Spreading Patterns of NDM-Producing Enterobacteriaceae in Clinical and Environmental Settings in Yangon, Myanmar

Abstract

The spread of carbapenemase-producing Enterobacteriaceae (CPE), contributing to widespread carbapenem resistance, has become a global concern. However, the specific dissemination patterns of carbapenemase genes have not been intensively investigated in developing countries, including Myanmar, where NDM-type carbapenemases are spreading in clinical settings. In the present study, we phenotypically and genetically characterized 91 CPE isolates obtained from clinical (n = 77) and environmental (n = 14) samples in Yangon, Myanmar. We determined the dissemination of plasmids harboring genes encoding NDM-1 and its variants using whole-genome sequencing and plasmid analysis. IncFII plasmids harboring blaNDM-5 and IncX3 plasmids harboring blaNDM-4 or blaNDM-7 were the most prevalent plasmid types identified among the isolates. The IncFII plasmids were predominantly carried by clinical isolates of Escherichia coli, and their clonal expansion was observed within the same ward of a hospital. In contrast, the IncX3 plasmids were found in phylogenetically divergent isolates from clinical and environmental samples classified into nine species, suggesting widespread dissemination of plasmids via horizontal transfer. Half of the environmental isolates were found to possess IncX3 plasmids, and this type of plasmid was confirmed to transfer more effectively to recipient organisms at a relatively low temperature (25°C) compared to the IncFII plasmid. Moreover, various other plasmid types were identified harboring blaNDM-1, including IncFIB, IncFII, IncL/M, and IncA/C2, among clinical isolates of Klebsiella pneumoniae or Enterobacter cloacae complex. Overall, our results highlight three distinct patterns of the dissemination of blaNDM-harboring plasmids among CPE isolates in Myanmar, contributing to a better understanding of their molecular epidemiology and dissemination in a setting of endemicity.

<p>Emergence of Almost Identical F36:A-:B32 Plasmids Carrying <em>bla</em>_NDM-5 and <em>qepA</em> in <em>Escherichia coli </em>from Both Pakistan and Canada</p>

“…In E. coli C4109, bla NDM-7 was carried by a 49,828-bp IncX3 plasmid pHN4109c (MK088485), which shared 92% coverage and 99% identity with pKW53T-NDM (KX214669) from clinical E. coli in Kuwait, pNDM5_IncX3 (KU761328) from clinical K. pneumoniaee in China, and tig00000260 (CP021738) from E. coli in USA ( Figure 1A). IncX3 has dominated the spread of bla NDM in many countries, particularly in Asian countries, such as China, 9 Korea, 20 Myanmar, 21 and India. 22 To the best of our knowledge, this study was the first to identify bla NDM -positive IncX3 plasmid in Pakistan.…”

“…In the second part, bla NDM-5 gene was found embedded in an ISCR1 complex class 1 integron, which was sequentially organized as IS26-ΔISAba125-bla NDM-5 -ble MBL -trpF-tat-ISCR1-qacEΔ1-sul1-aad2-hp-dfrA12-ΔintI1, which was identical with the E. coli plasmid pM309-NDM5 (F36:A4:B-or F36:A20:B-, AP01 8833.1), pNDM-d2e9 (F2:A-:B-, CP026201.1), and pAMA1 167-NDM-5 (F1:A1:B49, CP024805.1) from Myanmar, USA, and Denmark, respectively. 21,25 The third part only contained one resistance gene, qepA. This genetic structure was sequentially organized as groEL/ΔintI1-ISCR3-qepA-ΔintI1-IS26-ΔTn2-ΔIS1, and was highly similar to that of pHN3A11 (JX997935.…”

Complete Nucleotide Sequence of Plasmids of Two Escherichia coli Strains Carrying blaNDM–5 and blaNDM–5 and blaOXA–181 From the Same Patient

“…pISV_IncI_CMY-42, that harbored the bla CMY-42 gene coding for beta-lactam resistance, exhibited high similarity to plasmid pCMY-42 (KY463221.1; 99.48% sequence similarity 93% query coverage) isolated in 2017 from an E. coli strain in Italy (Bitar et al, 2017). While pISV_IncX3_OXA181, which harbored genes coding for quinolone resistance (qnrS1) and betalactam resistance (bla OXA-181 ), showed 100% sequence similarity and coverage to several plasmids found in NCBI database (AP018837.1 (Sugawara et al, 2019); Myanmar, MG893567.1; China, CP024806; Denmark, MG570092; Lebanon (Bitar et al, 2018), KX894452.1; Germany, KX523903; Czechia).…”

Novel quinolone resistance determinant, qepA8, in Shigella flexneri isolated in the United States, 2016

“…Although, 2016AM-0877 was the first observed by Pathogen Detection (create date November 11, 2018), isolates cultured from specimens collected as early as 2010 were uploaded to NCBI and later found to be qepA8 -positive. A majority of the qepA8 -positive strains (n=15) were of clinical or environmental origin and were collected in Myanmar during August 2015-January 2017 (17, 18). Of the publicly available long-reads, one had a 149,768-bp plasmid—herein referred to as pM216_mF (Genbank LC492469)— which carried qepA8 in a complex composite transposon that appeared to be highly related (<10 single-nucleotide polymorphisms in the shared region [gray in Figure 1]) to that observed in 2016AM-0877.…”

“…Transformants were selected on LB plates containing 30 μg/mL of chloramphenicol. Plasmid size and qepA presence was confirmed by S1-PFGE (17) and PCR (5’-ATGTCCGCCACGCTCCACGAC-3’, 5’-TCAACCAGATGCGAGCGCTG-3’), respectively. Broth microdilution for the TOP10 transformants compared with untransformed E. coli TOP10 (performed in triplicate) found an at least eight-fold and a two-fold increase in MIC was observed for ciprofloxacin and levofloxacin (Table 1), respectively; however, MIC values remained significantly below clinical breakpoints (19).…”