Precise Species Identification by Whole-Genome Sequencing of Enterobacter Bloodstream Infection, China

AbstractEpidemiological and microbiological data on Vibrio cholerae isolated between 2004 and 2017 (n=836) and held in the Public Health England culture archive were reviewed. The traditional biochemical species identification and serological typing results were compared with the genome derived species identification and serotype for a sub-set of isolates (n=152). Of the 836 isolates, 750 (89.7%) were from faecal specimens, 206 (24.6%) belonged to serogroup O1 and seven (0.8%) were serogroup O139, and 792 (94.7%) isolates from patients reporting recent travel abroad, most commonly to India (n=209) and Pakistan (n=104). Of the 152 isolates of V. cholerae speciated by kmer identification, 149 (98.1%) were concordant with the traditional biochemical approach. Traditional serotyping results were 100% concordant with the whole genome sequencing (WGS) analysis for identification of serogroups O1 and O139 and Classical and El Tor biotypes. ctxA was detected in all isolates of V. cholerae O1 El Tor and O139 belonging to sequence type (ST) 69, and in V. cholerae O1 Classical variants belonging to ST73. A phylogeny of isolates belonging to ST69 from UK travellers clustered geographically, with isolates from India and Pakistan located on separate branches. Moving forward, WGS data from UK travellers will contribute to global surveillance programs, and the monitoring of emerging threats to public health and the global dissemination of pathogenic lineages. At the national level, these WGS data will inform the timely reinforcement of direct public health messaging to travellers and mitigate the impact of imported infections and the associated risks to public health.

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Evaluation of Whole-Genome Sequencing for Identification and Typing of Vibrio cholerae

Journal of Clinical Microbiology ◽

10.1128/jcm.00831-18 ◽

2018 ◽

Vol 56 (11) ◽

Cited By ~ 12

Author(s):

David R. Greig ◽

Ulf Schaefer ◽

Sophie Octavia ◽

Ebony Hunter ◽

Marie A. Chattaway ◽

...

Keyword(s):

Public Health ◽

Whole Genome Sequencing ◽

Vibrio Cholerae ◽

Species Identification ◽

Genome Sequencing ◽

National Level ◽

Whole Genome ◽

Content Type ◽

El Tor ◽

The Impact

ABSTRACT Epidemiological and microbiological data on Vibrio cholerae strains isolated between April 2004 and March 2018 (n = 836) and held at the Public Health England culture archive were reviewed. The traditional biochemical species identification and serological typing results were compared with the genome-derived species identification and serotype for a subset of isolates (n = 152). Of the 836 isolates, 750 (89.7%) were from a fecal specimen, 206 (24.6%) belonged to serogroup O1, and 7 (0.8%) were serogroup O139; 792 (94.7%) isolates were from patients reporting recent travel abroad, most commonly to India (n = 209) and Pakistan (n = 104). Of the 152 V. cholerae isolates identified by use of kmer, 149 (98.1%) were concordant with those identified using the traditional biochemical approach. Traditional serotyping results were 100% concordant with those of the whole-genome sequencing (WGS) analysis for the identification of serogroups O1 and O139 and classical and El Tor biotypes. ctxA was detected in all isolates of V. cholerae O1 El Tor and O139 belonging to sequence type 69 (ST69) and in V. cholerae O1 classical variants belonging to ST73. A phylogeny of isolates belonging to ST69 from U.K. travelers clustered geographically, with isolates from India and Pakistan located on separate branches. Moving forward, WGS data from U.K. travelers will contribute to global surveillance programs and the monitoring of emerging threats to public health and the global dissemination of pathogenic lineages. At the national level, these WGS data will inform the timely reinforcement of direct public health messaging to travelers and mitigate the impact of imported infections and the associated risks to public health.

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Genome-based characterization of Escherichia coli causing bloodstream infection through next-generation sequencing

PLoS ONE ◽

10.1371/journal.pone.0244358 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0244358

Author(s):

Rafika Indah Paramita ◽

Erni Juwita Nelwan ◽

Fadilah Fadilah ◽

Editha Renesteen ◽

Nelly Puspandari ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Whole Genome Sequencing ◽

Bloodstream Infection ◽

Genome Sequencing ◽

Virulence Genes ◽

Sequence Type ◽

Whole Genome ◽

National Hospital ◽

Sequence Types

Escherichia coli are one of the commonest bacteria causing bloodstream infection (BSI). The aim of the research was to identify the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance of E. coli isolated from bloodstream infection hospitalized patients in Cipto Mangunkusumo National Hospital Jakarta. We used whole genome sequencing methods rather than the conventional one, to characterized the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance (AMR) of E. coli. The composition of E. coli sequence types (ST) was as follows: ST131 (n = 5), ST38 (n = 3), ST405 (n = 3), ST69 (n = 3), and other STs (ST1057, ST127, ST167, ST3033, ST349, ST40, ST58, ST6630). Enteroaggregative E. coli (EAEC) and Extra-intestinal pathogenic E. coli (ExPEC) groups were found dominant in our samples. Twenty isolates carried virulence genes for host cells adherence and 15 for genes that encourage E. coli immune evasion by enhancing survival in serum. ESBL-genes were present in 17 E. coli isolates. Other AMR genes also encoded resistance against aminoglycosides, quinolones, chloramphenicol, macrolides and trimethoprim. The phylogeny analysis showed that phylogroup D is dominated and followed by phylogroup B2. The E. coli isolated from 22 patients in Cipto Mangunkusumo National Hospital Jakarta showed high diversity in serotypes, sequence types, virulence genes, and AMR genes. Based on this finding, routinely screening all bacterial isolates in health care facilities can improve clinical significance. By using Whole Genome Sequencing for laboratory-based surveillance can be a valuable early warning system for emerging pathogens and resistance mechanisms.

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Salmonella identified in pigs in Kenya and Malawi reveals the potential for zoonotic transmission in emerging pork markets

PLoS Neglected Tropical Diseases ◽

10.1371/journal.pntd.0008796 ◽

2020 ◽

Vol 14 (11) ◽

pp. e0008796 ◽

Cited By ~ 1

Author(s):

Catherine N. Wilson ◽

Caisey V. Pulford ◽

James Akoko ◽

Blanca Perez Sepulveda ◽

Alexander V. Predeus ◽

...

Keyword(s):

Lymph Node ◽

Whole Genome Sequencing ◽

Bloodstream Infection ◽

Genome Sequencing ◽

Mesenteric Lymph Node ◽

Zoonotic Transmission ◽

Whole Genome ◽

Foodborne Disease ◽

Mesenteric Lymph ◽

The Uk

Salmonella is a major cause of foodborne disease globally. Pigs can carry and shed non-typhoidal Salmonella (NTS) asymptomatically, representing a significant reservoir for these pathogens. To investigate Salmonella carriage by African domestic pigs, faecal and mesenteric lymph node samples were taken at slaughter in Nairobi, Busia (Kenya) and Chikwawa (Malawi) between October 2016 and May 2017. Selective culture, antisera testing and whole genome sequencing were performed on samples from 647 pigs; the prevalence of NTS carriage was 12.7% in Busia, 9.1% in Nairobi and 24.6% in Chikwawa. Two isolates of S. Typhimurium ST313 were isolated, but were more closely related to ST313 isolates associated with gastroenteritis in the UK than bloodstream infection in Africa. The discovery of porcine NTS carriage in Kenya and Malawi reveals potential for zoonotic transmission of diarrhoeal strains to humans in these countries, but not for transmission of clades specifically associated with invasive NTS disease in Africa.

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Clinical and Genomic Characterization of Recurrent Enterococcal Bloodstream Infection in Patients With Acute Leukemia

Open Forum Infectious Diseases ◽

10.1093/ofid/ofy107 ◽

2018 ◽

Vol 5 (6) ◽

Author(s):

Julia A Messina ◽

Rohita Sinha ◽

Kimberly Starr ◽

Mehreen Arshad ◽

Barbara D Alexander ◽

...

Keyword(s):

Acute Leukemia ◽

Whole Genome Sequencing ◽

Bloodstream Infection ◽

Genome Sequencing ◽

Genetic Relatedness ◽

Categorical Variables ◽

Genetic Lineage ◽

Whole Genome ◽

Sequencing Analysis ◽

Continuous Variables

Abstract Background Rates and risk factors for recurrent enterococcal bloodstream infection (R-EBSI) and whether the same genetic lineage causes index EBSI and R-EBSI are unknown in patients with acute leukemia (AL) receiving chemotherapy. Methods Ninety-two AL patients with EBSI from 2010 to 2015 were included. Enterococcal bloodstream infection was defined by 31 positive blood cultures for Enterococcus faecium or Enterococcus faecalis and fever, hypotension, or chills. Clearance was defined by 31 negative cultures 324 hours after last positive culture and defervescence. Recurrent enterococcal bloodstream infection was defined by a positive blood culture for Enterococcus 324 hours after clearance. Categorical variables were reported as proportions and compared by the χ2 test. Continuous variables were summarized by median and interquartile range (IQR) and compared by the Wilcoxon-Mann-Whitney Test. P values <.05 were considered significant. Whole-genome sequencing was performed on available paired BSI isolates from 7 patients. Results Twenty-four patients (26%) had 31 episodes of R-EBSI. Median time to R-EBSI (IQR) was 26 (13–50) days. Patients with R-EBSI had significantly longer durations of fever and metronidazole exposure during their index EBSI. Thirty-nine percent of E. faecium R-EBSI isolates became daptomycin-nonsusceptible Enterococcus (DNSE) following daptomycin therapy for index EBSI. Whole-genome sequencing analysis confirmed high probability of genetic relatedness of index EBSI and R-EBSI isolates for 4/7 patients. Conclusions Recurrent enterococcal bloodstream infection and DNSE are common in patients with AL and tend to occur within the first 30 days of index EBSI. Duration of fever and metronidazole exposure may be useful in determining risk for R-EBSI. Whole-genome sequencing analysis demonstrates that the same strain causes both EBSI and R-EBSI in some patients.

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Three cases of mcr-1-positive colistin-resistant Escherichia coli bloodstream infections in Italy, August 2016 to January 2017

Eurosurveillance ◽

10.2807/1560-7917.es.2017.22.16.30517 ◽

2017 ◽

Vol 22 (16) ◽

Cited By ~ 17

Author(s):

Marta Corbella ◽

Bianca Mariani ◽

Carolina Ferrari ◽

Francesco Comandatore ◽

Erika Scaltriti ◽

...

Keyword(s):

Escherichia Coli ◽

Multidrug Resistance ◽

Whole Genome Sequencing ◽

Bloodstream Infection ◽

Genome Sequencing ◽

Bloodstream Infections ◽

Tertiary Hospital ◽

Whole Genome ◽

E Coli ◽

Sequence Types

We describe three cases of bloodstream infection caused by colistin-resistant Escherichia coli in patients in a tertiary hospital in Italy, between August 2016 and January 2017. Whole genome sequencing detected the mcr-1 gene in three isolated strains belonging to different sequence types (STs). This occurrence of three cases with mcr-1-positive E. coli belonging to different STs in six months suggests a widespread problem in settings where high multidrug resistance is endemic such as in Italy.

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DNA extraction from primary liquid blood cultures for bloodstream infection diagnosis using whole genome sequencing

Journal of Medical Microbiology ◽

10.1099/jmm.0.000664 ◽

2018 ◽

Vol 67 (3) ◽

pp. 347-357 ◽

Cited By ~ 9

Author(s):

Luke W. Anson ◽

Kevin Chau ◽

Nicholas Sanderson ◽

Sarah Hoosdally ◽

Phelim Bradley ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Bloodstream Infection ◽

Dna Extraction ◽

Genome Sequencing ◽

Blood Cultures ◽

Whole Genome ◽

Infection Diagnosis

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Identification and Whole Genome Sequencing of the First Case of Kosakonia radicincitans Causing a Human Bloodstream Infection

Frontiers in Microbiology ◽

10.3389/fmicb.2017.00062 ◽

2017 ◽

Vol 8 ◽

Cited By ~ 3

Author(s):

Micah D. Bhatti ◽

Awdhesh Kalia ◽

Pranoti Sahasrabhojane ◽

Jiwoong Kim ◽

David E. Greenberg ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Bloodstream Infection ◽

Genome Sequencing ◽

Whole Genome ◽

First Case

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Draft Genome Sequence of Erysipelothrix rhusiopathiae, Isolated from a Canine Case of Diskospondylitis

Microbiology Resource Announcements ◽

10.1128/mra.00592-20 ◽

2020 ◽

Vol 9 (26) ◽

Author(s):

Sara V. Little ◽

Andrew E. Hillhouse ◽

Sara D. Lawhon

Keyword(s):

Whole Genome Sequencing ◽

Species Identification ◽

Genome Sequencing ◽

Ribosomal Dna ◽

Draft Genome ◽

Dna Amplification ◽

Whole Genome ◽

Erysipelothrix Rhusiopathiae ◽

Content Type ◽

16S Ribosomal Dna

ABSTRACT This is the draft genome of an Erysipelothrix rhusiopathiae strain isolated from the blood of a canine. Initial 16S ribosomal DNA amplification identified the isolate as belonging to the Erysipelothrix genus but could not elucidate the species due to previous misidentification of E. rhusiopathiae and E. tonsillarum. The species identification was confirmed by whole-genome sequencing.

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Characterization of an Enterobacter cloacae Strain Producing both KPC and NDM Carbapenemases by Whole-Genome Sequencing

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01275-15 ◽

2015 ◽

Vol 59 (10) ◽

pp. 6625-6628 ◽

Cited By ~ 27

Author(s):

Wenjing Wu ◽

Yu Feng ◽

Alessandra Carattoli ◽

Zhiyong Zong

Keyword(s):

Whole Genome Sequencing ◽

Bloodstream Infection ◽

Genome Sequencing ◽

Carbapenem Resistance ◽

Enterobacter Cloacae ◽

Whole Genome ◽

Content Type ◽

Carbapenem Resistant

ABSTRACTA carbapenem-resistantEnterobacter cloacaestrain, WCHECl-14653, causing a fatal bloodstream infection, was characterized by genome sequencing and conjugation experiments. The strain carried two carbapenemase genes,blaNDM-1andblaKPC-2, on separate IncF plasmids. The coexistence ofblaNDM-1andblaKPC-2conferred slightly higher-level carbapenem resistance compared with that ofblaNDM-1orblaKPC-2alone, and the coexistence of two IncF plasmids may generate new platforms for spreading carbapenemase genes.

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