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

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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Laboratory based Retrospective Study to determine the start of SARS-CoV-2 in Patients with Severe Acute Respiratory Illness in Egypt at El-Demerdash tertiary hospitals

10.21203/rs.3.rs-76216/v2 ◽

2020 ◽

Author(s):

Sara H.A.Agwa ◽

Hesham Elghazaly ◽

Sarah El-Nakeep ◽

Ahmad Moustafa ◽

Manal H El-Sayed ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Clinical Characteristics ◽

Severe Infection ◽

Respiratory Illness ◽

Morbidity And Mortality ◽

Whole Genome ◽

University Hospitals ◽

First Case ◽

Tertiary Hospitals

Abstract Purpose: COVID-19 is the most recent pandemic causing morbidity and mortality. Although a part of the pathogens causing SARI, it is unique in causing pulmonary thrombosis and lung fibrosis. Thus different management is needed. We aimed o explore the start of SARS-CoV-2 in preserved SARI samples to know the exact time of its emergence in our hospital, to conduct whole-genome sequencing in positive SARS-CoV-2 samples to define its strain. To assess the clinical characteristics of the severe respiratory infection admitted to El-Demerdash hospitals in that same period from our own file reports.Methods: We conducted a retrospective cohort study among SARI patients who were admitted to Ain Shams university hospitals. preserved nasopharyngeal& oropharyngeal swabs from 333 SARI patients were used in SARS-CoV-2 detection by RT-Real time PCR. Moreover, whole-genome sequencing of SARS-CoV-2 positive samples was performed. Clinical characteristics of the SARI patients were analyzed in the same period to show the relation to morbidity and mortality.Results: The first case of SARS-CoV-2 was detected in a 6months aged female patient on mid-April 2020, B.1.1.7, clade GR. Co-infection (with both bacterial and viral) was most prevalent in pediatrics than adults, but mortality was higher in adults than pediatrics (18.1% versus 7.1%). ICU admission was higher in adults than in the pediatric group (65% versus 12.8%). Co-morbidities were associated with higher mortality and more severe infection. The most common bacterial infection in both adults and pediatrics was Klebsiella pneumoniae, followed by Staphylococcus aureus and Streptococcus pneumoniae. Conclusion: COVID-19 didn’t start till mid-April in the Egyptian hospitals as remarked by this tertiary hospital’s data. Co-infection is the most prevalent in children and further research is needed in this area.

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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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First case of IMP-15-producing Pseudomonas aeruginosa in Switzerland: Challenging laboratory diagnosis using whole genome sequencing (WGS)

IDCases ◽

10.1016/j.idcr.2020.e00933 ◽

2020 ◽

Vol 22 ◽

pp. e00933

Author(s):

Daniel Goldenberger ◽

Danielle Vuichard-Gysin ◽

Kathrin Herzog ◽

Vladimira Hinić ◽

Helena Seth-Smith ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Laboratory Diagnosis ◽

Whole Genome ◽

First Case

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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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Discovery of SARS-CoV-2 strain of P.1 lineage harboring K417T/ E484K / N501Y by whole genome sequencing in the city, Japan

10.1101/2021.02.24.21251892 ◽

2021 ◽

Author(s):

Yosuke Hirotsu ◽

Masao Omata

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Japanese Patients ◽

Original Strain ◽

Whole Genome ◽

Sequencing Analysis ◽

Receptor Binding Domain ◽

Cruise Ship ◽

First Case ◽

The City

On the February 2020, the very first case was an American female from Diamond Princess cruise ship. Since, we have confirmed 136 patients infected with coronavirus disease 2019 (COVID-19) until February 2021. Here, we conducted the whole genome sequencing analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on samples from 70 of 136 patients (51.5%). These patients were infected in Diamond Princess cruise ship (n=1), Africa (n=2), Japan (n=66) and Brazil (n=1). The viral genome sequence of a patient on the Diamond Princess cruise ship in February 2020 was similar to that of original strain found in Wuhan, China (19A clade). Four patients, including two returnees from Africa and two lived in Japan, confirmed at the end of March 2020 had sequences similar to those of lineage with D614G mutation, which was endemic in Europe (20A [n=3] and 20B [n=1] clade). The 64 Japanese patients confirmed from September 2020 to January 2021 had sequences similar to those of the currently prevalent lineage (20B [n=58] and 20C clade [n=6]). Subsequent analysis revealed three mutations (K417T/ E484K / N501Y) in the receptor binding domain of the spike protein in a man in his 40s. The sequence was identical to the P.1 lineage (also known as 20J/501Y.V3) reported in Brazil. This is the first report of SARS-CoV-2 P.1 lineage identified in the city, Japan.

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