Last data update: Jun 03, 2024. (Total: 46935 publications since 2009)
Records 1-4 (of 4 Records) |
Query Trace: Ishaq MK [original query] |
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Notes from the Field: Legionnaires disease in a U.S. traveler after staying in a private vacation rental house in the U.S. Virgin Islands - United States, February 2022
Mac VV , Labgold K , Moline HL , Smith JC , Carroll J , Clemmons N , Edens C , Ellis B , Harrison C , Henderson KC , Ishaq MK , Kozak-Muiznieks NA , Kunz J , Lawrence M , Lucas CE , Walker HL , Willby MJ , Ellis EM . MMWR Morb Mortal Wkly Rep 2023 72 (20) 564-565 On February 1, 2022, the U.S. Virgin Islands (USVI) Department of Health (VIDOH) was notified of a confirmed case of Legionnaires disease in an adult U.S. resident (Figure). The patient, a man aged 55 years, returned to his U.S. state of residence from leisure travel in USVI on January 22 and developed a cough, shortness of breath, and fatigue on January 23. On January 29, he was hospitalized for shortness of breath and received a positive SARS-CoV-2 test result at admission. The combination of the patient’s symptoms and recent travel history prompted administration of a urinary antigen test (UAT) for Legionnaires disease specific to Legionella pneumophila serogroup 1 (Lp1); a positive result was returned on January 31. Inpatient treatment administered for COVID-19 pneumonia and Legionnaires disease included remdesivir, oral levofloxacin, oral and intravenous steroid therapy, and as-needed use of a bronchodilator inhaler and an expectorant. Remdesivir was discontinued during inpatient treatment because of elevated liver enzymes. The patient recovered and was discharged on February 2. |
Genomic heterogeneity differentiates clinical and environmental subgroups of Legionella pneumophila sequence type 1.
Mercante JW , Caravas JA , Ishaq MK , Kozak-Muiznieks NA , Raphael BH , Winchell JM . PLoS One 2018 13 (10) e0206110 Legionella spp. are the cause of a severe bacterial pneumonia known as Legionnaires' disease (LD). In some cases, current genetic subtyping methods cannot resolve LD outbreaks caused by common, potentially endemic L. pneumophila (Lp) sequence types (ST), which complicates laboratory investigations and environmental source attribution. In the United States (US), ST1 is the most prevalent clinical and environmental Lp sequence type. In order to characterize the ST1 population, we sequenced 289 outbreak and non-outbreak associated clinical and environmental ST1 and ST1-variant Lp strains from the US and, together with international isolate sequences, explored their genetic and geographic diversity. The ST1 population was highly conserved at the nucleotide level; 98% of core nucleotide positions were invariant and environmental isolates unassociated with human disease (n = 99) contained ~65% more nucleotide diversity compared to clinical-sporadic (n = 139) or outbreak-associated (n = 28) ST1 subgroups. The accessory pangenome of environmental isolates was also ~30-60% larger than other subgroups and was enriched for transposition and conjugative transfer-associated elements. Up to ~10% of US ST1 genetic variation could be explained by geographic origin, but considerable genetic conservation existed among strains isolated from geographically distant states and from different decades. These findings provide new insight into the ST1 population structure and establish a foundation for interpreting genetic relationships among ST1 strains; these data may also inform future analyses for improved outbreak investigations. |
Comparative genome analysis reveals a complex population structure of Legionella pneumophila subspecies.
Kozak-Muiznieks NA , Morrison SS , Mercante JW , Ishaq MK , Johnson T , Caravas J , Lucas CE , Brown E , Raphael BH , Winchell JM . Infect Genet Evol 2018 59 172-185 The majority of Legionnaires' disease (LD) cases are caused by Legionella pneumophila, a genetically heterogeneous species composed of at least 17 serogroups. Previously, it was demonstrated that L. pneumophila consists of three subspecies: pneumophila, fraseri and pascullei. During an LD outbreak investigation in 2012, we detected that representatives of both subspecies fraseri and pascullei colonized the same water system and that the outbreak-causing strain was a new member of the least represented subspecies pascullei. We used partial sequence based typing consensus patterns to mine an international database for additional representatives of fraseri and pascullei subspecies. As a result, we identified 46 sequence types (STs) belonging to subspecies fraseri and two STs belonging to subspecies pascullei. Moreover, a recent retrospective whole genome sequencing analysis of isolates from New York State LD clusters revealed the presence of a fourth L. pneumophila subspecies that we have termed raphaeli. This subspecies consists of 15 STs. Comparative analysis was conducted using the genomes of multiple members of all four L. pneumophila subspecies. Whereas each subspecies forms a distinct phylogenetic clade within the L. pneumophila species, they share more average nucleotide identity with each other than with other Legionella species. Unique genes for each subspecies were identified and could be used for rapid subspecies detection. Improved taxonomic classification of L. pneumophila strains may help identify environmental niches and virulence attributes associated with these genetically distinct subspecies. |
Genome-based discrimination between Group I Clostridium botulinum and Clostridium sporogenes strains: implications for bacterial taxonomy.
Weigand MR , Pena-Gonzalez A , Shirey TB , Broeker RG , Ishaq MK , Konstantinidis KT , Raphael BH . Appl Environ Microbiol 2015 81 (16) 5420-9 Taxonomic classification of Clostridium botulinum is based on the production of botulinum neurotoxin (BoNT) while closely-related, non-toxic organisms are classified as Clostridium sporogenes. However, this taxonomic organization does not accurately mirror phylogenetic relationships between these species. A phylogenetic reconstruction using 2,016 orthologous genes shared among strains of C. botulinum Group I and C. sporogenes clearly separated these two species into discrete clades which showed approximately 93% average nucleotide identity (ANI) between them. Clustering of strains based on the presence of variable orthologs revealed 143 C. sporogenes clade-specific genetic signatures, a subset of which was further evaluated for their ability to correctly classify a panel of presumptive C. sporogenes strains by PCR. Genome sequencing of several C. sporogenes strains lacking these signatures confirmed that they clustered with C. botulinum strains in a core genome phylogenetic tree. Our analysis also identified C. botulinum strains that contained C. sporogenes clade-specific signatures and phylogenetically clustered with C. sporogenes strains. The genome sequences of two bontB2-containing strains belonging to the C. sporogenes clade contained regions with similarity to a bont-encoding plasmid (pCLD) while two different strains belonging to the C. botulinum clade encoded bontB2 on the chromosome. These results indicate that bont/B2 was likely acquired by C. sporogenes strains through horizontal gene transfer. The genome-based classification of these species used to identify candidate genes for the development of rapid assays for molecular identification may be applicable to additional bacterial species that are challenging with respect to their classification. |
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