Lab Matters Fall 2020 - Page 43

APHL 2020 POSTER ABSTRACTS high risk patient cohort and whole genome sequening ( WGS ) performed on Illumina MiSeq platform at Dept . of State Health Services Lab , Texas . Parsnp was utilized to align GC core genomes assembly to study evolutionary hierarchy and genetic polymorphism . PubMLST databases were used for molecular typing and microbial genome diversity . Average Nucleotide Identity ( ANI ) allowed finding nucleotide-level genomic similarity between the coding regions of unknown strains against reference strain . NG-MAST sequence types were interpreted using CosmosID bioinformatics pipeline .
Results : Single nucleotide polymorphism ( SNP ) -based phylogenetic tree was generated upon core genome analysis grouped 97 isolates into 31 sequence types ( STs ) consisting of 3 clusters / clades with less than 10 SNPs . The most common STs were ST-9363 ( n = 16 ; 16.5 %), and ST-1579 ( n = 13 ; 13.4 %). Isolates with decreased susceptibility to azithromycin were associated with ST-1579 ( n = 12 ), ST-12093 ( n = 2 ), and ST-9363 ( n = 1 ). None of the study isolates had reduced susceptibility to Cefixime or Ceftriaxone . Ciprofloxacin resistance was associated with ST-1579 and ST-7363 . AMR markers penA , blaTEM , tetM , and 23S rRNA variants were also detected .
Conclusions : A wide variation in sequence types was obtained in surveillance jurisdiction , however almost all isolates with decreased susceptibility to azithromycin belonged to ST-1579 and also expressed gene markers for Ciprofloxacin resistance . This analysis demonstrates the necessity to incorporate advanced molecular methods like next generation sequencing ( NGS ) as a routine surveillance tool to aid in molecular epidemiology , evidence-based antibiotic treatment and better characterize sexually-transmitted disease clusters and / or public health outbreaks involving ARGC .
Presenter : Joshua Weiner , City of Milwaukee Health Department , Milwaukee , WI , jweine @ milwaukee . gov
Prevalence of Mycoplasma genitalium in High-Risk Patients Seeking Testing at a Local Public Health Laboratory
M . Khubbar 1 , J . Weiner 1 , T . Dasu 1 , Z . Amezquita-Montes 1 , M . Khubbar 1 , K . Schieble 1 , H . Hermus 1 , R . Kryshak 1 , J . Dalby 2 , S . Bhattacharyya 1 ; 1 City of Milwaukee Health Department , Milwaukee , WI , 2 University of Wisconsin- Madison , Madison , WI
Introduction : Mycoplasma genitalium ( MG ) is a slow growing , self-replicating bacterium , lacking cell wall and predominantly found in urogenital tract of both sexes . The infection may persist asymptomatic for months or years in individuals , or can be found in men with non-gonococcal urethritis and women with cervicitis and pelvic inflammatory disease . Early diagnosis and effective treatment are , therefore , important in preventing sequelae and ongoing transmission , particularly the transmission of drug-resistant strains to sex partners . Current treatment guidelines are inconsistent about the need for presumptive treatment of sexual contacts of M . genitalium – infected patients , which further complicates as found to be co-infected with commonly known sexually transmitted pathogens . Implementation of nucleic acid amplification ( NAAT ) assay improves monitoring disease prevalence , co-STI infections and implement best clinical practices .
Methods : Aptima ® analyte specific reagents ( ASR ) validation for MG NAAT involved 219 residual clinical specimens those previously tested for chlamydia , gonorrhea , trichomonas and / or herpes simplex virus were tested on the Panther ® System ( Hologic , Inc . Marlborough , MA ). A variety of sample types ( urine , urethral , vaginal , rectal ) and specimen transport tubes ( Aptima ® Urine , Unisex and
Multitest Specimen Transport Tube ; MicroTest™ M4 Transport Tube ) were validated in this process . Subsequent Aptima ® FDA-cleared IVD assay verification involved the use of 81 pre-qualified specimens ( 45 clinical specimens , 36 Validation Panel samples through Hologic , Inc .).
Samples received by STD clinic laboratory were analyzed for MG surveillance , monitoring positivity rate and co-infections .
Results : MG was detected in 148 of 763 samples tested . 15 % of the MG positive patients presented with at least one laboratory confirmed STI co-infection ( chlamydia , gonorrhea , trichomonas , and herpes ). There were more number of men tested than women and urine was the most common specimen type to be tested for MG . The sensitivity of the assay was comparable between urine and urethral swab in males . We only had one rectal swab submitted which turned out to be negative .
Conclusion : Overall prevalence of M . genitalium was determined to be 19 %, which is significantly higher than national gonorrhea or chlamydia prevalence . Prescription practices by the STI physicians has been optimized based on this data by treating non-specific urethritis ( NSU ) with doxycycline ; recurring infections are treated with moxifloxacin . Prior to launch of the MG assay , NSU and PID patients were empirically treated based on symptoms . Major achievement in public health practice is adequate treatment for high-risk STI public health clinic population . Our laboratory and STI clinic is exploring impact of macrolide resistance testing on jurisdictional patient cohort .
Presenter : Manjeet Khubbar , City of Milwaukee Health Department , Milwaukee , WI , mkhubb @ milwaukee . gov
Molecular Epidemiology of the First NDM-1-producing Klebsiella pneumoniae Outbreak in Minnesota
S . Namugenyi , J . Dale , B . Pattee , S . O ’ Malley , R . Lynfield and P . Snippes Vagnone , Minnesota Department of Health , St . Paul , MN
New Delhi-metallo-β-lactamase ( NDM ) is an enzyme , found in gram negative bacteria , capable of hydrolyzing penicillin , cephalosporin , monobactam , and carbapenem classes of antibiotics ; which contributes to bacterial resistance to these antimicrobials . Though uncommon in the United States , NDM-producing Enterobacteriaceae are more common in healthcare settings in other countries and are an emerging public health threat . In Minnesota , fewer than 10 cases were reported annually from 2012 – 2018 most of whom received recent healthcare abroad . Between December 2018 and May 2019 , the first outbreak of NDM-producing Klebsiella pneumoniae occurred in Minnesota among eleven cases with an epidemiologic link to one long-term care facility , and without patient history of international travel . One case also harbored an NDM-producing Escherichia coli .
Isolates were obtained from 9 / 11 cases . Whole genome sequencing ( WGS ), using the Illumina platform and single nucleotide polymorphism ( SNP ) analysis , demonstrated relatedness between all nine K . pneumoniae isolates with SNP differences ranging from 1 – 18 . WGS analysis also determined that all K . pneumoniae isolates were multi-locus sequence type 147 and harbored the blaNDM-1 gene . Additional genes conferring resistance to β-lactams , aminoglycosides , fluoroquinolones , phenicol , sulphonamide , and trimethoprim were identified in all nine isolates . Antimicrobial susceptibility testing by broth microdilution confirmed
Infectious Disease
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