Whole-genome analysis of mycobacteria from birds at the San Diego Zoo

Abstract

MethodsMycobacteria isolated from more than 100 birds diagnosed with avian mycobacteriosis at the San Diego Zoo and its Safari Park were cultured postmortem and had their whole genomes sequenced. Computational workflows were developed and applied to identify the mycobacterial species in each DNA sample, to find single-nucleotide polymorphisms (SNPs) between samples of the same species, to further differentiate SNPs between as many as three different genotypes within a single sample, and to identify which samples are closely clustered genomically.ResultsNine species of mycobacteria were found in 123 samples from 105 birds. The most common species were Mycobacterium avium and Mycobacterium genavense, which were in 49 and 48 birds, respectively. Most birds contained only a single mycobacterial species, but two birds contained a mixture of two species. The M. avium samples represent diverse strains of M. avium avium and M. avium hominissuis, with many pairs of samples differing by hundreds or thousands of SNPs across their common genome. By contrast, the M. genavense samples are much closer genomically; samples from 46 of 48 birds differ from each other by less than 110 SNPs. Some birds contained two, three, or even four genotypes of the same bacterial species. Such infections were found in 4 of 49 birds (8%) with M. avium and in 11 of 48 birds (23%) with M. genavense. Most were mixed infections, in which the bird was infected by multiple mycobacterial strains, but three infections with two genotypes differing by ≤ 10 SNPs were likely the result of within-host evolution. The samples from 31 birds with M. avium can be grouped into nine clusters within which any sample is ≤ 12 SNPs from at least one other sample in the cluster. Similarly, the samples from 40 birds with M. genavense can be grouped into ten such clusters. Information about these genomic clusters is being used in an ongoing, companion study of mycobacterial transmission to help inform management of bird collections.

Population Genomics of Nontuberculous Mycobacteria Recovered from United States Cystic Fibrosis Patients

“…The remaining CF-RDP M. intracellulare isolates were related to but genetically distinct from other reference strains (i.e. ATCC 13950 42 , MOTT-64 43 ), zoonotic isolates collected from birds in the US 44 , and M. yongonense. None of the CF-RDP M. chimaera isolates were genetically similar to isolates derived from contaminated HCU units mean = 15905 SNPs; 45,46 .…”

Use of molecular data in zoo and aquarium collection management: Benefits, challenges, and best practices

“…For zoos and aquariums, molecular data can be used to aid in disease detection in addition to various complex management applications related to disease. For example, diagnostic tests can be instrumental in establishing pathogen presence or absence within individuals (e.g., mycoplasma infections in desert tortoises, Gopherus agassizii ; Braun et al, ), while collection or population‐level studies can inform models of disease transmission (e.g., mycobacteria diversity and transmission dynamics given epidemiological links within a diverse bird collection; Pfeiffer, Braun, Burchell, Witte, & Rideout, ). Here, we focus on what our experience suggests to be the disease‐related inquiry of primary concern to cooperative breeding program managers: ascertaining disease heritability.…”

Methods for Detecting Mycobacterial Mixed Strain Infections–A Systematic Review

“…Of the 97 studies identified in Covidence, eight (8.2%) primarily used WGS to detect MSIs in humans (Bryant et al, 2013a ; Gan et al, 2016 ; Witney et al, 2017 ; Baffoe-Bonnie et al, 2019 ; Dippenaar et al, 2019 ; O'Donnell et al, 2019 ; Anyansi et al, 2020 ; Wollenberg et al, 2020 ), while three others (3.1%) used the method to detect MSIs in various animal species (Davidson et al, 2016 ; Pfeiffer et al, 2017 ; Silva-Pereira et al, 2019 ), only one of which focused on a MTBC bacteria (Silva-Pereira et al, 2019 ). Secondary searches found four more human studies on WGS and mycobacterial MSIs (Chan et al, 2013 ; Kay et al, 2015 ; Dheda et al, 2017 ; Nimmo et al, 2020 ), in addition to reports where the method was used to confirm such infection that were initially identified using other means ( Supplementary Table 2 ).…”