A hybridization target enrichment approach for pathogen genomics.

IMPORTANCE: Emerging infectious diseases require continuous pathogen monitoring. Rapid clinical diagnosis by nucleic acid amplification is limited to a small number of targets and may miss target detection due to new mutations in clinical isolates. Whole-genome sequencing (WGS) identifies genome-wide variations that may be used to determine a pathogen's drug resistance patterns and phylogenetically characterize isolates to track disease origin and transmission. WGS is typically performed using DNA isolated from cultured clinical isolates. Culturing clinical specimens increases turn-around time and may not be possible for fastidious bacteria. To overcome some of these limitations, direct sequencing of clinical specimens has been attempted using expensive capture probes to enrich the entire genomes of target pathogens. We present a method to produce a cost-effective, time-efficient, and large-scale synthesis of probes for whole-genome enrichment. We envision that our method can be used for direct clinical sequencing of a wide range of microbial pathogens for genomic epidemiology.

Rifabutin and rifampin resistance levels and associated rpoB mutations in clinical isolates of Mycobacterium tuberculosis complex.

Cross-resistance in rifamycins has been observed in rifampin (RIF)-resistant Mycobacterium tuberculosis complex isolates; some rpoB mutations do not confer broad in vitro rifamycin resistance. We examined 164 isolates, of which 102 were RIF-resistant, for differential resistance between RIF and rifabutin (RFB). A total of 42 unique single mutations or combinations of mutations were detected. The number of unique mutations identified exceeded that reported in any previous study. RFB and RIF MICs up to 8 µg/mL by MGIT 960 were studied; the cut-off values for susceptibility to RIF and RFB were 1 µg/mL and 0.5 µg/mL, respectively. We identified 31 isolates resistant to RIF but susceptible to RFB with the mutations D516V, D516F, 518 deletion, S522L, H526A, H526C, H526G, H526L, and two dual mutations (S522L + K527R and H526S + K527R). Clinical investigations using RFB to treat multidrug-resistant tuberculosis cases harboring those mutations are recommended.

A Case of Persistent and Possibly Treatment Resistant Pharyngeal Gonorrhea.

An HIV-negative man with pharyngeal gonorrhea had a positive test-of-cure (nucleic acid amplification test) result 7 days after treatment with ceftriaxone/azithromycin. Neisseria gonorrhoeae Multi-Antigen Sequencing Type 1407 and mosaic pen A (XXXIV) gene were identified in the test-of-cure specimen, and culture was negative. Retreatment with ceftriaxone 500 mg intramuscularly plus azithromycin 2 g orally yielded a negative test-of-cure result.

Expression of ESBL-like activity in infrequently encountered members of the family Enterobacteriaceae.

A collection of 94 unusual members of the Enterobacteriaceae were screened for the presence of extended spectrum ß-lactamases (ESBLs) using the MicroScan ESßL plus dried confirmation panel. Presumptively positive strains were then confirmed for the presence of an ESBL by double disk diffusion, E-test strips (AB Biodisk, Solna, Sweden) and PCR for SHV, TEM, and CTX-M2 genes. Of the 18 strains initially positive on the ESßL panel only three strains (Leminorella grimontii, Klebsiella ozaenae, and Kluyvera ascorbata) were positive by confirmation methods. These results suggest laboratories should be cautious regarding the methodology employed in screening for the presence of ESBLs in enteric bacteria. However, it should be noted that of the 94 strains, 29 were found to be resistant to two or more of the antibiotics present in the MicroScan ESßL plus panel indicating that there are potential treatment issues with these organisms despite their lack of ESBLs.

Rickettsia rickettsii (Rickettsiales: Rickettsiaceae) in Amblyomma americanum (Acari: Ixodidae) from Kansas.

The role of lone star ticks as vectors for Rocky Mountain spotted fever (RMSF) remains poorly described. We compared the entomological inoculation rates (EIRs) for Rickettsia spp. for representative sites in Missouri and Kansas, states that frequently report RMSF each year. Host-seeking ticks were collected during 2006 and pooled tick homogenates analyzed by polymerase chain reaction to detect probable R. rickettsii, with confirmation for multiple gene targets performed on individual ticks from pools that screened positive. Of 870 adult and nymphal lone star ticks, Amblyomma americanum (L.), 0.46% contained DNA of Rickettsia rickettsii. Interestingly, two of these positive ticks were concurrently infected by R. amblyommii. More than 90% of lone star tick pools contained R. amblyommii DNA. Of 169 dog ticks that were analyzed, none were infected by R. rickettsii. The entomological inoculation rate for spotted fever group (SFG) rickettsiae within lone star ticks was an order of magnitude greater than that for dog ticks. We conclude that lone star ticks may be epidemiologically significant vectors of Rocky Mountain spotted fever and of spotted fever group rickettsiae.

Diversity of Francisella species in environmental samples from Martha's Vineyard, Massachusetts.

We determined whether Francisella spp. are present in water, sediment, and soil from an active tularemia natural focus on Martha's Vineyard, Massachusetts, during a multiyear outbreak of pneumonic tularemia. Environmental samples were tested by polymerase chain reaction (PCR) targeting Francisella species 16S rRNA gene and succinate dehydrogenase A (sdhA) sequences; evidence of the agent of tularemia was sought by amplification of Francisella tularensis-specific sequences for the insertion element ISFTu2, 17-kDa protein gene tul4, and the 43-kDa outer membrane protein gene fopA. Evidence of F. tularensis subsp. tularensis, the causative agent of the human infections in this outbreak, was not detected from environmental samples despite its active transmission among ticks and animals in the sampling site. Francisella philomiragia was frequently detected from a brackish-water pond using Francisella species PCR targets, and subsequently F. philomiragia was isolated from an individual brackish-water sample. Distinct Francisella sp. sequences that are closely related to F. tularensis and Francisella novicida were detected from samples collected from the brackish-water pond. We conclude that diverse Francisella spp. are present in the environment where human cases of pneumonic tularemia occur.

Burden of tick-borne infections on American companion animals.

This review examines the biology of ticks and tick-borne infections in the United States. The most common tick-borne diseases in dogs and cats are discussed. We demonstrate that there is much interest in tick-borne infections at the level of the lay public (pet owners), describe trends in the distribution and prevalence of tick-borne infections in the United States, summarize some issues in understanding the degree of ill health due to tick-borne infections, and suggest some avenues for research that would clarify these issues.

Molecular detection of Bartonella schoenbuchensis from ectoparasites of deer in Massachusetts.

Deer keds (Lipoptena cervi) are thought to have been introduced into New England from Europe during the 1800 s. We sought to determine whether L. cervi from Massachusetts deer contained evidence of infection by Bartonella schoenbuchensis, which appears to be maintained by L. cervi in Europe. Five of 6 keds were found to contain B. schoenbuchensis DNA, and 2 deer ticks cofeeding on deer with such keds did as well. The detection of Bartonella DNA in deer ticks probably represents contamination by infected deer blood.

Raccoons and skunks as sentinels for enzootic tularemia.

We analyzed sera from diverse mammals of Martha's Vineyard, Massachusetts, for evidence of Francisella tularensis exposure. Skunks and raccoons were frequently seroreactive, whereas white-footed mice, cottontail rabbits, deer, rats, and dogs were not. Tularemia surveillance may be facilitated by focusing on skunks and raccoons.