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1.
Microorganisms ; 10(2)2022 Jan 26.
Artigo em Inglês | MEDLINE | ID: mdl-35208747

RESUMO

Whole genome sequencing (WGS) of Salmonella supports both molecular typing and detection of antimicrobial resistance (AMR). Here, we evaluated the correlation between phenotypic antimicrobial susceptibility testing (AST) and in silico prediction of AMR from WGS in Salmonella enterica (n = 1321) isolated from human infections in Canada. Phenotypic AMR results from broth microdilution testing were used as the gold standard. To facilitate high-throughput prediction of AMR from genome assemblies, we created a tool called Staramr, which incorporates the ResFinder and PointFinder databases and a custom gene-drug key for antibiogram prediction. Overall, there was 99% concordance between phenotypic and genotypic detection of categorical resistance for 14 antimicrobials in 1321 isolates (18,305 of 18,494 results in agreement). We observed an average sensitivity of 91.2% (range 80.5-100%), a specificity of 99.7% (98.6-100%), a positive predictive value of 95.4% (68.2-100%), and a negative predictive value of 99.1% (95.6-100%). The positive predictive value of gentamicin was 68%, due to seven isolates that carried aac(3)-IVa, which conferred MICs just below the breakpoint of resistance. Genetic mechanisms of resistance in these 1321 isolates included 64 unique acquired alleles and mutations in three chromosomal genes. In general, in silico prediction of AMR in Salmonella was reliable compared to the gold standard of broth microdilution. WGS can provide higher-resolution data on the epidemiology of resistance mechanisms and the emergence of new resistance alleles.

2.
MMWR Morb Mortal Wkly Rep ; 71(6): 206-211, 2022 02 11.
Artigo em Inglês | MEDLINE | ID: mdl-35143464

RESUMO

Genomic surveillance is a critical tool for tracking emerging variants of SARS-CoV-2 (the virus that causes COVID-19), which can exhibit characteristics that potentially affect public health and clinical interventions, including increased transmissibility, illness severity, and capacity for immune escape. During June 2021-January 2022, CDC expanded genomic surveillance data sources to incorporate sequence data from public repositories to produce weighted estimates of variant proportions at the jurisdiction level and refined analytic methods to enhance the timeliness and accuracy of national and regional variant proportion estimates. These changes also allowed for more comprehensive variant proportion estimation at the jurisdictional level (i.e., U.S. state, district, territory, and freely associated state). The data in this report are a summary of findings of recent proportions of circulating variants that are updated weekly on CDC's COVID Data Tracker website to enable timely public health action.† The SARS-CoV-2 Delta (B.1.617.2 and AY sublineages) variant rose from 1% to >50% of viral lineages circulating nationally during 8 weeks, from May 1-June 26, 2021. Delta-associated infections remained predominant until being rapidly overtaken by infections associated with the Omicron (B.1.1.529 and BA sublineages) variant in December 2021, when Omicron increased from 1% to >50% of circulating viral lineages during a 2-week period. As of the week ending January 22, 2022, Omicron was estimated to account for 99.2% (95% CI = 99.0%-99.5%) of SARS-CoV-2 infections nationwide, and Delta for 0.7% (95% CI = 0.5%-1.0%). The dynamic landscape of SARS-CoV-2 variants in 2021, including Delta- and Omicron-driven resurgences of SARS-CoV-2 transmission across the United States, underscores the importance of robust genomic surveillance efforts to inform public health planning and practice.


Assuntos
COVID-19/epidemiologia , COVID-19/virologia , SARS-CoV-2/genética , Centers for Disease Control and Prevention, U.S. , Genômica , Humanos , Prevalência , Vigilância em Saúde Pública/métodos , Estados Unidos/epidemiologia
3.
Foodborne Pathog Dis ; 19(3): 199-208, 2022 03.
Artigo em Inglês | MEDLINE | ID: mdl-34989634

RESUMO

In August 2016, the Wisconsin Department of Health Services notified the U.S. Centers for Disease Control and Prevention of multidrug-resistant (MDR) Salmonella enterica serovar Heidelberg infections in people who reported contact with dairy calves. Federal and state partners investigated this to identify the source and scope of the outbreak and to prevent further illnesses. Cases were defined as human Salmonella Heidelberg infection caused by a strain that had one of seven pulsed-field gel electrophoresis (PFGE) patterns or was related by whole genome sequencing (WGS), with illness onset from January 1, 2015, through July 2, 2018. Patient exposure and calf purchase information was collected and analyzed; calves were traced back from the point of purchase. Isolates obtained from animal and environmental samples collected on-farm were supplied by veterinary diagnostic laboratories and compared with patient isolates using PFGE and WGS. Antimicrobial susceptibility testing by standardized broth microdilution was performed. Sixty-eight patients from 17 states were identified. Forty (63%) of 64 patients noted cattle contact before illness. Thirteen (33%) of 40 patients with exposure to calves reported that calves were sick or had died. Seven individuals purchased calves from a single Wisconsin livestock market. One hundred forty cattle from 14 states were infected with the outbreak strain. WGS indicated that human, cattle, and environmental isolates from the livestock market were genetically closely related. Most isolates (88%) had resistance or reduced susceptibility to antibiotics of ≥5 antibiotic classes. This resistance profile included first-line antibiotic treatments for patients with severe salmonellosis, including ampicillin, ceftriaxone, and ciprofloxacin. In this outbreak, MDR Salmonella Heidelberg likely spread from sick calves to humans, emphasizing the importance of illness surveillance in animal populations to prevent future spillover of this zoonotic disease.


Assuntos
Salmonella enterica , Animais , Antibacterianos/farmacologia , Bovinos , Surtos de Doenças/veterinária , Farmacorresistência Bacteriana Múltipla , Eletroforese em Gel de Campo Pulsado , Humanos , Testes de Sensibilidade Microbiana , Salmonella , Estados Unidos/epidemiologia
4.
Clin Infect Dis ; 74(3): 455-460, 2022 02 11.
Artigo em Inglês | MEDLINE | ID: mdl-33993224

RESUMO

BACKGROUND: In 2018, the Centers for Disease Control and Prevention and the Vermont Department of Health investigated an outbreak of multidrug-resistant Shigella sonnei infections in a retirement community that offered a continuum of care from independent living through skilled nursing care. The investigation identified 24 culture-confirmed cases. Isolates were resistant to trimethoprim-sulfamethoxazole, ampicillin, and ceftriaxone, and had decreased susceptibility to azithromycin and ciprofloxacin. METHODS: To evaluate clinical and microbiologic response, we reviewed inpatient and outpatient medical records for treatment outcomes among the 24 patients with culture-confirmed S. sonnei infection. We defined clinical failure as diarrhea (≥3 loose stools per day) for ≥1 day after treatment finished, and microbiologic failure as a stool culture that yielded S. sonnei after treatment finished. We used broth microdilution to perform antimicrobial susceptibility testing, and whole genome sequencing to identify resistance mechanisms. RESULTS: Isolates contained macrolide resistance genes mph(A) and erm(B) and had azithromycin minimum inhibitory concentrations above the Clinical and Laboratory Standards Institute epidemiological cutoff value of ≤16 µg/mL. Among 24 patients with culture-confirmed Shigella infection, 4 were treated with azithromycin; all had clinical treatment failure and 2 also had microbiologic treatment failure. Isolates were susceptible to ciprofloxacin but contained a gyrA mutation; 2 patients failed treatment with ciprofloxacin. CONCLUSIONS: These azithromycin treatment failures demonstrate the importance of clinical breakpoints to aid clinicians in identifying alternative treatment options for resistant strains. Additionally, these treatment failures highlight a need for comprehensive susceptibility testing and systematic outcome studies, particularly given the emergence of multidrug-resistant Shigella among an expanding range of patient populations.


Assuntos
Disenteria Bacilar , Shigella , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Azitromicina/farmacologia , Azitromicina/uso terapêutico , Ciprofloxacina/farmacologia , Ciprofloxacina/uso terapêutico , Surtos de Doenças , Farmacorresistência Bacteriana/genética , Disenteria Bacilar/tratamento farmacológico , Disenteria Bacilar/epidemiologia , Humanos , Macrolídeos/uso terapêutico , Testes de Sensibilidade Microbiana , Aposentadoria , Shigella sonnei/genética , Resultado do Tratamento , Vermont
5.
JAMA Netw Open ; 4(9): e2125203, 2021 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-34524434

RESUMO

Importance: Extensively drug-resistant Campylobacter jejuni infections cannot be treated with any commonly recommended antibiotics and pose an increasing public health threat. Objectives: To investigate cases of extensively drug-resistant C jejuni associated with pet store puppies and describe the epidemiologic and laboratory characteristics of these infections. Design, Setting, and Participants: In August 2017, health officials identified, via survey, patients with C jejuni infections who reported contact with puppies sold by pet stores. In conjunction with state and federal partners, the Centers for Disease Control and Prevention investigated cases of culture-confirmed C jejuni infections in US patients with an epidemiologic or molecular association with pet store puppies between January 1, 2016, and February 29, 2020. Available records from cases occurring before 2016 with genetically related isolates were also obtained. Main Outcomes and Measures: Patients were interviewed about demographic characteristics, health outcomes, and dog exposure during the 7 days before illness onset. Core genome multilocus sequence typing was used to assess isolate relatedness, and genomes were screened for resistance determinants to predict antibiotic resistance. Isolates resistant to fluoroquinolones, macrolides, and 3 or more additional antibiotic classes were considered to be extensively drug resistant. Cases before 2016 were identified by screening all sequenced isolates submitted for surveillance using core genome multilocus sequence typing. Results: A total of 168 patients (median [interquartile range] age, 37 [19.5-51.0] years; 105 of 163 female [64%]) with an epidemiologic or molecular association with pet store puppies were studied. A total of 137 cases occurred from January 1, 2016, to February 29, 2020, with 31 additional cases dating back to 2011. Overall, 117 of 121 patients (97%) reported contact with a dog in the week before symptom onset, of whom 69 of 78 (88%) with additional information reported contact with a pet store puppy; 168 isolates (88%) were extensively drug resistant. Traceback investigation did not implicate any particular breeder, transporter, distributer, store, or chain. Conclusions and Relevance: Strains of extensively drug-resistant C jejuni have been circulating since at least 2011 and are associated with illness among pet store customers, employees, and others who come into contact with pet store puppies. The results of this study suggest that practitioners should ask about puppy exposure when treating patients with Campylobacter infection, especially when they do not improve with routine antibiotics, and that the commercial dog industry should take action to help prevent the spread of extensively drug-resistant C jejuni from pet store puppies to people.


Assuntos
Zoonoses Bacterianas/epidemiologia , Infecções por Campylobacter/epidemiologia , Campylobacter jejuni , Surtos de Doenças , Doenças do Cão/transmissão , Animais de Estimação , Adulto , Animais , Infecções por Campylobacter/microbiologia , Infecções por Campylobacter/veterinária , Cães , Farmacorresistência Bacteriana , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Estudos Retrospectivos , Estados Unidos/epidemiologia
6.
Antibiotics (Basel) ; 10(3)2021 Mar 05.
Artigo em Inglês | MEDLINE | ID: mdl-33807748

RESUMO

Salmonella Infantis, a common contaminant of poultry products, is known to harbor mobile genetic elements that confer multi-drug resistance (MDR) and have been detected in many continents. Here, we report four MDR S. Infantis strains recovered from poultry house environments in Santa Cruz Island of the Galapagos showing extended-spectrum ß-lactamase (ESBL) resistance and reduced fluoroquinolone susceptibility. Whole-genome sequencing (WGS) revealed the presence of the ESBL-conferring blaCTX-M-65 gene in an IncFIB-like plasmid in three S. Infantis isolates. Multi-locus sequence typing (MLST) and single nucleotide variant/polymorphism (SNP) SNVPhyl analysis showed that the S. Infantis isolates belong to sequence type ST32, likely share a common ancestor, and are closely related (1-3 SNP difference) to blaCTX-M-65-containing clinical and veterinary S. Infantis isolates from the United States and Latin America. Furthermore, phylogenetic analysis of SNPs following core-genome alignment (i.e., ParSNP) inferred close relatedness between the S. Infantis isolates from Galapagos and the United States. Prophage typing confirmed the close relationship among the Galapagos S. Infantis and was useful in distinguishing them from the United States isolates. This is the first report of MDR blaCTX-M-65-containing S. Infantis in the Galapagos Islands and highlights the need for increased monitoring and surveillance programs to determine prevalence, sources, and reservoirs of MDR pathogens.

7.
J Open Source Softw ; 6(60)2021 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-35360664

RESUMO

Laboratories that run Whole Genome Sequencing (WGS) produce a tremendous amount of data, up to 10 gigabytes for some common instruments. There is a need to standardize the quality assurance and quality control process (QA/QC). Therefore we have created SneakerNet to automate the QA/QC for WGS.

8.
Genes (Basel) ; 11(12)2020 12 18.
Artigo em Inglês | MEDLINE | ID: mdl-33352984

RESUMO

Salmonella Infantis carrying extended spectrum ß-lactamase blaCTX-M-65 on a pESI-like megaplasmid has recently emerged in United States poultry. In order to determine the carriage rate and gene content variability of this plasmid in U.S. Salmonella Infantis, whole genome sequences of Salmonella isolates from humans and animals in the U.S. and internationally containing the pESI-like plasmid were analyzed. The U.S. Department of Agriculture Food Safety and Inspection Service (FSIS) identified 654 product sampling isolates containing pESI-like plasmids through hazard analysis and critical control point (HACCP) verification testing in 2017 and 2018. The Centers for Disease Control and Prevention identified 55 isolates with pESI-like plasmids in 2016-2018 through the National Antimicrobial Resistance Monitoring System. Approximately 49% of pESI-like plasmids from FSIS verification isolates and 71% from CDC NARMS contained blaCTX-M-65. Pan-plasmid genome analysis was also performed. All plasmids contained traN and more than 95% contained 172 other conserved genes; 61% contained blaCTX-M-65. In a hierarchical clustering analysis, some plasmids from U.S. animal sources clustered together and some plasmids from South America clustered together, possibly indicating multiple plasmid lineages. However, most plasmids contained similar genes regardless of origin. Carriage of the pESI-like plasmid in U.S. appears to be limited to Salmonella Infantis and carriage rates increased from 2017 to 2018.


Assuntos
Genes Bacterianos , Plasmídeos/genética , Doenças das Aves Domésticas/microbiologia , Salmonelose Animal/microbiologia , Infecções por Salmonella/microbiologia , Salmonella/genética , Animais , Proteínas de Bactérias/genética , Portador Sadio , Bovinos/microbiologia , Doenças dos Bovinos/epidemiologia , Doenças dos Bovinos/microbiologia , Galinhas/microbiologia , Análise por Conglomerados , Carne/microbiologia , Doenças das Aves Domésticas/epidemiologia , Salmonella/enzimologia , Salmonella/isolamento & purificação , Intoxicação Alimentar por Salmonella/epidemiologia , Intoxicação Alimentar por Salmonella/microbiologia , Infecções por Salmonella/epidemiologia , Salmonelose Animal/epidemiologia , Alinhamento de Sequência , Perus/microbiologia , Estados Unidos/epidemiologia , beta-Lactamases/genética
9.
MMWR Morb Mortal Wkly Rep ; 69(20): 618-622, 2020 May 22.
Artigo em Inglês | MEDLINE | ID: mdl-32437343

RESUMO

Ceftriaxone-resistant Salmonella enterica serotype Typhi (Typhi), the bacterium that causes typhoid fever, is a growing public health threat. Extensively drug-resistant (XDR) Typhi is resistant to ceftriaxone and other antibiotics used for treatment, including ampicillin, chloramphenicol, ciprofloxacin, and trimethoprim-sulfamethoxazole (1). In March 2018, CDC began enhanced surveillance for ceftriaxone-resistant Typhi in response to an ongoing outbreak of XDR typhoid fever in Pakistan. CDC had previously reported the first five cases of XDR Typhi in the United States among patients who had spent time in Pakistan (2). These illnesses represented the first cases of ceftriaxone-resistant Typhi documented in the United States (3). This report provides an update on U.S. cases of XDR typhoid fever linked to Pakistan and describes a new, unrelated cluster of ceftriaxone-resistant Typhi infections linked to Iraq. Travelers to areas with endemic Typhi should receive typhoid vaccination before traveling and adhere to safe food and water precautions (4). Treatment of patients with typhoid fever should be guided by antimicrobial susceptibility testing whenever possible (5), and clinicians should consider travel history when selecting empiric therapy.


Assuntos
Ceftriaxona/farmacologia , Surtos de Doenças , Resistência Microbiana a Medicamentos , Salmonella typhi/efeitos dos fármacos , Doença Relacionada a Viagens , Febre Tifoide/epidemiologia , Febre Tifoide/microbiologia , Adolescente , Adulto , Idoso , Ceftriaxona/uso terapêutico , Criança , Pré-Escolar , Feminino , Humanos , Lactente , Iraque/epidemiologia , Masculino , Pessoa de Meia-Idade , Paquistão/epidemiologia , Febre Tifoide/tratamento farmacológico , Estados Unidos/epidemiologia , Adulto Jovem
10.
Open Forum Infect Dis ; 7(4): ofaa113, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32341933

RESUMO

In 2017, state health departments notified the Centers for Disease Control and Prevention about 4 patients with shigellosis who experienced persistent illness after treatment with oral third-generation cephalosporins. Given increasing antibiotic resistance among Shigella, these cases highlight the need to evaluate the efficacy of oral cephalosporins for shigellosis.

11.
Emerg Infect Dis ; 26(5): 1030-1033, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32310060

RESUMO

A multidrug-resistant Salmonella enterica serotype Anatum strain reported in Taiwan was isolated in the United States from patients and from seafood imported from Asia. Isolates harbored 11 resistance determinants, including quinolone and inducible cephalosporin resistance genes. Most patients had traveled to Asia. These findings underscore the need for global One Health resistance surveillance.


Assuntos
Farmacorresistência Bacteriana Múltipla , Salmonella enterica , Antibacterianos/farmacologia , Ásia/epidemiologia , Humanos , Testes de Sensibilidade Microbiana , Salmonella/genética , Salmonella enterica/genética , Alimentos Marinhos , Sorogrupo , Taiwan , Estados Unidos/epidemiologia
12.
Microbiol Resour Announc ; 9(13)2020 Mar 26.
Artigo em Inglês | MEDLINE | ID: mdl-32217683

RESUMO

A large outbreak of extensively drug-resistant (XDR) Salmonella enterica serotype Typhi infections is ongoing in Pakistan, predominantly in Sindh Province. Here, we report the sequencing and characterization of five XDR Salmonella Typhi isolates from the Punjab province of Pakistan that are closely related to the outbreak strain and carry the same IncY plasmid.

13.
Artigo em Inglês | MEDLINE | ID: mdl-31527028

RESUMO

Enterobacteriaceae, quinolone resistance is largely attributed to mutations in the quinolone resistance-determining regions (QRDR) of gyrA, gyrB, parC, and parE, and plasmid-italiciated quinolone resistance (PMQR) genes (e.g., qnr genes, aac(6')-Ib-cr, or qepA).….

14.
MMWR Morb Mortal Wkly Rep ; 68(33): 713-717, 2019 Aug 23.
Artigo em Inglês | MEDLINE | ID: mdl-31437141

RESUMO

In September 2018, CDC identified Salmonella enterica serotype Newport (Newport) infections that were multidrug resistant (MDR), with decreased susceptibility to azithromycin, a recommended oral treatment agent. Until 2017, decreased susceptibility to azithromycin had occurred in fewer than 0.5% of Salmonella isolates from U.S. residents. This report summarizes the investigation of a multistate MDR Salmonella outbreak conducted by CDC, state and local health departments, and the U.S. Department of Agriculture's Food Safety and Inspection Service. During June 2018-March 2019, 255 cases of infection with the outbreak strain were identified in 32 states; 43% of patients (89 of 206 with information on travel) reported recent travel to Mexico. Infections were linked to consumption of soft cheese obtained in Mexico and beef obtained in the United States. Consumers should avoid eating soft cheese that could be made from unpasteurized milk, regardless of the source of the cheese. When preparing beef, a food thermometer should be used to ensure that appropriate cooking temperatures are reached. When antibiotic treatment is needed for a patient, clinicians should choose antibiotics based on susceptibility testing wherever possible.


Assuntos
Azitromicina/farmacologia , Surtos de Doenças , Farmacorresistência Bacteriana Múltipla , Intoxicação Alimentar por Salmonella/epidemiologia , Salmonella/efeitos dos fármacos , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Queijo/microbiologia , Criança , Pré-Escolar , Feminino , Microbiologia de Alimentos , Humanos , Lactente , Masculino , México , Pessoa de Meia-Idade , Carne Vermelha/microbiologia , Salmonella/genética , Intoxicação Alimentar por Salmonella/tratamento farmacológico , Doença Relacionada a Viagens , Estados Unidos/epidemiologia , Adulto Jovem
15.
J Antimicrob Chemother ; 74(1): 38-41, 2019 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-30202900

RESUMO

Background: Trimethoprim/sulfamethoxazole is a synthetic antibiotic combination recommended for the treatment of complicated non-typhoidal Salmonella infections in humans. Resistance to trimethoprim/sulfamethoxazole is mediated by the acquisition of mobile genes, requiring both a dfr gene (trimethoprim resistance) and a sul gene (sulfamethoxazole resistance) for a clinical resistance phenotype (MIC ≥4/76 mg/L). In 2017, the CDC investigated a multistate outbreak caused by a Salmonella enterica serotype Heidelberg strain with trimethoprim/sulfamethoxazole resistance, in which sul genes but no known dfr genes were detected. Objectives: To characterize and describe the molecular mechanism of trimethoprim resistance in a Salmonella Heidelberg outbreak isolate. Methods: Illumina sequencing data for one outbreak isolate revealed a 588 bp ORF encoding a putative dfr gene. This gene was cloned into Escherichia coli and resistance to trimethoprim was measured by broth dilution and Etest. Phylogenetic analysis of previously reported dfrA genes was performed using MEGA. Long-read sequencing was conducted to determine the context of the novel dfr gene. Results and conclusions: The novel dfr gene, named dfrA34, conferred trimethoprim resistance (MIC ≥32 mg/L) when cloned into E. coli. Based on predicted amino acid sequences, dfrA34 shares less than 50% identity with other known dfrA genes. The dfrA34 gene is located in a class 1 integron in a multiresistance region of an IncC plasmid, adjacent to a sul gene, thus conferring clinical trimethoprim/sulfamethoxazole resistance. Additionally, dfrA34 is associated with ISCR1, enabling easy transmission between other plasmids and bacterial strains.


Assuntos
Surtos de Doenças , Genes Bacterianos , Infecções por Salmonella/epidemiologia , Infecções por Salmonella/microbiologia , Salmonella enterica/efeitos dos fármacos , Salmonella enterica/isolamento & purificação , Resistência a Trimetoprima , Clonagem Molecular , Escherichia coli/efeitos dos fármacos , Escherichia coli/genética , Expressão Gênica , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Testes de Sensibilidade Microbiana , Salmonella enterica/genética , Estados Unidos/epidemiologia
16.
Emerg Infect Dis ; 24(12): 2284-2291, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30457533

RESUMO

Extended-spectrum ß-lactamases (ESBLs) confer resistance to clinically important third-generation cephalosporins, which are often used to treat invasive salmonellosis. In the United States, ESBLs are rarely found in Salmonella. However, in 2014, the US Food and Drug Administration found blaCTX-M-65 ESBL-producing Salmonella enterica serotype Infantis in retail chicken meat. The isolate had a rare pulsed-field gel electrophoresis pattern. To clarify the sources and potential effects on human health, we examined isolates with this pattern obtained from human surveillance and associated metadata. Using broth microdilution for antimicrobial susceptibility testing and whole-genome sequencing, we characterized the isolates. Of 34 isolates, 29 carried the blaCTX-M-65 gene with <9 additional resistance genes on 1 plasmid. Of 19 patients with travel information available, 12 (63%) reported recent travel to South America. Genetically, isolates from travelers, nontravelers, and retail chicken meat were similar. Expanded surveillance is needed to determine domestic sources and potentially prevent spread of this ESBL-containing plasmid.


Assuntos
Infecções por Salmonella/epidemiologia , Infecções por Salmonella/microbiologia , Salmonella enterica/classificação , beta-Lactamases/genética , DNA Bacteriano , Humanos , Filogenia , Filogeografia , Polimorfismo Genético , Salmonella enterica/genética , Sorogrupo , Estados Unidos/epidemiologia
17.
MMWR Morb Mortal Wkly Rep ; 67(37): 1032-1035, 2018 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-30235182

RESUMO

Campylobacter causes an estimated 1.3 million diarrheal illnesses in the United States annually (1). In August 2017, the Florida Department of Health notified CDC of six Campylobacter jejuni infections linked to company A, a national pet store chain based in Ohio. CDC examined whole-genome sequencing (WGS) data and identified six isolates from company A puppies in Florida that were highly related to an isolate from a company A customer in Ohio. This information prompted a multistate investigation by local and state health and agriculture departments and CDC to identify the outbreak source and prevent additional illness. Health officials from six states visited pet stores to collect puppy fecal samples, antibiotic records, and traceback information. Nationally, 118 persons, including 29 pet store employees, in 18 states were identified with illness onset during January 5, 2016-February 4, 2018. In total, six pet store companies were linked to the outbreak. Outbreak isolates were resistant by antibiotic susceptibility testing to all antibiotics commonly used to treat Campylobacter infections, including macrolides and quinolones. Store record reviews revealed that among 149 investigated puppies, 142 (95%) received one or more courses of antibiotics, raising concern that antibiotic use might have led to development of resistance. Public health authorities issued infection prevention recommendations to affected pet stores and recommendations for testing puppies to veterinarians. This outbreak demonstrates that puppies can be a source of multidrug-resistant Campylobacter infections in humans, warranting a closer look at antimicrobial use in the commercial dog industry.


Assuntos
Infecções por Campylobacter/epidemiologia , Campylobacter jejuni/efeitos dos fármacos , Surtos de Doenças , Cães/microbiologia , Farmacorresistência Bacteriana Múltipla , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Animais , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Infecções por Campylobacter/tratamento farmacológico , Infecções por Campylobacter/prevenção & controle , Campylobacter jejuni/isolamento & purificação , Criança , Pré-Escolar , Busca de Comunicante , Surtos de Doenças/prevenção & controle , Fezes/microbiologia , Feminino , Humanos , Lactente , Masculino , Pessoa de Meia-Idade , Estados Unidos/epidemiologia , Adulto Jovem , Zoonoses
18.
Zoonoses Public Health ; 65(7): 838-849, 2018 11.
Artigo em Inglês | MEDLINE | ID: mdl-30027554

RESUMO

Invasive Salmonella infections in adults are commonly treated with fluoroquinolones, a critically important antimicrobial class. Historically, quinolone resistance was the result of chromosomal mutations, but plasmid-mediated quinolone resistance (PMQR) has emerged and is increasingly being reported in Enterobacteriaceae worldwide. PMQR may facilitate the spread of quinolone resistance, lead to higher-level quinolone resistance, and make infections harder to treat. To better understand the epidemiology of PMQR in non-typhoidal Salmonella causing human infections in the United States, we looked at trends in quinolone resistance among isolates submitted to the Centers for Disease Control and Prevention. We reviewed demographic, exposure and outcome information for patients with isolates having a PMQR-associated phenotype during 2008-2014 and tested isolates for quinolone resistance mechanisms. We found that PMQR is emerging among non-typhoidal Salmonella causing human infections in the United States and that international travel, reptile and amphibian exposure, and food are likely sources of human infection.


Assuntos
Doenças Transmissíveis Emergentes/microbiologia , Farmacorresistência Bacteriana , Quinolonas/farmacologia , Infecções por Salmonella/epidemiologia , Infecções por Salmonella/microbiologia , Antibacterianos/farmacologia , Doenças Transmissíveis Emergentes/epidemiologia , Surtos de Doenças , Humanos , Plasmídeos/genética , Salmonella/efeitos dos fármacos , Salmonella/genética , Fatores de Tempo , Estados Unidos/epidemiologia
20.
PLoS One ; 13(12): e0208735, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30596673

RESUMO

Enterotoxigenic Escherichia coli (ETEC) are an important cause of diarrhea globally, particularly among children under the age of five in developing countries. ETEC O6 is the most common ETEC serogroup, yet the genome wide population structure of isolates of this serogroup is yet to be determined. In this study, we have characterized 40 ETEC O6 isolates collected between 1975-2016 by whole genome sequencing (WGS) and by phenotypic antimicrobial susceptibility testing. To determine the relatedness of isolates, we evaluated two methods-whole genome high-quality single nucleotide polymorphism (whole genome-hqSNP) and core genome SNP analyses using Lyve-SET and Parsnp respectively. All isolates were tested for antimicrobial susceptibility using a panel of 14 antibiotics. ResFinder 2.1 and a custom quinolone resistance determinants workflow were used for resistance determinant detection. VirulenceFinder 1.5 was used for prediction of the virulence genes. Thirty-seven isolates clustered into three major clades (I, II, III) by whole genome-hqSNP and core genome SNP analyses, while three isolates included in the whole genome-hqSNP analysis only did not cluster with clades I-III by both analyses and formed a distantly related outgroup, designated clade IV. Median number of pairwise whole genome-hqSNPs in clonal ETEC O6 outbreaks ranged from 0 to 5. Of the 40 isolates tested for antimicrobial susceptibility, 18 isolates were pansusceptible. Twenty-two isolates were resistant to at least one antibiotic, nine of which were multidrug resistant. Phenotypic antimicrobial resistance (AR) correlated with AR determinants in 22 isolates. Thirty-two isolates harbored both enterotoxin virulence genes while the remaining 8 isolates had only one of the two virulence genes. In summary, whole genome-hqSNP and core genome SNP analyses from this study revealed similar evolutionary relationships and an overall diversity of ETEC O6 isolates independent of time of isolation. Less than 5 pairwise hqSNPs between ETEC O6 isolates is circumstantially indicative of an outbreak cluster. Findings from this study will be a basis for quicker outbreak detection and control by efficient subtyping by WGS.


Assuntos
Escherichia coli Enterotoxigênica/genética , Infecções por Escherichia coli/epidemiologia , Infecções por Escherichia coli/microbiologia , Antibacterianos/farmacologia , Biologia Computacional , DNA Bacteriano , Surtos de Doenças , Farmacorresistência Bacteriana/genética , Escherichia coli Enterotoxigênica/efeitos dos fármacos , Escherichia coli Enterotoxigênica/isolamento & purificação , Escherichia coli Enterotoxigênica/patogenicidade , Genoma Bacteriano , Humanos , Testes de Sensibilidade Microbiana , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA , Sorogrupo , Fatores de Virulência/genética
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