Antimicrobial-Resistant Escherichia coli Strains and Their Plasmids in People, Poultry, and Chicken Meat in Laos

Antimicrobial resistant (AMR) Enterobacterales are widely distributed among the healthy population of the Indochinese peninsula, including Laos. However, the local reservoir of these pathogens are currently not known and possible sources such as agricultural settings and food have rarely been analyzed. In this work, we investigated the extended-spectrum cephalosporin- (ESC-) and colistin-resistant Escherichia coli strains (CST-R-Ec) isolated from the gut of local people, feces of poultry, and from chicken meat (60 samples each group) in Laos. Whole-genome sequencing (WGS) analysis based on both short- and long-read sequencing approaches were implemented. The following prevalence of ESC-R-Ec and CST-R-Ec were recorded, respectively: local people (70 and 15%), poultry (20 and 23.3%), and chicken meat (21.7 and 13.3%). Core-genome analysis, coupled with sequence type (ST)/core-genome ST (cgST) definitions, indicated that no common AMR-Ec clones were spreading among the different settings. ESC-R-Ec mostly possessed blaCTX–M–15 and blaCTX–M–55 associated to ISEcp1 or IS26. The majority of CST-R-Ec carried mcr-1 on IncX4, IncI2, IncP1, and IncHI1 plasmids similar or identical to those described worldwide; strains with chromosomal mcr-1 or possessing plasmid-mediated mcr-3 were also found. These results indicate a high prevalence of AMR-Ec in the local population, poultry, and chicken meat. While we did not observe the same clones among the three settings, most of the blaCTX–Ms and mcr-1/-3 were associated with mobile-genetic elements, indicating that horizontal gene transfer may play an important role in the dissemination of AMR-Ec in Laos. More studies should be planned to better understand the extent and dynamics of this phenomenon.

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Travellers returning from the island of Zanzibar colonized with MDR Escherichia coli strains: assessing the impact of local people and other sources

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkaa457 ◽

2020 ◽

Author(s):

Aline I Moser ◽

Esther Kuenzli ◽

Thomas Büdel ◽

Edgar I Campos-Madueno ◽

Odette J Bernasconi ◽

...

Keyword(s):

Escherichia Coli ◽

Low Income ◽

Core Genome ◽

Chicken Meat ◽

Local People ◽

Low Income Countries ◽

Local Sources ◽

Genome Analyses ◽

Almost All ◽

The Impact

Abstract Objectives Many travellers to low-income countries return home colonized at the intestinal level with extended-spectrum cephalosporin-resistant (ESC-R) and/or colistin-resistant (CST-R) Escherichia coli (Ec) strains. However, nothing is known about the local sources responsible for the transmission of these pathogens to the travellers. Methods We compared the ESC-R- and CST-R-Ec strains found in the pre- (n = 23) and post-trip (n = 37) rectal swabs of 37 travellers from Switzerland to Zanzibar with those (i) contemporarily isolated from local people, poultry, retailed chicken meat (n = 31), and (ii) from other sources studied in the recent past (n = 47). WGS and core-genome analyses were implemented. Results Twenty-four travellers returned colonized with ESC-R- (n = 29) and/or CST-R- (n = 8) Ec strains. Almost all ESC-R-Ec were CTX-M-15 producers and belonged to heterogeneous STs/core-genome STs (cgSTs), while mcr-positive strains were not found. Based on the strains’ STs/cgSTs, only 20 subjects were colonized with ESC-R- and/or CST-R-Ec that were not present in their gut before the journey. Single nucleotide variant (SNV) analysis showed that three of these 20 travellers carried ESC-R-Ec (ST3489, ST3580, ST361) identical (0–20 SNVs) to those found in local people, chicken meat, or poultry. Three further subjects carried ESC-R-Ec (ST394, ST648, ST5173) identical or highly related (15–55 SNVs) to those previously reported in local people, fish, or water. Conclusions This is the first known study comparing the ESC-R- and/or CST-R-Ec strains obtained from travellers and local sources using solid molecular methods. We showed that for at least one-third of the returning travellers the acquired antibiotic-resistant Ec had a corresponding strain among resident people, food, animal and/or environmental sources.

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Household Clustering of Escherichia coli Sequence Type 131 Clinical and Fecal Isolates According to Whole Genome Sequence Analysis

Open Forum Infectious Diseases ◽

10.1093/ofid/ofw129 ◽

2016 ◽

Vol 3 (3) ◽

Cited By ~ 31

Author(s):

James R. Johnson ◽

Gregg Davis ◽

Connie Clabots ◽

Brian D. Johnston ◽

Stephen Porter ◽

...

Keyword(s):

Escherichia Coli ◽

Genome Sequence ◽

Core Genome ◽

Sequence Type ◽

Whole Genome Sequence ◽

Whole Genome ◽

The Core ◽

Genome Phylogeny ◽

Genome Level ◽

Repeated Infections

Abstract Background. Within-household sharing of strains from the resistance-associated H30R1 and H30Rx subclones of Escherichia coli sequence type 131 (ST131) has been inferred based on conventional typing data, but it has been assessed minimally using whole genome sequence (WGS) analysis. Methods. Thirty-three clinical and fecal isolates of ST131-H30R1 and ST131-H30Rx, from 20 humans and pets in 6 households, underwent WGS analysis for comparison with 52 published ST131 genomes. Phylogenetic relationships were inferred using a bootstrapped maximum likelihood tree based on core genome sequence polymorphisms. Accessory traits were compared between phylogenetically similar isolates. Results. In the WGS-based phylogeny, isolates clustered strictly by household, in clades that were distributed widely across the phylogeny, interspersed between H30R1 and H30Rx comparison genomes. For only 1 household did the core genome phylogeny place epidemiologically unlinked isolates together with household isolates, but even there multiple differences in accessory genome content clearly differentiated these 2 groups. The core genome phylogeny supported within-household strain sharing, fecal-urethral urinary tract infection pathogenesis (with the entire household potentially providing the fecal reservoir), and instances of host-specific microevolution. In 1 instance, the household's index strain persisted for 6 years before causing a new infection in a different household member. Conclusions. Within-household sharing of E coli ST131 strains was confirmed extensively at the genome level, as was long-term colonization and repeated infections due to an ST131-H30Rx strain. Future efforts toward surveillance and decolonization may need to address not just the affected patient but also other human and animal household members.

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Presence of β-Lactamase-producing Enterobacterales and Salmonella Isolates in Marine Mammals

International Journal of Molecular Sciences ◽

10.3390/ijms22115905 ◽

2021 ◽

Vol 22 (11) ◽

pp. 5905

Author(s):

Olivia M. Grünzweil ◽

Lauren Palmer ◽

Adriana Cabal ◽

Michael P. Szostak ◽

Werner Ruppitsch ◽

...

Keyword(s):

Escherichia Coli ◽

Marine Mammals ◽

Virulence Genes ◽

Multidrug Resistant ◽

Healthcare Sector ◽

Whole Genome ◽

E Coli ◽

High Prevalence ◽

Lactamase Gene ◽

Sequence Types

Marine mammals have been described as sentinels of the health of marine ecosystems. Therefore, the aim of this study was to investigate (i) the presence of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Enterobacterales, which comprise several bacterial families important to the healthcare sector, as well as (ii) the presence of Salmonella in these coastal animals. The antimicrobial resistance pheno- and genotypes, as well as biocide susceptibility of Enterobacterales isolated from stranded marine mammals, were determined prior to their rehabilitation. All E. coli isolates (n = 27) were screened for virulence genes via DNA-based microarray, and twelve selected E. coli isolates were analyzed by whole-genome sequencing. Seventy-one percent of the Enterobacterales isolates exhibited a multidrug-resistant (MDR) pheno- and genotype. The gene blaCMY (n = 51) was the predominant β-lactamase gene. In addition, blaTEM-1 (n = 38), blaSHV-33 (n = 8), blaCTX-M-15 (n = 7), blaOXA-1 (n = 7), blaSHV-11 (n = 3), and blaDHA-1 (n = 2) were detected. The most prevalent non-β-lactamase genes were sul2 (n = 38), strA (n = 34), strB (n = 34), and tet(A) (n = 34). Escherichia coli isolates belonging to the pandemic sequence types (STs) ST38, ST167, and ST648 were identified. Among Salmonella isolates (n = 18), S. Havana was the most prevalent serotype. The present study revealed a high prevalence of MDR bacteria and the presence of pandemic high-risk clones, both of which are indicators of anthropogenic antimicrobial pollution, in marine mammals.

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Extraintestinal pathogenic Escherichia coli sequence type 131 H30-R and H30-Rx subclones in retail chicken meat, Italy

International Journal of Food Microbiology ◽

10.1016/j.ijfoodmicro.2016.04.004 ◽

2016 ◽

Vol 228 ◽

pp. 10-13 ◽

Cited By ~ 7

Author(s):

Arash Ghodousi ◽

Celestino Bonura ◽

Paola Di Carlo ◽

Willem B. van Leeuwen ◽

Caterina Mammina

Keyword(s):

Escherichia Coli ◽

Chicken Meat ◽

Sequence Type ◽

Pathogenic Escherichia Coli ◽

Retail Chicken Meat

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Sequence Type 273 Carbapenem-Resistant Klebsiella pneumoniae Carrying bla NDM-1 and bla IMP-4

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00160-18 ◽

2018 ◽

Vol 62 (6) ◽

Cited By ~ 4

Author(s):

Lu Liu ◽

Yu Feng ◽

Haiyan Long ◽

Alan McNally ◽

Zhiyong Zong

Keyword(s):

Klebsiella Pneumoniae ◽

Southeast Asia ◽

Human Blood ◽

Sequence Type ◽

Whole Genome Sequence ◽

Whole Genome ◽

Content Type ◽

Carbapenem Resistant ◽

Transmissible Plasmid ◽

Long Read

ABSTRACT A carbapenem-resistant Klebsiella pneumoniae isolate was recovered from human blood. Its whole-genome sequence was obtained using Illumina and long-read MinION sequencing. The strain belongs to sequence type 273 (ST273), which was found recently and caused an outbreak in Southeast Asia. It has two carbapenemase genes, bla NDM-1 (carried by an ST7 IncN self-transmissible plasmid) and bla IMP-4 (located on a self-transmissible IncHI5 plasmid). Non-KPC-producing ST237 may represent a lineage of carbapenem-resistant K. pneumoniae , which warrants further monitoring.

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Draft Genome Sequences of Colistin-Resistant MCR-1-Producing Escherichia coli ST1850 and ST74 Strains Isolated from Commercial Chicken Meat

Genome Announcements ◽

10.1128/genomea.00329-17 ◽

2017 ◽

Vol 5 (20) ◽

Cited By ~ 6

Author(s):

Daniel F. Monte ◽

Miriam R. Fernandes ◽

Louise Cerdeira ◽

Tiago A. de Souza ◽

Andressa Mem ◽

...

Keyword(s):

Escherichia Coli ◽

Draft Genome ◽

Chicken Meat ◽

Sequence Type ◽

Genome Sequences ◽

Content Type ◽

Commercial Chicken

ABSTRACT We present here the draft genome sequences of two colistin-resistant mcr-1-carrying Escherichia coli strains belonging to sequence type 74 (ST74) and ST1850, isolated from commercial chicken meat in Brazil. Assembly of this draft genome resulted in 5,022,083 and 4,950,681 bp, respectively, revealing the presence of the IncX4 plasmid-mediated mcr-1 gene responsible for resistance to colistin.

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Comparison of different technologies for the decipherment of the whole genome sequence of Campylobacter jejuni BfR-CA-14430

Gut Pathogens ◽

10.1186/s13099-019-0340-7 ◽

2019 ◽

Vol 11 (1) ◽

Author(s):

Lennard Epping ◽

Julia C. Golz ◽

Marie-Theres Knüver ◽

Charlotte Huber ◽

Andrea Thürmer ◽

...

Keyword(s):

Campylobacter Jejuni ◽

Genome Sequence ◽

Bacterial Species ◽

Illumina Miseq ◽

Chicken Meat ◽

Whole Genome ◽

Short Read ◽

Plasmid Sequence ◽

Depth Analysis ◽

Long Read

Abstract Background Campylobacter jejuni is a zoonotic pathogen that infects the human gut through the food chain mainly by consumption of undercooked chicken meat, raw chicken cross-contaminated ready-to-eat food or by raw milk. In the last decades, C. jejuni has increasingly become the most common bacterial cause for food-born infections in high income countries, costing public health systems billions of euros each year. Currently, different whole genome sequencing techniques such as short-read bridge amplification and long-read single molecule real-time sequencing techniques are applied for in-depth analysis of bacterial species, in particular, Illumina MiSeq, PacBio and MinION. Results In this study, we analyzed a recently isolated C. jejuni strain from chicken meat by short- and long-read data from Illumina, PacBio and MinION sequencing technologies. For comparability, this strain is used in the German PAC-CAMPY research consortium in several studies, including phenotypic analysis of biofilm formation, natural transformation and in vivo colonization models. The complete assembled genome sequence most likely consists of a chromosome of 1,645,980 bp covering 1665 coding sequences as well as a plasmid sequence with 41,772 bp that encodes for 46 genes. Multilocus sequence typing revealed that the strain belongs to the clonal complex CC-21 (ST-44) which is known to be involved in C. jejuni human infections, including outbreaks. Furthermore, we discovered resistance determinants and a point mutation in the DNA gyrase (gyrA) that render the bacterium resistant against ampicillin, tetracycline and (fluoro-)quinolones. Conclusion The comparison of Illumina MiSeq, PacBio and MinION sequencing and analyses with different assembly tools enabled us to reconstruct a complete chromosome as well as a circular plasmid sequence of the C. jejuni strain BfR-CA-14430. Illumina short-read sequencing in combination with either PacBio or MinION can substantially improve the quality of the complete chromosome and epichromosomal elements on the level of mismatches and insertions/deletions, depending on the assembly program used.

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Whole genome analysis of cephalosporin-resistant Escherichia coli from bloodstream infections in Australia, New Zealand and Singapore: high prevalence of CMY-2 producers and ST131 carrying blaCTX-M-15 and blaCTX-M-27

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkx466 ◽

2017 ◽

Vol 73 (3) ◽

pp. 634-642 ◽

Cited By ~ 20

Author(s):

Patrick N A Harris ◽

Nouri L Ben Zakour ◽

Leah W Roberts ◽

Alexander M Wailan ◽

Hosam M Zowawi ◽

...

Keyword(s):

Escherichia Coli ◽

New Zealand ◽

Genome Analysis ◽

Bloodstream Infections ◽

Whole Genome ◽

Whole Genome Analysis ◽

High Prevalence

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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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