Phylogenetic inference of Coxiella burnetii by 16S rRNA gene sequencing

Bacterial burden and molecular characterization of Coxiella burnetii in shedding pregnant and postpartum ewes from Saint Kitts

This study aimed to evaluate the bacterial burden and perform molecular characterization of Coxiella burnetii during shedding in pregnant (vaginal, mucus and feces) and postpartum (vaginal mucus, feces and milk) ewes from Saint Kitts. Positive IS1111 DNA (n=250) for C. burnetii samples from pregnant (n=87) and postpartum (n=74) Barbados Blackbelly ewes in a previous investigation were used for this study. Vaginal mucus (n=118), feces (n=100), and milk (n=32) positive IS1111 C. burnetii-DNA were analysed by real time qPCR (icd gene). For molecular characterization of C. burnetii, selected (n=10) IS1111 qPCR positive samples were sequenced for fragments of the IS1111 element and the 16 S rRNA gene. nBLAST, phylogenetic and haplotype analyses were performed. Vaginal mucus, feces and milk had estimated equal amounts of bacterial DNA (icd copies), and super spreaders were detected within the fecal samples. C. burnetii haplotypes had moderate to high diversity, were ubiquitous worldwide and similar to previously described in ruminants and ticks and humans.

Molecular detection and genetic characterization of Coxiella-like endosymbionts in dogs and ticks infesting dogs in Northeast India

An epidemiological study was performed to determine the role of dogs and ticks infesting dogs in the transmission of Q fever in humans and animals from April 2019 to March 2020 in the northeastern hill states of India. In total, 245 pet and stray dogs irrespective of age or sex were sampled, without specific inclusion or exclusion criteria. In total, 478 ticks belonging to three species were detected, namely Rhipicephalus sanguineus, Rhipicephalus (Boophilus) microplus and Hyalomma anatolicum anatolicum. The DNA extracted from blood and tick samples was assayed for molecular characterization of Coxiella burnetii targeting the 16S rRNA and superoxide dismutase (SOD) genes. Amplified PCR products were purified, cloned and custom sequenced. PCR assay showed 3.3% (8/245) of the dogs were positive for Coxiella-like bacteria. Coxiella-like bacterial DNA was detected in adult fully engorged females of R. sanguineus (7.7%, 13/168), R. (B.) microplus (3.3%, 4/123) and H. anatolicum (1.9%, 1/54). Coxiella-like bacterial DNA lacked in adult male or nymphal stage. The infection rate did not vary significantly between seasons, nor according to sex or age of the host. Six nucleotide sequences of 16S rRNA and SOD genes are discussed.

16S rDNA and ITS Sequence Diversity of Burkholderia mallei Isolated from Glanders-Affected Horses and Mules in India (2013-2019)

Glanders is a highly contagious and fatal infection of equids caused by the bacteria known as Burkholderia mallei. It is one of the notifiable equine diseases and is still present in Asia, South America and Africa. In India, glanders re-emerged in 2006, and thereafter, increasing numbers of cases were reported in different regions of the country. Between 2013 and 2019, 39 B. mallei were isolated from glanders-affected horses (n = 30) and mules (n = 9) from seven states of India such as Uttar Pradesh, Haryana, Delhi, Himachal Pradesh, Gujarat, Maharashtra and Tamil Nadu. In this study, the phylogenetic relationships of these isolates were assessed by sequence analysis of 16S rDNA gene and ITS region. Purified PCR-amplified products of 16S rDNA gene and ITS region were sequenced, aligned and phylogenetic trees were constructed using MEGA 11 software. Additionally, B. mallei 16S rDNA (n = 36) and ITS (n = 18) sequences available in the GenBank were also included for analysis to determine the diversity of older B. mallei isolates with recent Indian isolates. Both the phylogeny showed that the majority of the recent isolates from India are closely related to each other, but are genetically diverse from older isolates that originated from India. Nucleotide substitutions were also observed in a single and double position in 12 recent and two old Indian isolates. The study also indicates that similar B. mallei strains were responsible for glanders outbreaks in different states (Uttar Pradesh- Himachal Pradesh and Uttar Pradesh- Haryana) and this is due to the migration of infected animals from one state to another state. This study implies that 16S rDNA and ITS region may be used for molecular characterization of B. mallei associated with glanders in resource-limited settings.

Antimicrobial Susceptibility of Western Hemisphere Isolates of Burkholderia pseudomallei: Phenotypic and Genomic Analyses

Current antimicrobial treatment recommendations for melioidosis, the disease caused by Burkholderia pseudomallei, are largely based on studies of strains isolated from the Eastern Hemisphere (EH), where most human cases are identified and reported. In this study, we evaluated the antimicrobial susceptibility of 26 strains in the CDC (Centers for Diseases Control and Prevention) collection from the Western Hemisphere (WH) isolated from 1960 to 2015. Minimal inhibitory concentration (MIC) values were measured by standard broth microdilution for 16 antimicrobials following Clinical and Laboratory Standards Institute (CLSI) guidelines. Twenty-four of the 26 WH strains were susceptible to the six antimicrobials with CLSI-defined MIC susceptibility interpretive criteria for B. pseudomallei: amoxicillin/clavulanate, ceftazidime, imipenem, doxycycline, tetracycline, and trimethoprim/sulfamethoxazole. One WH strain demonstrated intermediate amoxicillin/clavulanate resistance and another strain had intermediate resistance to tetracycline. For all antimicrobials tested, the susceptibility profiles of WH isolates were comparable with previously reported MIC results of EH strains. The overall similarities suggest that the same antimicrobials are useful for melioidosis treatment in both the WH and EH. Using in silico analyses of WH genomes, we identified a novel amino acid substitution P258S in the beta-lactamase PenA, which may contribute to decreased susceptibility to amoxicillin/clavulanate in B. pseudomallei.

Correlating Genotyping Data of Coxiella burnetii with Genomic Groups

Coxiella burnetii is a zoonotic pathogen that resides in wild and domesticated animals across the globe and causes a febrile illness, Q fever, in humans. Several distinct genetic lineages or genomic groups have been shown to exist, with evidence for different virulence potential of these lineages. Multispacer Sequence Typing (MST) and Multiple-Locus Variable number tandem repeat Analysis (MLVA) are being used to genotype strains. However, it is unclear how these typing schemes correlate with each other or with the classification into different genomic groups. Here, we created extensive databases for published MLVA and MST genotypes of C. burnetii and analysed the associated metadata, revealing associations between animal host and human disease type. We established a new classification scheme that assigns both MST and MLVA genotypes to a genomic group and which revealed additional sub-lineages in two genomic groups. Finally, we report a novel, rapid genomotyping method for assigning an isolate into a genomic group based on the Cox51 spacer sequence. We conclude that by pooling and streamlining existing datasets, associations between genotype and clinical outcome or host source were identified, which in combination with our novel genomotyping method, should enable an estimation of the disease potential of new C. burnetii isolates.

First isolation and molecular phylogenetic analysis of Coxiella burnetii in lactating cows

Q fever is an infectious disease of animals and humans, caused by globally distributed C. burnetii. In Iraq, there are no previous studies associated with the detection of the organism in cattle. An overall of 130 lactating cows were submitted to direct collection of milk samples. Initially, the samples of milk were tested using the molecular polymerase chain reaction (PCR) assay targeting three genes (16S rRNA, IS1111a transposase, and htpB). However, positive results (18.46%; 24/130) were detected only with the 16s rRNA gene. Concerning risk factors, the highest prevalence of C. burnetii was showed in the district of Badra (42.86%), whereas the lowest - in Al-Numaniyah and Al-Suwaira districts (P=0.025). There was no significant variation in positivity between the months of sampling period (P=0.082) and between age groups (P=0.076). Crossbred cows (20.69%) showed a higher positivity than local and pure breeds (P=0.043). Milk of positive samples (n=24) was used for cultivation of C. burnetii into specific pathogen free-embryonated chicken eggs (SPF-ECEs). After three passages into SPF-ECEs, contents of yolk sac were collected, subjected for DNA extraction, and re-tested by PCR assay using the primer of 16s rRNA gene only. Of 24 cultivated milk samples, 12.5% (3/24) were positive for C. burnetii. Finally, the positive local isolates were analysed phylogenetically and reported in NCBI-Genbank under the accession numbers of MN121700.1, MN121701.1, and MN121702.1. In conclusion, this is a unique study as it detected C. burnetii in Iraqi lactating cows, and confirmed that organism was shed actively through milk, suggesting that these animals can play a role as a reservoir for organism with potential risk for transmission of infection from these animals to humans as well as to other animal species.

Coxiella burnetii is widespread in ticks (Ixodidae) in the Xinjiang areas of China

Background

The gram-negative Coxiella burnetii bacterium is the pathogen that causes Q fever. The bacterium is transmitted to animals via ticks, and manure, air, dead infected animals, etc. and can cause infection in domestic animals, wild animals, and humans. Xinjiang, the provincial-level administrative region with the largest land area in China, has many endemic tick species. The infection rate of C. burnetii in ticks in Xinjiang border areas has not been studied in detail.

Results

For the current study, 1507 ticks were collected from livestock at 22 sampling sites in ten border regions of the Xinjiang Uygur Autonomous region from 2018 to 2019. C. burnetii was detected in 205/348 (58.91%) Dermacentor nuttalli; in 110/146 (75.34%) D. pavlovskyi; in 66/80 (82.50%) D. silvarum; in 15/32 (46.90%) D. niveus; in 28/132 (21.21%) Hyalomma rufipes; in 24/25 (96.00%) H. anatolicum; in 219/312 (70.19%) H. asiaticum; in 252/338 (74.56%) Rhipicephalus sanguineus; and in 54/92 (58.70%) Haemaphysalis punctata. Among these samples, C. burnetii was detected in D. pavlovskyi for the first time. The infection rate of Rhipicephalus was 74.56% (252/338), which was the highest among the four tick genera sampled, whereas the infection rate of H. anatolicum was 96% (24/25), which was the highest among the nine tick species sampled. A sequence analysis indicated that 63 16S rRNA sequences could be found in four newly established genotypes: MT498683.1 (n = 18), MT498684.1 (n = 33), MT498685.1 (n = 6), and MT498686.1 (n = 6).

Conclusions

This study indicates that MT498684.1 might represent the main C. burnetii genotype in the ticks in Xinjiang because it was detected in eight of the tick species studied. The high infection rate of C. burnetii detected in the ticks found in domestic animals may indicate a high likelihood of Q fever infection in both domestic animals and humans.

Molecular epidemiology of Rickettsia sp. and Coxiella burnetii collected from Hyalomma asiaticum in Bactrian camels (Camelus bactrianus) in inner Mongolia of China

The purpose of the present study was to determine the presence of Rickettsia sp. and Coxiella burnetii in Hyalomma asiaticum collected from Bactrian camels (Camelus bactrianus) in Inner Mongolia of China. A total of 385 H. asiaticum adults collected from Bactrian camels from Alxa in Inner Mongolia from 2017 to 2018 were examined using PCR combined with sequencing. The results indicated that 18 (4.7 %) and 5 (1.3 %) samples tested positive for Rickettsia and C. burnetii, respectively. The corresponding nucleotide identities among detected genes ranged between 99.7 % and 100 % for the sequences of 17 kD and ompB from Rickettsia and 16S rRNA and FtsX from C. burnetii. Two representative strains-Rickettsia IMA-1 strain and C. burnetii IMA-1 strain-were used for subsequent analysis. NCBI BLAST and phylogenetic analyses demonstrated that the detected strain Rickettsia IMA-1 may represent a novel species of spotted fever group (SFG) rickettsiae. The C. burnetii IMA-1 strain was grouped with Coxiella burnetii str. RSA439 (GenBank: CP040059.1). In addition, the Rickettsia sp. was successfully isolated from the ticks in Vero cells incubated at 28 °C. These findings indicate that the H. asiaticum collected off Bactrian camels in Inner Mongolia carried SFG Rickettsia species and C. burnetii and could contribute to the etiology of febrile illness in animals and humans.