Primers used in this study for PCR and sequencing.

<p>Primers used in this study for PCR and sequencing.</p

Faecal Carriage of Gram-Negative Multidrug-Resistant Bacteria among Patients Hospitalized in Two Centres in Ulaanbaatar, Mongolia

<div><p>Gram-negative multidrug-resistant organisms (GN-MDRO) producing β-lactamases (ESBL, plasmid-mediated AmpC β-lactamases and carbapenemases) are increasingly reported throughout Asia. The aim of this surveillance study was to determine the rate of bacterial colonization in patients from two hospitals in the Mongolian capital Ulaanbaatar. Rectal swabs were obtained from patients referred to the National Traumatology and Orthopaedics Research Centre (NTORC) or the Burn Treatment Centre (BTC) between July and September 2014, on admission and again after 14 days. Bacteria growing on selective chromogenic media (CHROMagar ESBL/KPC) were identified by MALDI-ToF MS. We performed susceptibility testing by disk diffusion and PCR (<i>bla</i>_IMP-1, <i>bla</i>_VIM, <i>bla</i>_GES, <i>bla</i>_NDM, <i>bla</i>_KPC, <i>bla</i>_OXA-48, <i>bla</i>_GIM-1, <i>bla</i>_OXA-23, <i>bla</i>_OXA-24/40, <i>bla</i>_OXA-51, <i>bla</i>_OXA-58, <i>bla</i>_OXA-143, <i>bla</i>_OXA-235, <i>bla</i>_CTX-M, <i>bla</i>_SHV <i>bla</i>_TEM and plasmid-mediated <i>bla</i>_AmpC). Carbapenemase-producing isolates were additionally genotyped by PFGE and MLST. During the study period 985 patients in the NTORC and 65 patients in the BTC were screened on admission. The prevalence of GN-MDRO-carriage was 42.4% and 69.2% respectively (<i>p</i><0.001). Due to the different medical specialities the two study populations differed significantly in age (<i>p<</i>0.029<i>)</i> and gender (<i>p</i><0.001) with younger and more female patients in the burn centre (BTC). We did not observe a significant difference in colonization rate in the respective age groups in the total study population. In both centres most carriers were colonized with CTX-M-producing <i>E</i>. <i>coli</i>, followed by CTX-M-producing <i>K</i>. <i>pneumoniae</i> and CTX-M-producing <i>E</i>. <i>cloacae</i>. 158 patients from the NTORC were re-screened after 14 days of whom 99 had acquired a new GN-MDRO (<i>p</i><0.001). Carbapenemases were detected in both centres in four OXA-58-producing <i>A</i>. <i>baumannii</i> isolates (ST642) and six VIM-2-producing <i>P</i>. <i>aeruginosa</i> isolates (ST235). This study shows a high overall prevalence of GN-MDRO in the study population and highlights the importance of routine surveillance, appropriate infection control practice and antibiotic prescribing policies to prevent further spread especially of carbapenemases.</p></div

Patient characteristics of the study population with univariable analysis of the two study sites.

<p>Patient characteristics of the study population with univariable analysis of the two study sites.</p

GN-MDRO grouped by species and resistance mechanisms at the two sampling sites.

<p>GN-MDRO grouped by species and resistance mechanisms at the two sampling sites.</p

Resistance rates of relevant Gram-negative multidrug-resistant bacteria.

<p>Resistance rates of relevant Gram-negative multidrug-resistant bacteria.</p

Molecular epidemiology of SARS‐CoV‐2 in Mongolia, first experience with nanopore sequencing in lower‐ and middle‐income countries setting

Abstract Background Coronavirus disease (COVID‐19) has had a significant impact globally, and extensive genomic research has been conducted on severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) lineage patterns and its variants. Mongolia's effective response resulted in low prevalence until vaccinations became available. However, due to the lack of systematically collected data and absence of whole genome sequencing capabilities, we conducted a two‐stepped, nationally representative molecular epidemiologic study of SARS‐CoV‐2 in Mongolia for 2020 and 2021. Methods We used retrospective analysis of stored biological samples from November 2020 to October 2021 and a variant‐specific real‐time reverse transcription polymerase chain reaction (RT‐PCR) test to detect SARS‐CoV‐2 variants, followed by whole genome sequencing by Nanopore technology. Samples were retrieved from different sites and stored at −70°C deep freezer, and tests were performed on samples with cycle threshold <30. Results Out of 4879 nucleic acid tests, 799 whole genome sequencing had been carried out. Among the stored samples of earlier local transmission, we found the 20B (B.1.1.46) variant predominated in the earlier local transmission period. A slower introduction and circulation of alpha and delta variants were observed compared to global dynamics in 2020 and 2021. Beta or Gamma variants were not detected between November 2020 and September 2021 in Mongolia. Conclusions SARS‐CoV‐2 variants of concerns including alpha and delta were delayed in circulation potentially due to public health stringencies in Mongolia. We are sharing our initial experience with whole genome sequencing of SARS‐CoV‐2 from Mongolia, where sequencing data is sparse