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Lit Review April #1

April 6, 2018

Disclaimer: this compilation of synopses have been collected from multiple sources, including Mark Crislip's Puscast, Journal Watch Infectious Diseases, Medscape Infectious Diseases, CDC MMWR, AMA Morning Rounds, ProMED Mail, Journal of Clinical Microbiology, Antimicrobial Agents and Chemotherapy, Clinical Infectious Diseases, and more. I chose these articles based on their relevance to clinical microbiology and would be of interest to my fellows, and some other pieces that I found amusing to read. All credit goes to these original contributors. I'm just a messenger :).


Leading Photo by CDC (

Distinct fermentation and antibiotic sensitivity profiles exist in salmonellae of canine and human origin


  • S. enterica is pathogenic in both humans and dogs, but no evidence showing possibility of transfer between dog and owner

  • Looked at 88 human and 86 dog isolates (clinical)

  • Carbon utilization profiles between two groups was different (determined using a phenotypic array ala API

  • Canine isolates seemed to have higher AMP, AMX, CHL MICs compared to human isolates

  • Suggested separated reservoirs for disease

  • WGS would have given a better resolution

Salmonella enterica Serotype 4,[5],12:i:- in Swine in the United States Midwest: An Emerging Multidrug-Resistant Clade

  • Examples of Kauffmann-White-Le Minor scheme (from WHO document)

  • "4,[5],12" = somatic O antigen

  • ":i:-" = H antigen phase 1 is "i"

  • "-" = no phase 2 H antigen


  • Emerging globally, including in pork in the US, lacks the second-phase flagellar antigen

  • Compared WGS data from hundreds of 4,[5],12:i:- and Typhimurium from US and Europe, with a focus on isolates from pork in the US Midwest

  • 4,[5],12:i:- regardless of source could be divided into two clades – B I and B II

    • 85% of US isolates from 2014-15 in clade B II, which is emerging globally

  • R to AMP, STR, sulfonamides, TET

  • Subset of isolates R to enrofloxacin or ceftiofur associated with presence of plasmid-mediated resistance genes (qnrB19/qnrB2/qnrS1 for FQ and blaCMY-2/blaSHV-12 for ceph), with FQ resistance probably acquired in the US


Epidemiology, Microbiological Diagnosis, and Clinical Outcomes in Pyogenic Vertebral Osteomyelitis: A 10-year Retrospective Cohort Study


  • PVO: difficult to treat, sometimes culture-negative, pt on broad-spectrum treatment for a long time with little benefit compared to a shorter course, besides reduction of relapse in some studies

  • A study from Australia looking at 129 patients over 10 years

    • Most patients had blood culture, 44% had vertebral samples (open Bx better yield than core or FNA)

    • 78% organism identified, MSSA or gram positive most prevalent, these patients were more likely to be febrile and had elevated CRP on admission – makes sense

    • 22% - only 5 patients had histology results, with varying evidence of inflammation, 16s PCR in these patients was not conclusive

  • Overall clinical outcomes poor regardless of organism ID (only 15% complete recovery upon D/C)

  • However, not having org ID associated with more risk of adverse outcomes (mortality during index admission or attributable readmission within 2 years due to stuff like pain, disability, or need for more investigation)

  • It may be reasonable to go above and beyond to get a microbiological diagnosis to guide treatment instead of empirical


Systemic Antibiotics for the Treatment of Skin and Soft Tissue Abscesses: A Systematic Review and Meta-Analysis


  • To use or not to use antibiotics after I&D? Classical way of thinking is that antibiotics wouldn’t add much

  • Meta-analysis looking at 2400 patients

    • About half had MRSA

    • Treated with SXT or CLI

    • Treatment failure in antibiotic group (7.7%) less than placebo (16.1%)

    • Antibiotic also reduced risk of developing more lesions, while increase in adverse effects was minimal and mild (GI, rash, etc)

  • Mark Crislip on his podcast: DOX and LZD result in less chance of developing C. diff


Management of an Outbreak of Exophiala dermatitidis Bloodstream Infections at an Outpatient Oncology Clinic

  • Dematiaceous, may cause CNS infection in IC hosts, resp pathogen in CF patients



  • Photo: Mycology Online:

  • May 2016 NY: 4 cases of E. dermatitidis in oncology patients receiving infusion through port-a-cath at a clinic

  • Identified a total of 15 cases of fungemia with E. dermatitidis and 2 with Rhodotorula mucilaginosa, some positive in all cultures (peripheral, CVC-drawn blood, CVC device), most are asymptomatic

  • Source of contamination: IV flush solution containing saline, VAN, CAZ, heparin

    • Compounded in the clinic in substandard conditions, in 1 L bags, kept for 4-8 weeks with multiple access per day until bag was depleted

    • 38 patients exposed to potentially contaminated fluids

  • Isolates confirmed by WGS to be the same

  • Pts with positive blood culture had CVC removed, treated with mainly voriconazole, 3 died


mcr-3 and mcr-4 Variants in Carbapenemase-Producing Clinical Enterobacteriaceae Do Not Confer Phenotypic Polymyxin Resistance

  • Fact: mcr-1 isolates don’t always have NWT CST MICs (>=4): choosing isolates to screen is challenging

  • Singapore: sequenced a bunch of Enterobacteriaceae

    • Found mcr-3-like element in E. coli

      • Initial assembly showed a 9kb contig with this element

      • Claimed to not be plasmid-associated: mapping reads onto closest reference genome and re-assemble reads that did not match, found no plasmid-associated gene on the 9kb contig containing this element

      • Seems to be associated with transposable elements

      • I have a problem with this approach

        • Plasmid are notoriously difficult to assemble, lots of repeated sequences

        • One cannot make this assumption without long read sequencing

        • Transposable elements can be on a plasmid too

        • Was PlasmidFinder used on assembled contigs? Any origin of replication?

    • Found mcr-4-like elements in E. cloacae

      • 7.7kb contig with this element matched existing mcr-4 harboring plasmid

    • Both isolates S to CST, cloned genetic elements in E. coli did not confer resistance either

    • Why is this exciting?


Two Cases of Meningococcal Disease in One Family Separated by an Extended Period — Colorado, 2015–2016


  • Transmitted through large respiratory droplets

  • April 2015 in CO: 75 yo F came down with sepsis, GS CFF positive for GNDP but culture neg, BCB positive, treated and survived

  • 7 family members were prescribed PEP, but compliance unknown

    • Adults CIP PO single dose

    • Children RIF q12 for 2 days or CRO IM one dose

  • 15 mo later, a 3 mo grandbaby of patient came down also with meningococcemia

    • WGS: same bug

  • Treatment in patients usually eradicate organisms

  • Where did the bug come from?

    • Baby shared close unknown contact with index patient

    • Circulating strain

    • Incomplete eradication during PEP


Notes from the Field: Fatalities Associated with Human Adenovirus Type 7 at a Substance Abuse Rehabilitation Facility — New Jersey, 2017