Genomic Characterization of Drug-Resistant Mycobacterium tuberculosis L2/Beijing Isolates from Astana, Kazakhstan.

Kazakhstan ranks among the countries with the highest number of MDR-TB patients per 100,000 population worldwide. The successful transmission of local MDR strains of Mycobacterium tuberculosis (Mtb) poses a significant threat to disease control. In this study, we employed whole-genome sequencing to examine drug resistance, compensatory mutations, population structure, and transmission patterns in a sample of 24 clinical isolates of L2/Beijing Mtb collected in Astana, Kazakhstan between 2021 and 2022. The genotypic prediction of Mtb susceptibility to anti-TB agents was consistent with the phenotypic susceptibility, except for bedaquiline. An analysis of resistance-associated genes characterized most of the isolates as pre-extensively drug-resistant tuberculosis (pre-XDR-TB) (n = 15; 62.5%). The phylogenetic analysis grouped the isolates into four transmission clusters; the dominant cluster was assigned to the "aggressive" Central Asia outbreak (CAO) clade of L2/Beijing (n = 15; 62.5%). Thirteen mutations with putative compensatory effects were observed exclusively in Mtb isolates containing the rpoB S450L mutation. The putative compensatory mutations had a stabilizing effect on RpoABC protein stability and dynamics. The high prevalence of the CAO clade in the population structure of Mtb may explain the rapid spread of MDR-TB in Kazakhstan.

Association of different microbes and pathogenic factors in cases of infectious bovine keratoconjunctivitis in cattle from Eastern Kazakhstan.

Background and Aim: Infectious bovine keratoconjunctivitis (IBK) causes a significant economic loss to cattle industries in many countries, including Kazakhstan. Although Moraxella bovis is recognized as an etiologic agent of IBK, other bacterial and viral agents have been suspected to play a role in the pathogenesis of this disease. This study aimed to evaluate samples collected from the eyes of IBK-affected cattle in Eastern Kazakhstan at different stages of IBK for the presence of Mor. bovis, Moraxella bovoculi, Mycoplasma bovis, Mycoplasma bovoculi, and Bovine Herpes Virus Type 1 (BHV-1) and to characterize Mor. bovoculi pilA gene sequence diversity from Mor. bovoculi positive samples. Materials and Methods: Individual ocular swabs (n = 168) were collected from cattle that had clinical signs of IBK during the summer of 2022 on farms in the Abay region of Kazakhstan. Eye lesion scores (1, 2, and 3) were assigned depending on the degree of ocular damage. Infectious bovine keratoconjunctivitis-associated organisms were detected using a multiplex real-time polymerase chain reaction assay. The Mor. bovoculi pilA gene was sequenced from Mor. bovoculi positive samples. Results: Mycoplasma bovis and BHV-1 were not detected in any of the collected samples. Mycoplasma bovoculi was identified in the majority of samples overall, usually in mixed infection with Moraxella spp. Moraxella bovoculi was detected in 76.2% of animals and predominated in animals with eye lesion scores 2 and 3. Mycoplasma bovoculi was detected only in association with Mor. bovis and/or Mor. bovoculi in animals with eye lesion scores 2 and 3. Moraxella bovis was found in 57.7% of animals and was always identified in association with another organism. Sequencing of the pilA gene in 96 samples from Mor. bovoculi positive samples identified five PilA groups. The majority belonged to PilA group A. However, three new PilA groups were identified and designated PilA groups N, O, and P. Conclusion: The results indicate a high prevalence of Myc. bovoculi and Mor. bovoculi in eyes of cattle with IBK on livestock farms in Eastern Kazakhstan. Additional novel Mor. bovoculi PilA groups were identified.

Brucella abortus in Kazakhstan, population structure and comparison with worldwide genetic diversity.

Brucella abortus is the main causative agent of brucellosis in cattle, leading to severe economic consequences in agriculture and affecting public health. The zoonotic nature of the infection increases the need to control the spread and dynamics of outbreaks in animals with the incorporation of high resolution genotyping techniques. Based on such methods, B. abortus is currently divided into three clades, A, B, and C. The latter includes subclades C1 and C2. This study presents the results of whole-genome sequencing of 49 B. abortus strains isolated in Kazakhstan between 1947 and 2015 and of 36 B. abortus strains of various geographic origins isolated from 1940 to 2004. In silico Multiple Locus Sequence Typing (MLST) allowed to assign strains from Kazakhstan to subclades C1 and to a much lower extend C2. Whole-genome Single-Nucleotide Polymorphism (wgSNP) analysis of the 46 strains of subclade C1 with strains of worldwide origins showed clustering with strains from neighboring countries, mostly North Caucasia, Western Russia, but also Siberia, China, and Mongolia. One of the three Kazakhstan strains assigned to subclade C2 matched the B. abortus S19 vaccine strain used in cattle, the other two were genetically close to the 104 M vaccine strain. Bayesian phylodynamic analysis dated the introduction of B. abortus subclade C1 into Kazakhstan to the 19th and early 20th centuries. We discuss this observation in view of the history of population migrations from Russia to the Kazakhstan steppes.

Highly pathogenic avian influenza virus of the A/H5N8 subtype, clade 2.3.4.4b, caused outbreaks in Kazakhstan in 2020.

Background: Large poultry die-offs happened in Kazakhstan during autumn of 2020. The birds' disease appeared to be avian influenza. Northern Kazakhstan was hit first and then the disease propagated across the country affecting eleven provinces. This study reports the results of full-genome sequencing of viruses collected during the outbreaks and investigation of their relationship to avian influenza virus isolates in the contemporary circulation in Eurasia. Methods: Samples were collected from diseased birds during the 2020 outbreaks in Kazakhstan. Initial virus detection and subtyping was done using RT-PCR. Ten samples collected during expeditions to Northern and Southern Kazakhstan were used for full-genome sequencing of avian influenza viruses. Phylogenetic analysis was used to compare viruses from Kazakhstan to viral isolates from other world regions. Results: Phylogenetic trees for hemagglutinin and neuraminidase show that viruses from Kazakhstan belong to the A/H5N8 subtype and to the hemagglutinin H5 clade 2.3.4.4b. Deduced hemagglutinin amino acid sequences in all Kazakhstan's viruses in this study contain the polybasic cleavage site (KRRKR-G) indicative of the highly pathogenic phenotype. Building phylogenetic trees with the Bayesian phylogenetics results in higher statistical support for clusters than using distance methods. The Kazakhstan's viruses cluster with isolates from Southern Russia, the Russian Caucasus, the Ural region, and southwestern Siberia. Other closely related prototypes are from Eastern Europe. The Central Asia Migratory Flyway passes over Kazakhstan and birds have intermediate stops in Northern Kazakhstan. It is postulated that the A/H5N8 subtype was introduced with migrating birds. Conclusion: The findings confirm the introduction of the highly pathogenic avian influenza viruses of the A/Goose/Guangdong/96 (Gs/GD) H5 lineage in Kazakhstan. This virus poses a tangible threat to public health. Considering the results of this study, it looks justifiable to undertake measures in preparation, such as install sentinel surveillance for human cases of avian influenza in the largest pulmonary units, develop a human A/H5N8 vaccine and human diagnostics capable of HPAI discrimination.

Genome Sequence of Atyrau-5BJN(IL18), a Recombinant Lumpy Skin Disease Virus with Knockout of Virulence Genes.

Here, we present the coding sequence of the genome of the recombinant lumpy skin disease virus (LSDV) Atyrau-5BJN(IL18), obtained by knocking out four genes in the genome of a virulent field LSDV isolate. Genome sequencing confirmed the deletion of genes and the insertion of a foreign sequence in the viral genome.

Whole genome sequence analysis of Neisseria meningitidis strains circulating in Kazakhstan, 2017-2018.

Neisseria meningitidis (meningococcus) is a cosmopolitan bacterium that is often found in the upper respiratory tract of asymptomatic humans. However, N. meningitidis also causes meningeal inflammation and/or sepsis in humans with a periodic resurgence in incidence and high mortality rates. The pathogen is highly diverse genetically and antigenically, so that genotyping is considered important for vaccine matching to circulating strains. Annual incidence of meningococcal disease in Kazakhstan ranges between 0.2 and 2.5 cases per 100 thousand population. In total, 78 strains of N. meningitidis were isolated from clinical patients and contact persons during the years 2017-2018 in Kazakhstan. Of these, 41 strains including four from the patients and 37 from contacts, were sequenced using Illumina MiSeq. In silico typing was completed using the Neisseria pipeline 1.2 on the Galaxy Workflow Management System and PubMLST. Whole genome SNP (single nucleotide polymorphisms) trees were built using BioNumerics 8. Seven-gene multilocus sequence typing (MLST) identified ten sequence types (ST), two of which have not been previously described (ST-16025; ST-16027). ST-16025 was detected in two patients with invasive meningococcal disease in 2017 and 2018 in Akmola region and 16 contacts in 2017 in Turkistan region. This prevalent type ST-16025 demonstrates considerable intertypic diversity as it consists of three subcomplexes with a distance of more than 2000 SNPs. Invasive and carrier strains belong to different serogroups (MenB and MenC), PorA and FetA_VR. Two invasive strains were MenB, one MenC and one MenW (Hajj lineage). The strains from the contact persons were: MenC (n = 18), cnl (n = 9), MenY (n = 7), MenW (n = 1), MenB (n = 1) and one unidentifiable. Different numbers of alleles were present: 12, 11, 7, and 7 alleles for PorA, FetA, fHbp, and NHBA, respectively. This study is the first report of the genetic diversity of N. meningitidis strains in Kazakhstan. Despite limitations with the studied sample size, important conclusions can be drawn based on data produced. This study provides evidence for regulatory authorities with regard to changing routine diagnostic protocols to increase the collecting of samples for WGS.

Analysis of Bacteroides fragilis Clinical Strains Isolated in Kazakhstan.

Our aim was to study the nucleotide sequences of 9 previously undescribed strains of B. fragilis collected from patients with intra-abdominal diseases at city hospitals in Nur-Sultan, Kazakhstan.

Bacillus anthracis Phylogeography: New Clues From Kazakhstan, Central Asia.

This article describes Bacillus anthracis strains isolated in Kazakhstan since the 1950s until year 2016 from sixty-one independent events associated with anthrax in humans and animals. One hundred and fifty-four strains were first genotyped by Multiple Locus VNTR (variable number of tandem repeats) Analysis (MLVA) using 31 VNTR loci. Thirty-five MLVA31 genotypes were resolved, 28 belong to the A1/TEA group, five to A3/Sterne-Ames group, one to A4/Vollum and one to the B clade. This is the first report of the presence of the B-clade in Kazakhstan. The MLVA31 results and epidemiological data were combined to select a subset of seventy-nine representative strains for draft whole genome sequencing (WGS). Strains from Kazakhstan significantly enrich the known phylogeny of the Ames group polytomy, including the description of a new branch closest to the Texas, United States A.Br.Ames sublineage stricto sensu. Three among the seven currently defined branches in the TEA polytomy are present in Kazakhstan, "Tsiankovskii", "Heroin", and "Sanitary Technical Institute (STI)". In particular, strains from the STI lineage are largely predominant in Kazakhstan and introduce numerous deep branching STI sublineages, demonstrating a high geographic correspondence between "STI" and Kazakhstan, Central Asia. This observation is a strong indication that the TEA polytomy emerged after the last political unification of Asian steppes in the fourteenth century of the Common Era. The phylogenetic analysis of the Kazakhstan data and of currently available WGS data of worldwide origin strengthens our understanding of B. anthracis geographic expansions in the past seven centuries.

Coding-Complete Genome Sequence of Swine Influenza Virus Isolate A/Swine/Karaganda/04/2020 (H1N1) from Kazakhstan.

Here, we report the coding-complete genome sequence of a clinical sample of influenza virus obtained from a pig at a livestock farm in Karaganda, Central Kazakhstan, during a pig study in 2020. Isolate A/Swine/Karaganda/04/2020 (H1N1) belongs to clade 1A.3.2.2 lineage 1A, which includes the 2009 H1N1 pandemic strains.

Draft Genome Sequences of Three Pasteurella multocida Strains Isolated from Domestic Animals in Kazakhstan.

We report here the draft genome sequences of three strains of Pasteurella multocida isolated in Kazakhstan from domestic animals that died due to hemorrhagic septicemia.

Draft Genome Sequence of Moraxella bovoculi Strain KZ-1, Isolated from Cattle in North Kazakhstan.

Moraxella bovoculi strain KZ-1 was isolated from cattle that had symptoms of infectious bovine keratoconjunctivitis (IBK) in northern Kazakhstan. Here, we report the draft genome sequence of this strain.

Retrospective Analysis of the Relationship between Two Anthrax Outbreaks in Kazakhstan Based on Genomic Data.

We present a retrospective analysis of strains from two anthrax outbreaks in western Kazakhstan in 2009. The outbreaks occurred during the same period and in the same area located close to main roads, favoring a single source of infection. However, multilocus variable-number tandem-repeat analysis (MLVA), canonical single-nucleotide polymorphism (CanSNP) analysis, and genome-wide analysis demonstrated that the outbreaks were not connected.

Draft Genome Sequence of the Strain Francisella tularensis subsp. mediasiatica 240, Isolated in Kazakhstan.

Francisella tularensis subsp. mediasiatica is the least studied among the four F. tularensis subspecies. We present here the genome data of F. tularensis subsp. mediasiatica 240, isolated in the southern region of Kazakhstan.

Draft Genome Sequence of a Potential Commercial Biocellulose Producer, Strain Komagataeibacter europaeus GH1.

In this work, we present the draft genome sequence of Komagataeibacter europaeus strain GH1, which is an extremely efficient biocellulose producer.