Whole genome sequencing reveals high clonal diversity of Escherichia coli isolated from patients in a tertiary care hospital in Moshi, Tanzania

Sonda, Tolbert; Kumburu, Happiness; Zwetselaar, Marco van; Alifrangis, Michael; Mmbaga, Blandina T.; Aarestrup, Frank Møller; Kibiki, Gibson; Lund, Ole

doi:10.1186/s13756-018-0361-x

Cited by 26 publications

(32 citation statements)

References 48 publications

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“…Relatively little data concerning the genomics of E. coli exist in Africa to date. [21][22][23][24] The isolates sequenced as part of our project collected in Lilongwe, in the central region of Malawi, are highly phylogenetically similar to those seen in a previous study conducted in Blantyre, Malawi, in the southern region. [27] Interestingly, there are multiple branches that contain nearly identical isolates sequenced between the two studies despite the fact that the collection sites are over 300km apart from each other and our isolates were on average collected several years later.…”

Section: Discussionsupporting

confidence: 70%

“…[27] Although globally there is a strong association between ST131 and presence of the bla CTX-M-15 gene, here we identify the bla CTX-M-15 gene across a diverse set of lineages. [11] This finding is similar to other studies in Tanzania and Malawi, where the bla CTX-M-15 gene was found across numerous ST. [22,27] We see the bla gene in 8 different sequence types, including ST131. The ST that most commonly contained the bla CTX-M-15 gene was ST410.…”

Section: Discussionmentioning

confidence: 99%

“…[11,19,20] There is growing evidence in SSA that ST 131 CTX-M-15 E. coli strains are increasing, but there remains a limited number of studies assessing the clonality of E.coli , the distribution of ST131 and the presence of bla genes using whole genome sequencing. [21][22][23][24] In Malawi, specifically, there has been growing concern about increasing rates of antimicrobial resistance to most empirically used antimicrobials. [25,26] A recent genomic epidemiology study of 94 E. coli isolates collected at Queen Elizabeth Central Hospital, a tertiary care center in southern Malawi, and analyzed by whole genome sequencing (WGS), has shown that ST131 is the most common ST in southern Malawi at 14.9% of isolates sequenced.…”

Section: Introductionmentioning

confidence: 99%

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Genomic Epidemiology ofEscherichia coliIsolates from a Tertiary Referral Center in Lilongwe, Malawi

Tegha¹,

Ciccone

Krysiak³

et al. 2020

Preprint

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Antimicrobial resistance (AMR) is a global threat, including in sub-Saharan Africa. However, little is known about the genetics of resistant bacteria in the region. In Malawi, there is growing concern about increasing rates of antimicrobial resistance to most empirically used antimicrobials. The highly drug resistant Escherichia coli sequence type (ST) 131, which is associated with the extended spectrum β-lactamase bla , has been increasing in prevalence globally. Previous data from isolates collected between 2006-2013 in southern Malawi have shown the presence of ST131 and the bla CTX-M-15 gene in the country. We performed whole genome sequencing (WGS) of 58 clinical E. coli isolates at Kamuzu Central Hospital, a tertiary care center in central Malawi, collected from 2012-2018. We used Oxford Nanopore Technologies (ONT) sequencing, which was performed in Malawi. We show that ST131 has become more prevalent (14.9% increasing to 32.8%) and that the bla gene is occurring at a higher frequency (21.3% increasing to 44.8%). Phylogenetics show isolates are highly related between the central and southern geographic regions and confirm that ST131isolates are contained in a single group consistent with recent expansion. All AMR genes, including bla CTX-M-15 , were widely distributed across sequence types. We also identified an increased number of ST410 isolates, which in this study tend to carry a plasmid-located copy of bla gene at a higher frequency than bla occurs in ST131. This study confirms the expanding nature of ST131 and the wide distribution of the bla gene in Malawi. We also highlight the feasibility of conducting longitudinal genomic epidemiology studies of important bacteria with the sequencing done on site using a nanopore platform that requires minimal infrastructure.

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Section: Discussionsupporting

confidence: 70%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Genomic Epidemiology ofEscherichia coliIsolates from a Tertiary Referral Center in Lilongwe, Malawi

Tegha¹,

Ciccone

Krysiak³

et al. 2020

Preprint

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“…There also has been no clear time-dependent shifting of these lineages, though it appears that ST167 and ST617 are the dominant O89b-containing strains. ST617 strains are also known to carry many antibiotic resistance genes (30–33).…”

Section: Resultsmentioning

confidence: 99%

Comparative Genome Analysis of an Extensively Drug-Resistant Isolate of Avian Sequence Type 167 Escherichia coli Strain Sanji with Novel In Silico Serotype O89b:H9

Zhang

Chi

et al. 2019

mSystems

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Extensive drug resistance (XDR) is an escalating global problem. Escherichia coli strain Sanji was isolated from an outbreak of pheasant colibacillosis in Fujian province, China, in 2011. This strain has XDR properties, exhibiting sensitivity to carbapenems but no other classes of known antibiotics. Whole-genome sequencing revealed a total of 32 known antibiotic resistance genes, many associated with insertion sequence 26 (IS26) elements. These were found on the Sanji chromosome and 2 of its 6 plasmids, pSJ_255 and pSJ_82. The Sanji chromosome also harbors a type 2 secretion system (T2SS), a type 3 secretion system (T3SS), a type 6 secretion system (T6SS), and several putative prophages. Sanji and other ST167 strains have a previously uncharacterized O-antigen (O89b) that is most closely related to serotype O89 as determined on the basis of analysis of the wzm-wzt genes and in silico serotyping. This O89b-antigen gene cluster was also found in the genomes of a few other pathogenic sequence type 617 (ST617) and ST10 complex strains. A time-scaled phylogeny inferred from comparative single nucleotide variant analysis indicated that development of these O89b-containing lineages emerged about 30 years ago. Comparative sequence analysis revealed that the core genome of Sanji is nearly identical to that of several recently sequenced strains of pathogenic XDR E. coli belonging to the ST167 group. Comparison of the mobile elements among the different ST167 genomes revealed that each genome carries a distinct set of multidrug resistance genes on different types of plasmids, indicating that there are multiple paths toward the emergence of XDR in E. coli. IMPORTANCE E. coli strain Sanji is the first sequenced and analyzed genome of the recently emerged pathogenic XDR strains with sequence type ST167 and novel in silico serotype O89b:H9. Comparison of the genomes of Sanji with other ST167 strains revealed distinct sets of different plasmids, mobile IS elements, and antibiotic resistance genes in each genome, indicating that there exist multiple paths toward achieving XDR. The emergence of these pathogenic ST167 E. coli strains with diverse XDR capabilities highlights the difficulty of preventing or mitigating the development of XDR properties in bacteria and points to the importance of better understanding of the shared underlying virulence mechanisms and physiology of pathogenic bacteria.

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“…GZ04-0086 belonged to phylogenetic group A and sequence type ST44. E. coli ST44 has been frequently isolated from clinical settings (Kanamori et al, 2017;Runcharoen et al, 2017;Sonda et al, 2018). A phylogenetic analysis of E. coli ST44 revealed that GZ04-0086 was closest to isolates DO40 from canine and RDK06_431D from a patient in Tanzania, with 51 and 54 SNPs, respectively (Supplementary Figure S2).…”

Section: Genomic Insights Through Short-read and Long-read Sequencingmentioning

confidence: 99%

Coexistence of Two blaNDM–5 Genes Carried on IncX3 and IncFII Plasmids in an Escherichia coli Isolate Revealed by Illumina and Nanopore Sequencing

Yang

Lin

et al. 2020

Front. Microbiol.

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The emergence of carbapenem-resistant Enterobacteriaceae poses a significant threat to public health worldwide. Here, we reported a multidrug-resistant Escherichia coli strain with two different bla NDM-5-carrying plasmids from China. Illumina short-read and MinION long-read whole genome sequencing were performed. Genomic analysis found that one bla NDM-5 gene together with mphA was located on a 55-kb IncX3 plasmid, while the other bla NDM-5 gene was on a novel 68-kb IncFII plasmid. Susceptibility testing and quantitative reverse transcription PCR results further indicated that the transconjugants with the IncX3 plasmid exhibited higher-level carbapenem resistance and expression of bla NDM-5 than those with both plasmids or the IncFII plasmid. Two other β-lactamase genes (bla CTX−M-15 and bla OXA-1) were also detected on another 160-kb IncF plasmid. This is the first report of coexistence of two bla NDM-5-carrying plasmids in a single bacterial isolate, highlighting the genetic complexity of NDM-5 carbapenemase circulation, and the urgent need for continued active surveillance.

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Whole genome sequencing reveals high clonal diversity of Escherichia coli isolated from patients in a tertiary care hospital in Moshi, Tanzania

Cited by 26 publications

References 48 publications

Genomic Epidemiology ofEscherichia coliIsolates from a Tertiary Referral Center in Lilongwe, Malawi

Genomic Epidemiology ofEscherichia coliIsolates from a Tertiary Referral Center in Lilongwe, Malawi

Comparative Genome Analysis of an Extensively Drug-Resistant Isolate of Avian Sequence Type 167 Escherichia coli Strain Sanji with Novel In Silico Serotype O89b:H9

Coexistence of Two blaNDM–5 Genes Carried on IncX3 and IncFII Plasmids in an Escherichia coli Isolate Revealed by Illumina and Nanopore Sequencing

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