia
17.
BMC Microbiol ; 21(1): 64, 2021 02 25.
Artigo em Inglês | MEDLINE | ID: mdl-33632119

RESUMO

BACKGROUND: To date, information on healthy female urinary microbiota is available mostly at genus level and at one time point. However, profound species-level characterization of healthy urinary microbiome and its stability over time are essential for further correct interpretation of its role in healthy urogenital tract. In this study, we investigated female urogenital microbiome (FUM) at two timepoints (within 2.5-year interval) in young asymptomatic European women. We used culturomics with accurate isolates' identification (MALDI-TOF MS and gene markers sequencing) to understand species stability within healthy FUM. RESULTS: Extended culturomics of voided midstream urine sample pairs revealed a mean Shannon diversity index of 1.25 and mean of 19 species/sample (range 5-39 species; total of 115 species; 1830 isolates). High overall species variability between individuals was captured by beta diversity and a variety of community structure types, with the largest cluster characterized by Lactobacillus crispatus, often in combination with Gardnerella vaginalis or Gardnerella genomospecies 3. Significant FUM composition differences, related to Finegoldia magna and Streptococcus anginosus, according to smoking status were found. A high species variability within individuals (Shannon index SD > 0.5 in 7 out of 10 sample pairs) with a mean of 29% of shared species (range 9.1-41.7%) was observed. Moreover, 4 out of 10 sample pairs clustered in the same community structure type. The stable FUM sample pairs presented high abundance of Lactobacillus crispatus, Streptococcus agalactiae or Lactobacillus paragasseri and Bifidobacterium spp.. Moreover, Gardnerella vaginalis, Gardnerella genomospecies 3 or Gardnerella swidsinskii were often maintained within individuals in high abundance. CONCLUSIONS: Shift in species composition at two distant timepoints was frequently observed among urogenital microbiome of European asymptomatic women. This suggests possible interchange of particular species in healthy FUM and the existence of multiple health-associated FUM compositions in certain individuals. Additionally, we provided additional evidence on resilience of particular bacterial communities and identified certain species more prone to persist in urogenital tract. This study revealed important details on the FUM composition complexity relevant for studies aiming to understand microbiota role in the urogenital tract health and for identification of eubiotic and dysbiotic FUM.


Assuntos
Bactérias/genética , Portador Sadio/microbiologia , Portador Sadio/urina , Microbiota/genética , Vagina/microbiologia , Adulto , Bactérias/classificação , Bactérias/metabolismo , Fenômenos Fisiológicos Bacterianos , Disbiose , Europa (Continente) , Feminino , Humanos , Microbiota/fisiologia , RNA Ribossômico 16S/genética , Fatores de Tempo
18.
Antimicrob Resist Infect Control ; 10(1): 30, 2021 02 04.
Artigo em Inglês | MEDLINE | ID: mdl-33541419

RESUMO

BACKGROUND: Antimicrobial resistance in neonatal intensive care unit (NICU) patients is a threat, due to the frequent use of antimicrobial treatment and invasive devices in fragile babies. Since 2014 an active surveillance program of multidrug-resistant Gram-negative bacteria (MDR-GNB) carriage has been in place in the five NICUs of Palermo, Italy. In 2017 an increase in the prevalence of MDR-GNB, and in particular of extended-spectrum ß-lactamases-producing Klebsiella pneumoniae (ESBL-KP), was observed in "Civico" hospital NICU. AIM: To assess the impact of a coordinated intervention strategy in achieving long-lasting reduction of MDR-GNB prevalence in the NICU. METHODS: Rectal swabs were obtained monthly and processed to detect MDR-GNB using standard methods. MDR-GNB were characterized by pulsed-field gel electrophoresis (PFGE). Since November 2017 the following intervention measures were applied: (a) two-months intensification of sample collection; (b) stakeholders meetings; (c) improvement of prevention measures and antimicrobial policies. FINDINGS: During the intensified microbiological surveillance MDR-GNB and ESBL-KP were detected in rectal swabs (34.8%; 23.2%), nasal swabs (24.6%; 14.5%), oral swabs (14.5%; 5.4%), milk samples (32.1%; 17.9%), pacifiers swabs (30.8%; 17.9%) and from sub-intensive room surfaces. Thirteen ESBL-KP strains isolated from clinical and environmental samples showed identical PFGE patterns. The prevalence of MDR-GNB and ESBL-KP carriage significantly decreased in the year after intervention compared to the previous year (20.6% vs 62.2%; p < 0.001 and 11.1% vs 57.8%; p < 0.001). MDR-GNB were not detected at all for three months and ESBL-KP for five months. Multivariate analysis of the principal exposure variables showed that admission in the post-intervention period significantly reduced the risk of MDR-GNB carriage (adj-OR = 0.21, 95% CI = 0.076-0.629; p < 0.001). CONCLUSIONS: MDR-GNB broadly circulate in NICU setting, they can colonize different body sites and spread through various vehicles. A coordinated strategy of multiple interventions with active cooperation between epidemiologists and clinicians in the NICU can effectively reduce their circulation and in particular the carriage of the most dangerous ESBL-KP strains.


Assuntos
Portador Sadio/diagnóstico , Farmacorresistência Bacteriana Múltipla , Infecções por Bactérias Gram-Negativas/prevenção & controle , Controle de Infecções/métodos , Unidades de Terapia Intensiva Neonatal , Portador Sadio/microbiologia , Infecção Hospitalar/microbiologia , Infecção Hospitalar/prevenção & controle , Eletroforese em Gel de Campo Pulsado , Feminino , Bactérias Gram-Negativas/isolamento & purificação , Infecções por Bactérias Gram-Negativas/epidemiologia , Humanos , Recém-Nascido , Itália , Masculino , Testes de Sensibilidade Microbiana
19.
Antimicrob Resist Infect Control ; 10(1): 37, 2021 02 17.
Artigo em Inglês | MEDLINE | ID: mdl-33597029

RESUMO

BACKGROUND: According to WHO ( CISMAC. Centre for Intervention Science in Maternal and Child health), the antimicrobial resistant bacteria considered to be clinically most important for human health and earmarked for surveillance include extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, carbapenem-resistant bacteria, methicillin-resistant (MRSA) and, macrolide-lincosamide-streptogramin B -resistant vancomycin-resistant (VRSA) Staphylococcus aureus and vancomycin-resistant Enterococcus (VRE). If these bacteria are carried in the female genital tract, they may be transmitted to the neonate causing local or systemic neonatal infections that can be difficult to treat with conventionally available antimicrobials. In order to develop effective treatment strategies, there is need for updated information about the prevalence of colonization with important antimicrobial-resistant pathogens. OBJECTIVE: We sought to estimate the prevalence of vaginal colonization with potentially pathogenic and clinically important AMR bacteria among women in labour in Uganda and to identify factors associated with colonization. METHODS: We conducted a cross-sectional study among HIV-1 and HIV-2 negative women in labour at three primary health care facilities in Uganda. Drug susceptibility testing was done using the disk diffusion method on bacterial isolates cultured from vaginal swabs. We calculated the prevalence of colonization with potentially pathogenic and clinically important AMR bacteria, in addition to multidrug-resistant (MDR) bacteria, defined as bacteria resistant to antibiotics from ≥ 3 antibiotic classes. RESULTS: We found that 57 of the 1472 enrolled women (3.9% prevalence; 95% Confidence interval [CI] 3.0%, 5.1%) were colonized with ESBL-producing Enterobacteriaceace, 27 (1.8%; 95% CI 1.2%, 2.6%) were colonized with carbapenem-resistant Enterobacteriaceae, and 85 (5.8%; 95% CI 4.6%, 7.1%) were colonized with MRSA. The prevalence of colonization with MDR bacteria was high (750/1472; 50.9%; 95% CI 48.4%, 53.5%). Women who were ≥ 30 years of age had higher odds of being colonized with MDR bacteria compared to women aged 20-24 years (OR 1.6; 95% CI 1.1, 2.2). CONCLUSION: Most of the women included in our study were vaginally colonized with potentially pathogenic MDR and other clinically important AMR bacteria. The high prevalence of colonization with these bacteria is likely to further increase the incidence of difficult-to-treat neonatal sepsis.


Assuntos
Portador Sadio/epidemiologia , Farmacorresistência Bacteriana Múltipla , Enterobacteriaceae/isolamento & purificação , Staphylococcus aureus Resistente à Meticilina/isolamento & purificação , Vagina/microbiologia , Adulto , Portador Sadio/microbiologia , Estudos Transversais , Feminino , Humanos , Testes de Sensibilidade Microbiana , Gravidez , Prevalência , Uganda/epidemiologia , Adulto Jovem
20.
PLoS One ; 16(2): e0245790, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33544742

RESUMO

BACKGROUND: The study objective was to reveal reservoirs potentially leading to Staphylococcus aureus infections in haemodialysis clinic clients in the tropical north of the Australian Northern Territory (NT). This client population are primarily Aboriginal Australians who have a greater burden of ill health than other Australians. Reservoir identification will enhance infection control in this client group, including informing potential S. aureus decolonisation strategies. METHODS AND FINDINGS: The study participants were 83 clients of four haemodialysis clinics in the Darwin region of the NT, and 46 clinical staff and researchers who had contact with the clinic clients. The study design was longitudinal, encompassing swabbing of anatomical sites at two month intervals to yield carriage isolates, and also progressive collection of infection isolates. Swab sampling was performed for all participants, and infection isolates collected for dialysis clients only. Analysis was based on the comparison of 139 carriage isolates and 27 infection isolates using whole genome sequencing. Genome comparisons were based on of 20,651 genome-wide orthologous SNPs, presence/absence of the mecA and pvl genes, and inferred multilocus sequence type and clonal complex. Pairs of genomes meeting the definition of "not discriminated" were classed as defining potential transmission events. The primary outcome was instances of potential transmission between a carriage site other than a skin lesion and an infection site, in the same individual. Three such instances were identified. Two involved ST762 (CC1) PVL- MRSA, and one instance ST121 PVL+ MSSA. Three additional instances were identified where the carriage strains were derived from skin lesions. Also identified were six instances of potential transmission of a carriage strains between participants, including transmission of strains between dialysis clients and staff/researchers, and one potential transmission of a clinical strain between participants. There were frequent occurrences of longitudinal persistence of carriage strains in individual participants, and two examples of the same strain causing infection in the same participants at different times. Strains associated with infections and skin lesions were enriched for PVL and mecA in comparison to strains associated with long term carriage. CONCLUSIONS: This study indicated that strains differ with respect to propensity to stably colonise sites such as the nose, and cause skin infections. PVL+ strains were associated with infection and skin lesions and were almost absent from the carriage sites. PVL- MRSA (mainly CC1) strains were associated with infection and also with potential transmission events involving carriage sites, while PVL- MSSA were frequently observed to stably colonise individuals without causing infection, and to be rarely transmitted. Current clinical guidelines for dialysis patients suggest MRSA decolonisation. Implementation in this client group may impact infections by PVL- MRSA, but may have little effect on infection by PVL+ strains. In this study, the PVL+ strains were predominant causes of infection but rarely colonised typical carriage sites such as the nose, and in the case of ST121, were MSSA. The important reservoirs for infection by PVL+ strains appeared to be prior infections.


Assuntos
Portador Sadio/epidemiologia , Portador Sadio/transmissão , Genes Bacterianos , Diálise Renal , Dermatopatias Infecciosas/epidemiologia , Dermatopatias Infecciosas/transmissão , Infecções Estafilocócicas/epidemiologia , Infecções Estafilocócicas/transmissão , Staphylococcus aureus/genética , Adulto , Austrália/epidemiologia , Proteínas de Bactérias/genética , Toxinas Bacterianas/genética , Portador Sadio/microbiologia , Exotoxinas/genética , Humanos , Leucocidinas/genética , Estudos Longitudinais , Tipagem de Sequências Multilocus/métodos , Proteínas de Ligação às Penicilinas/genética , Polimorfismo de Nucleotídeo Único , Estudos Prospectivos , Dermatopatias Infecciosas/microbiologia , Infecções Estafilocócicas/microbiologia , Sequenciamento Completo do Genoma/métodos
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