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Kanje LE, Kumburu H, Kuchaka D, Shayo M, Juma MA, Kimu P, Beti M, van Zwetselaar M, Wadugu B, Mmbaga BT, Mkumbaye SI, Sonda T. Short reads-based characterization of pathotype diversity and drug resistance among Escherichia coli isolated from patients attending regional referral hospitals in Tanzania. BMC Med Genomics 2024; 17:110. [PMID: 38671498 PMCID: PMC11055328 DOI: 10.1186/s12920-024-01882-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Escherichia coli is known to cause about 2 million deaths annually of which diarrhea infection is leading and typically occurs in children under 5 years old. Although Africa is the most affected region there is little information on their pathotypes diversity and their antimicrobial resistance. OBJECTIVE To determine the pathotype diversity and antimicrobial resistance among E. coli from patients attending regional referral hospitals in Tanzania. MATERIALS AND METHODS A retrospective cross-section laboratory-based study where a total of 138 archived E. coli isolates collected from 2020 to 2021 from selected regional referral hospitals in Tanzania were sequenced using the Illumina Nextseq550 sequencer platform. Analysis of the sequences was done in the CGE tool for the identification of resistance genes and virulence genes. SPSS version 20 was used to summarize data using frequency and proportion. RESULTS Among all 138 sequenced E. coli isolates, the most prevalent observed pathotype virulence genes were of extraintestinal E. coli UPEC fyuA gene 82.6% (114/138) and NMEC irp gene 81.9% (113/138). Most of the E. coli pathotypes observed exist as a hybrid due to gene overlapping, the most prevalent pathotypes observed were NMEC/UPEC hybrid 29.7% (41/138), NMEC/UPEC/EAEC hybrid 26.1% (36/138), NMEC/UPEC/DAEC hybrid 18.1% (25/138) and EAEC 15.2% (21/138). Overall most E. coli carried resistance gene to ampicillin 90.6% (125/138), trimethoprim 85.5% (118/138), tetracycline 79.9% (110/138), ciprofloxacin 76.1% (105/138) and 72.5% (100/138) Nalidixic acid. Hybrid pathotypes were more resistant than non-hybrid pathotypes. CONCLUSION Whole genome sequencing reveals the presence of hybrid pathotypes with increased drug resistance among E. coli isolated from regional referral hospitals in Tanzania.
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Affiliation(s)
- Livin E Kanje
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania.
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania.
| | - Happiness Kumburu
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Clinical Laboratory, Kilimanjaro Christian Medical Center, Kilimanjaro, Tanzania
| | - Davis Kuchaka
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Mariana Shayo
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Masoud A Juma
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- State University of Zanzibar, Zanzibar, Tanzania
| | - Patrick Kimu
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Melkiory Beti
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | | | - Boaz Wadugu
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Blandina T Mmbaga
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Clinical Laboratory, Kilimanjaro Christian Medical Center, Kilimanjaro, Tanzania
| | - Sixbert Isdory Mkumbaye
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Clinical Laboratory, Kilimanjaro Christian Medical Center, Kilimanjaro, Tanzania
| | - Tolbert Sonda
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Clinical Laboratory, Kilimanjaro Christian Medical Center, Kilimanjaro, Tanzania
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Campos-Madueno EI, Aldeia C, Perreten V, Sendi P, Moser AI, Endimiani A. Detection of blaCTX-M and blaDHA genes in stool samples of healthy people: comparison of culture- and shotgun metagenomic-based approaches. Front Microbiol 2023; 14:1236208. [PMID: 37720151 PMCID: PMC10501143 DOI: 10.3389/fmicb.2023.1236208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/16/2023] [Indexed: 09/19/2023] Open
Abstract
We implemented culture- and shotgun metagenomic sequencing (SMS)-based methods to assess the gut colonization with extended-spectrum cephalosporin-resistant Enterobacterales (ESC-R-Ent) in 42 volunteers. Both methods were performed using native and pre-enriched (broth supplemented with cefuroxime) stools. Native culture screening on CHROMID® ESBL plates resulted in 17 positive samples, whereas the pre-enriched culture (gold-standard) identified 23 carriers. Overall, 26 ESC-R-Ent strains (24 Escherichia coli) were identified: 25 CTX-M and 3 DHA-1 producers (2 co-producing CTX-Ms). Using the SMS on native stool ("native SMS") with thresholds ≥60% for both identity and coverage, only 7 of the 23 pre-enriched culture-positive samples resulted positive for blaCTX-M/blaDHA genes (native SMS reads mapping to blaCTX-M/blaDHAs identified in gold-standard: sensitivity, 59.0%; specificity 100%). Moreover, an average of 31.5 and 24.6 antimicrobial resistance genes (ARGs) were detected in the 23 pre-enriched culture-positive and the 19 negative samples, respectively. When the pre-enriched SMS was implemented, more blaCTX-M/blaDHA genes were detected than in the native assay, including in stools that were pre-enriched culture-negative (pre-enriched SMS reads mapping to blaCTX-M/blaDHAs identified in gold-standard: sensitivity, 78.3%; specificity 75.0%). In addition, the pre-enriched SMS identified on average 38.6 ARGs/sample, whereas for the corresponding native SMS it was 29.4 ARGs/sample. Notably, stools resulting false-negative by using the native SMS had lower concentrations of ESC-R-Ent (average: ~105 vs. ~107 CFU/g) and E. coli classified reads (average: 193,959 vs. 1.45 million) than those of native SMS positive samples. Finally, the detection of blaCTX-M/blaDHA genes was compared with two well-established bioinformatic tools. In conclusion, only the pre-enriched SMS assured detection of most carriers of ESC-R-Ent. However, its performance was not comparable to the pre-enriched culture-based approach.
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Affiliation(s)
- Edgar I. Campos-Madueno
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Claudia Aldeia
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Parham Sendi
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Aline I. Moser
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
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Intestinal colonization with multidrug-resistant Enterobacterales: screening, epidemiology, clinical impact, and strategies to decolonize carriers. Eur J Clin Microbiol Infect Dis 2023; 42:229-254. [PMID: 36680641 PMCID: PMC9899200 DOI: 10.1007/s10096-023-04548-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/11/2023] [Indexed: 01/22/2023]
Abstract
The clinical impact of infections due to extended-spectrum β-lactamase (ESBL)- and/or carbapenemase-producing Enterobacterales (Ent) has reached dramatic levels worldwide. Infections due to these multidrug-resistant (MDR) pathogens-especially Escherichia coli and Klebsiella pneumoniae-may originate from a prior asymptomatic intestinal colonization that could also favor transmission to other subjects. It is therefore desirable that gut carriers are rapidly identified to try preventing both the occurrence of serious endogenous infections and potential transmission. Together with the infection prevention and control countermeasures, any strategy capable of effectively eradicating the MDR-Ent from the intestinal tract would be desirable. In this narrative review, we present a summary of the different aspects linked to the intestinal colonization due to MDR-Ent. In particular, culture- and molecular-based screening techniques to identify carriers, data on prevalence and risk factors in different populations, clinical impact, length of colonization, and contribution to transmission in various settings will be overviewed. We will also discuss the standard strategies (selective digestive decontamination, fecal microbiota transplant) and those still in development (bacteriophages, probiotics, microcins, and CRISPR-Cas-based) that might be used to decolonize MDR-Ent carriers.
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Pankok F, Fuchs F, Loderstädt U, Kaase M, Balczun C, Scheithauer S, Frickmann H, Hagen RM. Molecular Epidemiology of Escherichia coli with Resistance against Third-Generation Cephalosporines Isolated from Deployed German Soldiers-A Retrospective Assessment after Deployments to the African Sahel Region and Other Sites between 2007 and 2016. Microorganisms 2022; 10:microorganisms10122448. [PMID: 36557701 PMCID: PMC9788009 DOI: 10.3390/microorganisms10122448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Colonization and infection with bacteria with acquired antibiotic resistance are among the risks for soldiers on international deployments. Enterobacterales with resistance against third-generation cephalosporines are amongst the most frequently imported microorganisms. To contribute to the scarcely available epidemiological knowledge on deployment-associated resistance migration, we assessed the molecular epidemiology of third-generation cephalosporine-resistant Escherichia coli isolated between 2007 and 2016 from German soldiers after deployments, with a particular focus on the African Sahel region. A total of 51 third-generation cephalosporine-resistant E. coli isolated from 51 military returnees from deployment collected during the assessment period between 2007 and 2016 were subjected to short-read next-generation sequencing analysis. Returnees from the Sahel region (Djibouti, Mali, South Sudan, Sudan, Sudan, and Uganda) comprised a proportion of 52.9% (27/51). Repeatedly isolated sequence types according to the Warwick University scheme from returnees from the Sahel region were ST38, ST131, and ST648, confirming previous epidemiological assessments from various sub-Saharan African regions. Locally prevalent resistance genes in isolates from returnees from the Sahel region associated with third-generation resistance were blaCTX-M-15, blaCTX-M-27, blaCTX-M-1, blaTEM-169, blaCTX-M-14, blaCTX-M-99-like, blaCTX-M-125, blaSHV-12, and blaDHA-1, while virulence genes were east1, sat, and tsh in declining order of frequency of occurrence each. In line with phenotypically observed high resistance rates for aminoglycosides and trimethoprim/sulfamethoxazole, multiple associated resistance genes were observed. A similar, slightly more diverse situation was recorded for the other deployment sites. In summary, this assessment provides first next-generation sequencing-based epidemiological data on third-generation cephalosporine-resistant E. coli imported by deployed German soldiers with a particular focus on deployments to the Sahel region, thus serving as a small sentinel. The detected sequence types are well in line with the results from previous epidemiological assessments in sub-Saharan Africa.
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Affiliation(s)
- Frederik Pankok
- Institute for Infection Control and Infectious Diseases, University Medical Center Göttingen, 37075 Göttingen, Germany
- Correspondence: (F.P.); (U.L.)
| | - Frieder Fuchs
- Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, 56070 Koblenz, Germany
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Medical Faculty and University Hospital of Cologne, 50931 Cologne, Germany
| | - Ulrike Loderstädt
- Institute for Infection Control and Infectious Diseases, University Medical Center Göttingen, 37075 Göttingen, Germany
- Correspondence: (F.P.); (U.L.)
| | - Martin Kaase
- Institute for Infection Control and Infectious Diseases, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Carsten Balczun
- Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, 56070 Koblenz, Germany
| | - Simone Scheithauer
- Institute for Infection Control and Infectious Diseases, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Hagen Frickmann
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, 20359 Hamburg, Germany
- Institute for Medical Microbiology, Virology and Hospital Hygiene, University Medicine Rostock, 18057 Rostock, Germany
| | - Ralf Matthias Hagen
- Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, 56070 Koblenz, Germany
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Genome stability during serial subculturing in hyperepidemic multidrug-resistant Klebsiella pneumoniae and Escherichia coli. J Glob Antimicrob Resist 2022; 31:152-161. [PMID: 36049731 DOI: 10.1016/j.jgar.2022.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/19/2022] [Accepted: 08/09/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES Core-genome single nucleotide variant (cgSNV) analysis represents a powerful tool for epidemiological investigations of multidrug-resistant (MDR) bacteria. However, cgSNV thresholds to confirm whether isolates are the same clone are not formally defined. METHODS We implemented hybrid whole-genome sequencing to study the genomic changes of four MDR isolates belonging to hyperepidemic sequence types (STs) during 20 propagation steps (T20) on MacConkey and CHROMID(R) ESBL plates. The following strains were analyzed: Klebsiella pneumoniae AE-2247421 (OXA-48/NDM-1-producing, ST101), K. pneumoniae MCL-2017-2 (CTX-M-15-producing, ST307), Escherichia coli Ec-042 (OXA-181-producing, ST410), and E. coli Ec-050 (NDM-5-producing, ST167). The genome assembly at T5 and T20 was compared to that at time point zero (T0) and to two reference genomes. RESULTS At T20, AE-2247421 lost the IncL blaOXA-48-carrying plasmid when grown on CHROMID(R) ESBL plates, while a large fragment encompassing blaNDM-1 was lost from its IncC plasmid when grown on both plates. In contrast, no structural changes were noted for the other three strains. Regarding the cgSNVs, the following results were obtained at T5 and T20 (ranges considering the different agar plates and reference genomes): AE-2247421 (1-8 and 2-12 cgSNVs), MCL-2017-2 (both 1-2 cgSNVs), Ec-042 (both 0 cgSNVs), and Ec-050 (0-6 and 0-9 cgSNVs). CONCLUSION We showed that structural changes and accumulation of cgSNVs can occur in few propagation steps under laboratory conditions. These changes might also arise in the clinical context in a short time, especially under antibiotics treatment. This phenomenon should be carefully considered because it might affect the final interpretation of epidemiological genomic analyses.
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Arieti F, Savoldi A, Rejendran NB, Sibani M, Tebon M, Pezzani MD, Gorska A, Wozniak TM, Tacconelli E. The antimicrobial resistance travel tool, an interactive evidence-based educational tool to limit antimicrobial resistance spread. J Travel Med 2022; 29:6554586. [PMID: 35348740 PMCID: PMC9282094 DOI: 10.1093/jtm/taac045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 11/14/2022]
Abstract
BACKGROUND International travel has been recognized as a risk factor contributing to the spread of antimicrobial resistance (AMR). However, tools focused on AMR in the context of international travel and designed to guide decision-making are limited. We aimed at developing an evidence-based educational tool targeting both healthcare professionals (HCPs) and international travellers to help prevent the spread of AMR. METHODS A literature review on 12 antimicrobial-resistant bacteria (ARB) listed as critical and high tiers in the WHO Pathogen Priority List covering four key areas was carried out: AMR surveillance data; epidemiological studies reporting ARB prevalence data on carriage in returning travellers; guidance documents reporting indications on screening for ARB in returning travellers and recommendations for ARB prevention for the public. The evidence, catalogued at country-level, provided the content for a series of visualizations that allow assessment of the risk of AMR acquisition through travel. RESULTS Up to January 2021, the database includes data on: (i) AMR surveillance for 2.018.241 isolates from 86 countries; (ii) ARB prevalence of carriage from 11.679 international travellers and (iii) 15 guidance documents published by major public health agencies. The evidence allowed the development of a consultation scheme for the evaluation of risk factors, prevalence of carriage, proportion and recommendations for screening of AMR. For the public, pre-travel practical measures to minimize the risk of transmission were framed. CONCLUSIONS This easy-to-use, annually updated, freely accessible AMR travel tool (https://epi-net.eu/travel-tool/overview/), is the first of its kind to be developed. For HCPs, it can provide a valuable resource for teaching and a repository that facilitates a stepwise assessment of the risk of AMR spread and strengthen implementation of optimized infection control measures. Similarly, for travellers, the tool has the potential to raise awareness of AMR and outlines preventive measures that reduce the risk of AMR acquisition and spread.
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Affiliation(s)
- Fabiana Arieti
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Verona 37134, Italy
| | - Alessia Savoldi
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Verona 37134, Italy
| | - Nithya Babu Rejendran
- Division of Infectious Diseases, Department of Internal Medicine I, German Center for Infection Research, University of Tübingen, Tübingen 72074, Germany.,German Centre for Infection Research (DZIF), Clinical Research Unit for Healthcare Associated Infections, Tübingen 72074, Germany
| | - Marcella Sibani
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Verona 37134, Italy
| | - Maela Tebon
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Verona 37134, Italy
| | - Maria Diletta Pezzani
- Division of Infectious Diseases, Department of Medicine, Verona University Hospital, Verona 37134, Italy
| | - Anna Gorska
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Verona 37134, Italy
| | - Teresa M Wozniak
- Menzies School of Health Research, Charles Darwin University, Darwin 8100, Northern Territory, Australia.,Australian e-Health Research Centre CSIRO, Brisbane 4000, Qeensland Australia
| | - Evelina Tacconelli
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Verona 37134, Italy.,Division of Infectious Diseases, Department of Internal Medicine I, German Center for Infection Research, University of Tübingen, Tübingen 72074, Germany.,German Centre for Infection Research (DZIF), Clinical Research Unit for Healthcare Associated Infections, Tübingen 72074, Germany
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Moser AI, Campos-Madueno EI, Sendi P, Perreten V, Keller PM, Ramette A, Endimiani A. Repatriation of a patient with COVID-19 contributed to the importation of an emerging carbapenemase producer. J Glob Antimicrob Resist 2021; 27:267-272. [PMID: 34718203 PMCID: PMC8552635 DOI: 10.1016/j.jgar.2021.10.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/07/2021] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVES Patients hospitalised abroad can become colonised with multidrug-resistant bacteria and import them to their home countries. In this study, we characterised an OXA-484 carbapenemase-producing Escherichia coli strain from a Swiss patient infected by SARS-CoV-2 and repatriated from India. METHODS At admission to Switzerland (April 2021), the patient undertook a nasopharyngeal swab to search for SARS-CoV-2 and a rectal swab to detect multidrug-resistant bacteria. Both SARS-CoV-2 and E. coli isolates were whole-genome sequenced and analysed for phylogenetic relatedness. RESULTS The patient was infected with the SARS-CoV-2 B.1.617.2 lineage (VOC Delta), a lineage that began to be reported across Switzerland at that time. He was also colonised with a sequence type 410 (ST410) E. coli strain (L3452210II) producing OXA-484, a single amino acid variant of OXA-181. The blaOXA-484 gene was carried by a 51.5 kb IncX3 plasmid identical to those described in blaOXA-181-harbouring ST410 E. coli strains. Core genome analysis showed that L3452210II was identical (ΔSNV ≤23) to two ST410 OXA-484 producers recently reported in Qatar and Germany, but differed from other ST410 OXA-181 producers reported worldwide. CONCLUSION The patient was infected by an emerging SARS-CoV-2 variant and also imported an E. coli producing OXA-484, an OXA-48-like carbapenemase not yet reported in Switzerland. The genetic background of L3452210II indicated that blaOXA-484 shared the same plasmid as blaOXA-181, but its bacterial host differed from most of the pandemic OXA-181-producing ST410 strains reported previously. This case description underlines that the COVID-19 crisis can contribute to the worldwide spread of emerging carbapenemase producers.
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Affiliation(s)
- Aline I Moser
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001, Bern, Switzerland
| | - Edgar I Campos-Madueno
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Parham Sendi
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Peter M Keller
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001, Bern, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001, Bern, Switzerland.
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Moser AI, Kuenzli E, Campos-Madueno EI, Büdel T, Rattanavong S, Vongsouvath M, Hatz C, Endimiani A. Antimicrobial-Resistant Escherichia coli Strains and Their Plasmids in People, Poultry, and Chicken Meat in Laos. Front Microbiol 2021; 12:708182. [PMID: 34381435 PMCID: PMC8350485 DOI: 10.3389/fmicb.2021.708182] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/05/2021] [Indexed: 01/05/2023] Open
Abstract
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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Affiliation(s)
- Aline I Moser
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Esther Kuenzli
- Department of Public Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland.,Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Thomas Büdel
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | | | | | - Christoph Hatz
- Department of Public Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland.,Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Division of Infectious Diseases and Hospital Epidemiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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