Multilocus sequence typing and bla ESBL characterization of extended-spectrum beta-lactamase-producing Escherichia coli isolated from healthy humans and swine in Northern Thailand

Chakkraphong Seenama; Visanu Thamlikitkul; Panan Ratthawongjirakul

doi:10.2147/IDR.S209545

Multilocus sequence typing and bla _ESBL characterization of extended-spectrum beta-lactamase-producing Escherichia coli isolated from healthy humans and swine in Northern Thailand

Infect Drug Resist. 2019 Jul 19:12:2201-2214. doi: 10.2147/IDR.S209545. eCollection 2019.

Authors

Chakkraphong Seenama^{1

2}, Visanu Thamlikitkul², Panan Ratthawongjirakul³

Affiliations

¹ Program of Molecular Sciences in Medical Microbiology and Immunology, Department of Transfusion Medicine and Clinical Microbiology, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand.
² Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
³ Research Group of Innovative Diagnosis of Antimicrobial Resistance, Department of Transfusion Medicine and Clinical Microbiology, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand.

Abstract

Purpose: Here, we investigated the genetic relationships and characteristics of extended- spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli) isolates from healthy hosts, humans in the community and swine among the livestock of Amphor Mueang, Lamphun Province, Thailand.

Patients and methods: Four hundred and nine rectal swabs were collected from healthy people and swine. A total of 212 ESBL-E. coli was isolated and phenotypically confirmed by a combination disk method. Putative ESBL-encoding genes, including bla _CTX-M, bla _TEM, and bla _SHV, were examined by multiplex-PCR. Randomly selected 42 ESBL-E. coli isolates were whole genome sequenced to characterize the ESBL-encoding genes and identify additional antimicrobial resistance genes. The genetic relatedness of 212 ESBL-E. coli was investigated by multilocus sequence typing.

Results: Overall, bla _CTX-M was the dominant ESBL-encoding gene found in 95.75% of the isolates, followed by bla _TEM (60.85%) and bla _SHV (2.40%). While bla _CTX-M-55 was the most common bla _ESBL subgroup found in this study. Whole genome sequencing showed a total of 15 different antimicrobial resistance genes other than bla _ESBL, including sul, qnr, aph(3')-Ia, among the selected 42 ESBL-E. coli isolates. Over half of the ESBL-E. coli (56.60%) carried bla _CTX-M co-existing with bla _TEM. The most common sequence types (STs) identified from human isolates were ST131, ST101, and ST70 while those isolated from swine were ST10, ST48, and ST131. ST131 strains carrying bla _CTX-M were the major isolated ESBL-E. coli strains, supporting a previous study that considered this strain truly pathogenic. Noticeably, 66.51% of ESBL-E. coli strains shared 19 identical STs, including a host-restricted ST131 between humans and swine, suggesting that transmission between these two hosts might be possible.

Conclusion: Proof of a direct transfer of ESBL-E. coli from animals to humans, or vice versa, is required for further elucidation. The ESBL-E. coli isolated from both types of healthy hosts may serve as a reservoir for community-acquired antimicrobial resistance.

Keywords: ESBL-E. coli; MLST; and blaSHV; blaCTX-M; blaTEM; genetic relatedness.