Evidence map›Paper›PMID 42409369›Full record

ArticleThe Journal of infectious diseases2026

Diverse Genetic Lineages Spreading Across Healthcare and Community Boundaries Underlie Extended-Spectrum Cephalosporin-Resistant Enterobacterales Colonization Burden in Botswana.

Tiffany Wan, Ebbing Lautenbach, Naledi Mannathoko, Mosepele Mosepele, Ashley Styczynski, Gemma Parra, Rachel M Smith, Robert Gross, Leigh Cressman, Anne Jaskowiak-Barr and 9 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in The Journal of infectious diseases, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

19 authors.

Tiffany WanDepartment of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA.ORCID 0000-0001-8446-3114
Ebbing LautenbachDivision of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.ORCID 0000-0003-4772-2409
Naledi MannathokoDepartment of Biomedical Sciences, University of Botswana, Gaborone, Botswana.
Mosepele MosepeleDepartment of Internal Medicine, University of Botswana, Gaborone, Botswana.ORCID 0000-0002-6051-0999
Ashley StyczynskiDivision of Healthcare Quality Promotion, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA.ORCID 0000-0002-4682-8087
Gemma ParraDivision of Healthcare Quality Promotion, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA.
Rachel M SmithDivision of Healthcare Quality Promotion, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA.
Robert GrossDivision of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
Leigh CressmanCenter for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
Anne Jaskowiak-BarrCenter for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
Kevin AlbyDepartment of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina, USA.ORCID 0000-0003-4637-8474
Laurel GlaserDepartment of Pathology and Laboratory Medicine, University Pennsylvania, Philadelphia, Pennsylvania, USA.
Melissa Richard-GreenblattDepartment of Laboratory Medicine, Public Health Ontario, Toronto, Ontario, Canada.ORCID 0000-0001-6717-8856
Laura CowdenCenter for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.ORCID 0009-0002-6469-9271
Alexa PatelCenter for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
Dimpho OtukileDepartment of Medicine, Botswana-University of Pennsylvania Partnership (BUP), Gaborone, Botswana.
Giacomo M PaganottiDivision of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
Margaret MokomaneSchool of Allied Health Professions, University of Botswana, Gaborone, Botswana.ORCID 0000-0002-4406-3594
Evan SnitkinDepartment of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA.ORCID 0000-0001-8409-278X

Funding

Virus & Reservoirs CoreP30AI045008 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI DAVID S METZGER · 1999 to 2026
$78.6M
University of Michigan Training Program in Genomic ScienceT32HG000040 · NHGRI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Sebastian Zoellner · 1995 to 2026
$16.4M
Broad Agency Announcement 75D30118C02919Broad Agency Announcement FY2018-OADS-01Intramural CDC HHS CC999999JG CDC HHSNHGRI NIH HHS T32 HG000040NIAID NIH HHS P30 AI045008NIH HHS P30 AI 045008Penn Center for AIDS ResearchPrevention of Healthcare Associated Infections
6 · The paper itself

Abstract

backgroundAlthough extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE) are a global health challenge, molecular data from low- and middle-income countries are limited. We used whole-genome sequencing to characterize ESCrE in community and healthcare settings in Botswana.

methodsStudy isolates were collected from 3 hospitals and 6 outpatient clinics in Botswana, as well as from adults and children in the community. Enrollment occurred from 15 January to 4 September 2020 but was paused from 2 April to 21 May 2020 due to a countrywide coronavirus disease 2019 (COVID-19) lockdown. Isolates from rectal swab specimens obtained from participants testing positive for ESCrE underwent whole-genome sequencing. Genomic data were analyzed to characterize resistance genes, sequence types (STs), and exposures associated with putative interpersonal transmission.

resultsEscherichia coli and Klebsiella pneumoniae ESCrE were diverse, represented by 87 and 49 STs, respectively, carrying 16 distinct extended-spectrum β-lactamase (ESBL) gene alleles. Twelve E. coli STs accounted for most isolates, with these common STs observed in both community and healthcare settings and increasing in the proportion after lockdown (from 61% to 80%). Examination of factors associated with harboring genetically similar E. coli revealed shared household and social networks across lockdown periods, with differences in shared hospital exposure and participant age between lockdown periods.

conclusionsGenomic characterization of ESCrE in Botswana revealed diverse STs carrying common ESBL genes, with overlapping STs among hospital and community participants consistent with intersecting transmission networks. Risk analysis of transmission supported the role of direct human contact, with the COVID-19 lockdown affecting the diversity of ESCrE and transmission pathways, highlighting the potential for behavioral changes to affect ESCrE spread.

Indexed as

Cephalosporin ResistanceEnterobacteriaceaeEnterobacteriaceae InfectionsAdolescentAdultAnti-Bacterial AgentsBotswanaCephalosporinsChildChild, PreschoolCOVID-19Escherichia coliFemaleHumansKlebsiella pneumoniaeMaleAnti-Bacterial AgentsCephalosporinsantibiotic resistanceextended-spectrum cephalosporin-resistancegenomicsmiddle- and low-income country

Identifiers

PMID42409369
PMCPMC13668363

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.