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

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.

High Acquisition Rate of Gram-Negative Multi-Drug Resistant Organism Colonization During Hospitalization: A Perspective from a High Endemic Setting.

OBJECTIVE: The aim of the study was to compare the rate of gram-negative multi-drug resistant organism (GN-MDRO) colonization at admission and during hospitalization and to describe the strains and antibiotic resistance genes acquired during hospitalization. METHODS: Rectal swabs were collected from patients hospitalized at the National Trauma Center (NTC), Mongolia, at the time of admission and after 14 days of hospitalization as has been detailed on our previous study. GN-MDRO antibiotic resistance was determined using EUCAST standards, and resistance genes were detected using multiplex PCR. RESULTS: A total of 158 patients were screened, and baseline colonization rate at admission was 29.1% (46/158). The rate went up to 69.9% (110/158) after 14 days of hospitalization (p<0.001). Of all participants, 74 patients (46.8%) screened GN-MDRO negative at admission acquired colonization by day 14. Other 36 patients (22.8%) maintained colonization that was screened positive at both time points. Only 38 patients (24.0%) remained free of GN-MDRO during hospitalization. There was a difference in GN-MDRO acquisition between these groups. Patients who were negative at admission acquired up to 3 GN-MDRO species, and there were 10 different species isolated. Reversely, patients who were screened positive at both time points had fairly homogenous isolates; up to 5 species of Enterobacterales were identified at admission and day 14 hospitalization. Overall, Enterobacterales were the dominant colonizers (61.4%, 97/158), and all Enterobacterales were resistant to cefotaxime as CTX-M resistance was our inclusion criteria. CONCLUSION: GN-MDRO baseline colonization rate on admission was high and, alarmingly, doubled during hospitalization in the study area. Enterobacterales was the predominant colonizer and was highly resistant to 3rd generation cephalosporin. This data supports a need for an improved infection control policy including routine surveillance of the GN-MDROs and improved antibiotic stewardship program.

HPV genoprevalence and HPV knowledge in young women in Mongolia, five years following a pilot 4vHPV vaccination campaign.

BACKGROUND: In a 2012 pilot, 9111 Mongolian girls aged 11-17 years received three doses of the quadrivalent (4vHPV) vaccine, Gardasil®. This is the first study to measure early vaccine effectiveness and assess knowledge and attitudes of young women in Mongolia in relation to the human papillomavirus (HPV), the vaccine and cervical cancer. METHODS: A cohort of women vaccinated in 2012 (n = 726) and an unvaccinated cohort (n = 790) provided self-administered vaginal swabs for detection of high-risk HPV genotypes 16, 18/45, 31, 33, 35, 39, 51, 52, 56, 58, 59, 66, 68 five years following vaccination. Participant knowledge and attitudes were assessed through a questionnaire. RESULTS: A total of 1882 questionnaires and 1516 self-administered vaginal swabs were analyzed. The prevalence of any HRHPV was 39.5% among both cohorts. The prevalence of vaccine-targeted HPV types was significantly lower in the vaccinated cohort than unvaccinated: 4.8% and 17.2% respectively. The 4vHPV was shown to be protective against HRHPV 16, 18/45 with 75% vaccine effectiveness. Participant knowledge was low. CONCLUSIONS: This study demonstrates that the 4vHPV is associated with reduced vaccine-targeted HPV detection rates in young Mongolian women. The questionnaire results highlight a need for awareness-raising initiatives in Mongolia on HPV, the vaccine and cervical cancer.

Genetic and biochemical characterisation of CTX-M-37 extended-spectrum ß-lactamase from an Enterobacter cloacae clinical isolate from Mongolia.

OBJECTIVES: The aims of this study were to determine the resistance level of a blaCTX-M-37-carrying Enterobacter cloacae isolate from Mongolia, to analyse kinetic parameters of the purified enzyme and to compare the genetic environment of the gene. METHODS: Minimum inhibitory concentrations (MICs) were determined using the Clinical and Laboratory Standards Institute (CLSI) agar dilution method. Purified CTX-M-37 enzyme was used to determined kinetic parameters. The genetic environment of the blaCTX-M-37 gene in E. cloacae was compared with a Kluyvera cryocrescens isolate. RESULTS: The E. cloacae isolate showed relatively low-level resistance to cefotaxime (MIC=16mg/L) compared with a CTX-M-3-producing strain (MIC=256mg/L), and CTX-M-37 had a lower kcat/Km value for cefotaxime (2.0µM-1s-1) compared with CTX-M-3 (3.5µM-1s-1), possibly due to Asn114Asp substitution. The blaCTX-M-37 gene in the E. cloacae isolate was carried on a conjugative plasmid and was associated with an ISEcp1 element containing the -35 and -10 putative promoter sequences TTGAAA and TACAAT, respectively, unlike in the K. cryocrescens isolate. CONCLUSIONS: The CTX-M-37-producing E. cloacae isolate showed relatively low-level resistance to cefotaxime and the purified enzyme had lower kinetic parameters as the result of Asn114Asp substitution. Presence of an ISEcp1 element and putative promoters upstream of the blaCTX-M-37 gene in E. cloacae, but not in the K. cryocrescens isolate, indicated their roles in mobilisation and expression of the gene.

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

Gram-negative multidrug-resistant organisms (GN-MDRO) producing ß-lactamases (ESBL, plasmid-mediated AmpC ß-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 (blaIMP-1, blaVIM, blaGES, blaNDM, blaKPC, blaOXA-48, blaGIM-1, blaOXA-23, blaOXA-24/40, blaOXA-51, blaOXA-58, blaOXA-143, blaOXA-235, blaCTX-M, blaSHV blaTEM and plasmid-mediated blaAmpC). 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 (p<0.001). Due to the different medical specialities the two study populations differed significantly in age (p<0.029) and gender (p<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 E. coli, followed by CTX-M-producing K. pneumoniae and CTX-M-producing E. cloacae. 158 patients from the NTORC were re-screened after 14 days of whom 99 had acquired a new GN-MDRO (p<0.001). Carbapenemases were detected in both centres in four OXA-58-producing A. baumannii isolates (ST642) and six VIM-2-producing P. aeruginosa 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.

Sexually transmitted infections among pregnant women attending antenatal clinics in Mongolia: potential impact on the Mongolian HIV epidemic.

We conducted Mongolia's first nation-wide cross-sectional survey of sexually transmitted infections (STIs) among pregnant women attending prenatal care. Among our 2000 participants, 386 (19.3%) were infected with Chlamydia trachomatis, 133 (6.7%) with Trichomonas vaginalis, 121 (6.1%) with Neisseria gonorrhoeae, and 128 (6.4%) were seropositive for Treponemal antibodies. None of our participants were seropositive for HIV infection. Additionally, 605 (30.3%) of the women had at least one STI, 133 (6.7%) had a double infection, and 15 (0.8%) had a triple infection. Our results suggest that STIs are a serious problem in Mongolia. Pregnant women represent a lower-risk general population; these high STI rates suggest that at this nascent stage, the identification, treatment, and prevention of STIs as risk factors for HIV transmission are crucial in the prevention of the emerging Mongolian HIV epidemic.