Microregistrar Infection Newsletter · Tuesday 3 November 2026
H5N1 B3.13 in US dairy cattle: CIDRAP confirms the Yakima death as the first US H5N1 death of 2026, as the virus turns up in Colorado milk testing.
CIDRAP reported on 2 Nov that two more Yakima County, Washington, residents have been infected with H5N1, one of whom died after admission with severe illness. The patient had underlying conditions and had contact with infected dairy cows. CIDRAP describes this as the first US H5N1 death this year and the third since 2024, when the virus was first found in dairy cattle. The third case was not severely ill. All three Yakima cases had known contact with infected animals, and close contacts are being monitored, with no suggestion of human-to-human transmission.
According to state officials quoted by CIDRAP, Washington has recorded 34 infected herds in the past 30 days, all but one in Yakima County. Sequencing from two Yakima farms shows the cow-adapted B3.13 genotype that has circulated in US cattle since spring 2024. Colorado has also detected H5N1 in routine bulk milk testing, at a Weld County dairy, for the first time since 2024. For UK teams: take an occupational and travel history (dairy, poultry, raw milk) in severe influenza-like illness or conjunctivitis, and follow UKHSA’s avian influenza testing guidance.
Check before quoting: the death and third case were in yesterday’s lead from the county releases. What’s new today is CIDRAP’s confirmation that the infection was H5N1, the B3.13 sequencing and the Colorado detection. CIDRAP’s 34 herds in 30 days doesn’t match FluTrackers’ relay of USDA data (6 more premises, total 40), and the dates and denominators may differ. Indiana’s first infected dairy herd is a FluTrackers relay only. We still haven’t seen a CDC statement. Ebola could lead today under the once-a-week rule, but there were no verified new Ebola figures.
Counted from today’s digest. The Crossref sweep (online 2–3 Nov) found infection-relevant items in OFID, JID, AAC, JCM, JAC and JAC-AMR. JAC and JAC-AMR items already covered on 2 Nov are not repeated, and JAC and JCM items that are in the Journal Watch top 10 appear only there. Non-infection NEJM and JAMA items aren’t counted. The 3 agency items are UKHSA’s updated prenatal pertussis coverage page (data tables replaced), the MHRA #MedSafetyWeek essay competition, and UKHSA’s HCAI monthly data announcement. Links are unique content links, not counting our two website links.
Also today
The other headlines from today’s issue. Each card links to its source and to the full summary.
BARDA awards IAVI $36m for a one-dose Bundibugyo vaccine
CIDRAP reports that the award supports manufacturing rVSV-based vaccine doses for clinical evaluation and outbreak response. It is one of four platforms under evaluation; there is still no licensed Bundibugyo vaccine or treatment.
New York: first measles death in more than 30 years (press-reported)
FluTrackers relayed a news report of New York’s first measles death in over three decades. We haven’t seen the state health department statement.
CLSI and EUCAST agree on amphotericin B but not azoles for C. auris
Across 107 isolates, agreement was 100% for amphotericin B but only 44–72% for azoles. CDC breakpoints classed 33–44% of FKS1 mutants as non-resistant to echinocandins.
Plasma mould PCR outperforms mNGS for invasive mould disease
In 96 patients with proven or probable disease, plasma cfDNA mould PCR sensitivity was 62.5% vs 43.8% for mNGS, with very high specificity for both (Journal Watch #5).
Patient-directed antibiotic duration in pyelonephritis: pilot RCT
A multicentre, double-blind pilot trial in women found similar sustained clinical resolution and adverse events when patients stopped after symptom resolution, compared with a fixed course.
No new Moodle entries since yesterday
“Whats new?” still has the 31 Oct C. diphtheriae & C. ulcerans Interactive at the top.
What we could not confirm
The lead relies on CIDRAP and the county releases; we found no CDC statement, and the herd counts (34 in 30 days vs a relayed USDA total of 40) don’t match. The Indiana herd, the New York measles death and DRC Ebola figures (CFR reported back down to 48.8%) are relays only. There’s still no new WHO DON since DON622 and no UKHSA outbreaks update. CDC HAN is still blocked, and ECDC’s CDTR archive still stops at week 42.
Microregistrar Moodle update
No new entries. We read the Microregistrar moodlecloud sheet (Index tab, “Whats new?”) directly this morning (3 Nov). The list is unchanged since the 2 Nov issue.
C. diphtheriae & C. ulcerans Interactive
Still the top row in “Whats new?”; we reported it on 1 Nov. Moodle ›
Greenbook vaccine part 1 revision
Second entry; reported on 31 Oct. Sheet ›
The full list is in the Microregistrar moodlecloud sheet ›
Watched pages
We check nine pages every morning for anything new, compared with what we saw last time (checked on the morning of 3 Nov 2026). All nine were reached. The UKHSA organisation page and the JAC advance list have something new.
Health Protection Report (UKHSA)
No changeNo new HPR issue; HPR 20(10) of 29 Oct is still the latest. Its prenatal pertussis data tables were replaced on 2 Nov (see Agencies). HPR volume 20 ›
UK SMI News (RCPath)
No changeThere are still no open consultations and no new UK SMI documents. The page markup changed, but we found no new content. No Mail Sorter SMI forwards. Consultations ›
UKHSA organisation page (GOV.UK)
NewNew on 2 Nov: updated prenatal pertussis coverage page and new announcements for upcoming surveillance releases (flu/COVID-19, norovirus, RSV coverage, HCAI monthly data). The HCID country risk page hasn’t changed since 22 Oct. UKHSA › · HCID risk ›
NICE published guidance
No changeNo new infection guidance; listing data otherwise unchanged. NICE published ›
Journal of Antimicrobial Chemotherapy
NewIn the Crossref sweep for 2–3 Nov, the same three articles as yesterday (C. auris AFST, NSTI, bictegravir). Two are now Journal Watch picks. JAC advance articles ›
Agencies & guidance
A quiet Monday for UK and European agencies. UKHSA published scheduling announcements and replaced the prenatal pertussis coverage data tables. MHRA continued #MedSafetyWeek. ECDC posted no news and there was no new WHO DON. In the US, H5N1 in dairy cattle continues to spread.
Guidance changes
No new UK infection guidance
No new UKHSA, NICE, Green Book or UK SMI guidance appeared in the window. The DHSC consultation on restricting high-risk cosmetic procedures in England (2 Nov) touches on infection risk but isn’t infection guidance.
UKHSA / MHRA / England
Prenatal pertussis coverage page updated
On 2 Nov UKHSA replaced the associated data tables for the April to June 2026 prenatal pertussis coverage report (HPR 20(10)). The change log describes this only as a file substitution, with no new period.
Release dates: HCAI monthly data, flu/COVID-19 and norovirus reports
Monthly MRSA, MSSA, Gram-negative bacteraemia and C. difficile data (to October 2026) and the week 45 flu/COVID-19 and norovirus reports are announced but not yet out. Announcements for later weeks were also posted.
Patient safety essay competition launched
No new MHRA drug or device alerts in the window. MHRA launched its 2026 national patient safety essay competition as part of #MedSafetyWeek (2–8 Nov).
No infection mail in the window
The microregistrar2021 inbox had no Mail Sorter forwards and no UKHSA, RCPath or vaccine emails since yesterday; only an ONS health statistics newsletter and unrelated mail.
ECDC / Europe
No ECDC news; CDTR archive still at week 42
The ECDC news feed has nothing after 29 Oct, and the weekly threats archive still lists week 42 as the latest. ESCMID posted only course promotions on X. FluTrackers relayed a WOAH report of H5N1 in a mallard in Germany.
Global
Vaccine funding announced; DRC revises deaths downwards (relay)
- Vaccine: BARDA has awarded IAVI $36 million for its one-dose rVSV-based Bundibugyo vaccine, covering manufacture for clinical evaluation and outbreak response (CIDRAP). There is still no licensed vaccine or treatment.
- DRC (government, via FluTrackers): the latest update lowered the death count, bringing the reported CFR back down to 48.8% from 51.6%. We can’t check the revised numerator.
- Response: WHO/AFRO says over 330 health professionals are being trained at a new frontline responder training centre in Bunia.
- US travel: from today (3 Nov), international travellers to the US must attest that they haven’t recently been in the DRC (CIDRAP, 28 Oct).
- UK: no imported cases; UKHSA’s risk assessment is unchanged (low).
There’s no new WHO DON since DON622 (23 Oct) and no new UKHSA outbreaks report. Ebola was eligible to lead today, but there were no verified new figures.
CIDRAP › · @FluTrackers (DRC) › · @WHOAFRO › · CIDRAP travel rule ›
Relayed measles reports: South Africa and Belize
FluTrackers relayed local reports of rising measles cases in Helderberg (Western Cape) and 19 cases so far this year in Belize.
Press reports relayed by FluTrackers; not checked against national sources.
H5N1 in a wild leopard cat
Second H5N1 detection in a wild mammal in Korea, found in a carcass in Seosan (relay).
WHO
No new Disease Outbreak News in the window
The latest is still DON622 (Ebola, 23 Oct). WHO posted on #MedSafetyWeek and on seasonal influenza and COVID-19 protection.
CDC / US
H5N1 B3.13: first US death of 2026; Colorado milk detection; more herds
- Human cases (CIDRAP, 2 Nov): 3 Yakima County cases, all with known contact with infected animals; 1 death (underlying conditions), described as the first US H5N1 death this year and the third since 2024. There’s no suggestion of human-to-human spread.
- Herds: 34 Washington herds infected in the past 30 days, all but one in Yakima County (state officials via CIDRAP). FluTrackers relays USDA reports of 6 more premises, for a state total of 40, plus a backyard flock in Yakima.
- Genotype: sequencing from two Yakima farms shows B3.13, the cow-adapted strain circulating since spring 2024.
- Colorado: H5N1 found in routine bulk milk tank testing at a Weld County dairy, the first such detection there since 2024.
- Indiana (relay): the state reports its first H5N1-infected dairy herd, with 2 dairies in total in its latest statement.
For UK clinicians: ask returning travellers with severe respiratory illness or conjunctivitis about US farm, dairy or raw-milk exposure.
The 34 and 40 herd counts cover different periods and sources and don’t reconcile. The Indiana figures are FluTrackers relays only, and we found no CDC statement.
CIDRAP › · YHD page › · @FluTrackers (USDA) › · @FluTrackers (Indiana) ›
Salmonella Telelkebir linked to Virginia raw oysters: 28 cases
One new case brings the multistate outbreak to 28 cases in 13 states, with 5 admitted to hospital. The oysters came from the Little Wicomico River (harvested 18 Sep to 8 Oct) and have been recalled (CDC, FDA, via CIDRAP).
Florida’s 2026 dengue total reaches 485
CIDRAP reports 60 new cases in the past week, with Hillsborough County at the centre of the outbreak.
CIDRAP: a mother’s account of a child’s flu death
A feature on a 3-year-old’s influenza death and the case for vaccination, ahead of the northern hemisphere season.
Five new EID early-release articles; travel notices unchanged
New EID articles (2 Nov) include hypertransmissible C. hominis IfA12G1R5 in Spain and Neoehrlichia mikurensis in the Netherlands (see Journals), along with endemic C. gattii in Nova Scotia, Jamestown Canyon virus in Illinois mosquitoes and porcine deltacoronavirus exposure in the US. The HAN archive was blocked again.
Journals
New since the 2 Nov issue: our picks from a Crossref sweep of the 19 watched titles (online 2–3 Nov) and EID early release, then today’s full Journal Watch top 10. Journal Watch’s JCM and JAC items aren’t repeated in our picks. The Lancet titles, CID, IJID, ICHE, AJIC, J Hosp Infect, J Infect, CMI and Eurosurveillance had nothing new in Crossref, and NEJM and JAMA had no infection items.
OFID and JID
Patient-directed vs fixed antibiotic duration in acute pyelonephritis: pilot RCT
Faine B, Moran G, Krishnadasan A and colleagues. Multicentre, double-blind pilot trial in women. Stopping antibiotics on the patient’s decision after symptom resolution gave similar sustained clinical resolution and adverse events to fixed duration. The authors say a larger, adequately powered trial is justified.
Diagnostic stewardship practices: US national survey
Scruggs-Wodkowski E, Piasecki R, Blok A and colleagues. 2025 survey of VA and non-federal hospitals. Strategies to reduce inappropriate urine testing and GI pathogen panels were the most common and were adopted similarly in both. VA hospitals reported more penicillin allergy testing (36.6% vs 21%; p=0.005).
Shotgun metagenomics vs 16S rDNA Sanger for culture-negative endocarditis
Ben Brahim S, Royer G, Jacquier H and colleagues. Both methods were run on identical DNA extracts from culture-negative native valves. Positivity rates were similar, and metagenomics gave higher taxonomic resolution.
Long-term daily chlorhexidine foot cleansing and staphylococcal burden
Bode M, Lydecker A, Robinson G and colleagues. Follow-up microbiome analysis of a trial of daily chlorhexidine versus soap and water over 1 year in people with previous diabetic foot complications. The parent trial found no significant reduction in new ulcers; the title reports reduced staphylococcal burden.
S. pneumoniae genomic stability during experimental human colonisation and PCV13
Stanley S, El Safadi D, Gordon S and colleagues. In the Experimental Human Pneumococcal Challenge model, the authors compared SNPs, indels and pangenome elements in strains from PCV13 recipients and controls. Group sizes are small (n=5 PCV13).
AAC, JCM and EID
NDM-7 exported in outer membrane vesicles from K. pneumoniae
González A, Quiroz V, Soto K and colleagues. Membrane-anchored NDM, unlike periplasmic KPC, is incorporated into OMVs. The title reports that vesicle-borne NDM-7 compromises imipenem (and other agents).
Rapid antigen tests for six respiratory viruses in children vs multiplex PCR
Kitagawa D, Di Lorenzo A, Okamura T and colleagues. Prospective paired-swab study comparing ImunoAce antigen kits (SARS-CoV-2, influenza A/B, adenovirus, hMPV, RSV) with FilmArray, with qPCR viral loads to model how sensitivity depends on viral load.
Post-COVID emergence of hypertransmissible C. hominis IfA12G1R5, Spain
EID early release (2 Nov). Relevant to UK labs that subtype Cryptosporidium, given summer outbreak activity.
Neoehrlichia mikurensis infection in an immunocompromised patient, the Netherlands
EID early release (2 Nov). A European tick-borne pathogen to consider in immunocompromised patients with unexplained fever and vascular events.
Journal Watch top 10
Credited to Microregistrar Journal Watch (issue of 3 Nov 2026, from 19 new PubMed records for 2–3 Nov). They are ranked by Journal Watch, and notes restate the abstracts; this isn’t clinical advice. Items 3 and 8 were also in our 2 Nov issue.
Antibiotic-loaded cement spacers: a comprehensive review
Review (US) covering literature from 1988 to 2024. It reports persisting mechanical problems plus nephrotoxicity and allergic reactions from unknown systemic antibiotic absorption, and argues for multidisciplinary, patient-specific spacer dosing in chronic periprosthetic joint infection.
Risk of depression after syphilis: Danish nationwide matched cohort
3,636 seropositive individuals. Depression risk was raised compared with the background population (HR 1.8), but seronegative tested individuals showed a similar rise, suggesting the association reflects the tested population rather than syphilis itself.
CLSI vs EUCAST broth microdilution for C. auris
Single-centre study (Greece), 107 isolates. Agreement was 100% for amphotericin B but only 44–72% for azoles. CDC breakpoints classed 33–44% of FKS1 mutants as non-resistant to echinocandins. Also covered in our 2 Nov issue.
Strongyloides stercoralis VirClia IgG monotest
Diagnostic accuracy study (Netherlands), 69 confirmed cases and 210 controls. The random-access chemiluminescent assay had 98.6% sensitivity and 98.1% specificity.
Plasma cfDNA PCR vs mNGS for invasive mould disease
Diagnostic accuracy study (US), 96 patients with proven or probable mould disease. Plasma mould PCR was more sensitive than mNGS (62.5% vs 43.8%), and specificity was very high for both.
Borrelia burgdorferi binds serum amyloid A in adipose tissue
Laboratory study (US). Infection triggered an adipose-tissue immune response with downregulation of SAA. SAA binding reduced bacterial viability in vitro and enhanced uptake by white blood cells.
Emerging serological technologies for HTLV diagnosis
Narrative review (Brazil) of advances and limitations in HTLV-1/2 serology and confirmatory testing, including cost, turnaround time and the need for affordable point-of-care tests.
Microbiology, resistance and mortality in necrotising soft tissue infections
Retrospective cohort (China), 212 adults over 16 years. 90-day mortality was 29.7% and Gram-negative infections predominated (43.9%). Also covered in our 2 Nov issue.
Do infection cases need to be last on the orthopaedic list?
Retrospective study (US). Clean orthopaedic cases that followed an infection case in the same theatre showed no difference in 30-day SSI or return to theatre for incision and drainage.
Bruker IR Biotyper for S. pyogenes emm typing
Laboratory evaluation (Canada). A tiered FT-IR classifier achieved 98% accuracy for emm pattern and 96% for emm type on external validation, and 100% in a mock outbreak. Classification of emm1 sublineages was poor.
On X
Tuesday light check: searches of agency and society accounts (UKHSA, ECDC, WHO, WHO/AFRO, CDC, MHRA, CIDRAP, IDSA, ESCMID) and of FluTrackers, AFluDiary and CIDRAP posts on Ebola, H5N1, C. auris and measles, from 2 Nov 08:10 GMT to this morning. Each item links to the post we read.
Agencies and societies
MHRA: #MedSafetyWeek patient safety essay competition. @MHRAgovuk ›
WHO: #MedSafetyWeek on not dismissing unexpected symptoms @WHO ›, and on influenza and COVID-19 protection @WHO ›
WHO/AFRO: the Bunia Ebola responder training centre @WHOAFRO ›, and psychosocial support from a clinician whose wife had Ebola @WHOAFRO ›
IDSA: HCV elimination webinar recording (with AASLD, INHSU and ESCMID). @IDSAInfo ›
CIDRAP: the Yakima H5N1 report @CIDRAP ›, and Quick takes on oysters, Bundibugyo vaccine funding and HIV in Barbados @CIDRAP ›
No posts from UKHSA, ECDC or CDC in the window.
Outbreaks and AMR
H5N1, US: AFluDiary’s “B3.13 is just getting started this fall?” round-up @FluTrackers ›; Washington adds 6 herds (n=40) and Indiana reports its first herd @FluTrackers ›; turkey farm, Sac County, Iowa @FluTrackers ›
Ebola, DRC: deaths revised downwards; reported CFR now 48.8%. @FluTrackers ›
Measles: New York’s first measles death in over 30 years @FluTrackers ›; a confirmed case in Ripley County, Indiana @FluTrackers ›
H5N1, Germany: WOAH report of a mallard. @FluTrackers ›
Unverified: FluTrackers relays weren’t checked against primary sources, apart from the Washington cases (confirmed by CIDRAP).
What we could not confirm
We want you to know exactly where today’s issue has limits, so here are the 11 gaps we couldn’t close, plus the reports that simply weren’t out yet.
| Source | Issue |
|---|---|
| Lead (US H5N1) | Based on CIDRAP and the Yakima Health District; we found no CDC statement. CIDRAP’s 34 herds in 30 days and the relayed USDA state total of 40 don’t reconcile (different periods). Indiana’s first herd is a relay. |
| Ebola | There was no new WHO DON, UKHSA or AFRO situation report. The DRC death revision (CFR 48.8%) is a FluTrackers relay, and the revised numerator is unknown. |
| Measles (US / international) | The New York death, Indiana, South Africa and Belize reports are press items relayed by FluTrackers and weren’t checked against health departments. |
| Journals | Based on Crossref abstracts only; some abstracts are truncated, so findings for the CHG foot, JID and AAC papers rely partly on titles. Elsevier titles (IJID, AJIC, JHI, J Infect, CMI) and the Lancet titles returned nothing. The ARIC VAP paper from India had no abstract and isn’t included. The EID notes are based on titles. |
| Journal Watch | All 10 were included. Items 3 and 8 overlap our 2 Nov issue, and the notes restate abstracts without rechecking. |
| X (light) | Light Tuesday check only (2 searches). Relay accounts are secondary. |
| CDC | The HAN archive was blocked again (stub page). We didn’t check MMWR. The travel notice list wasn’t compared in detail. |
| ECDC | The CDTR archive still shows week 42 (weeks 43 and 44 are missing). There was no ECDC news in the window. |
| Watched pages | The RCPath SMI, Examinations and NICE pages differed from yesterday only in markup. We found no new content, but this was a quick text check. |
| Moodle | No new entries. We read the sheet only, not the Moodle site itself. |
| Mail Sorter / mailbox | There were no Mail Sorter forwards and no infection emails in the window. |
Not out yet
- UKHSA: week 45 flu/COVID-19 and norovirus reports (data to week 44); HCAI monthly data (to October 2026); measles (12 Nov); next outbreaks-under-monitoring report.
- ECDC: CDTR weeks 43 and 44 (overdue).
- WHO: the revised Ebola rapid risk assessment; the next DON and AFRO situation report.
- CDC: a statement on the Washington H5N1 death; the Ebola travel attestation starts today (3 Nov).
- MHRA: #MedSafetyWeek runs until 8 Nov.
Sources
What we checked for this issue. Every link in the issue was retrieved and checked during this run.
- Watched pages (9 of 9 checked on the morning of 3 Nov)
- Microregistrar moodlecloud Google Sheet (Index tab), read directly through the Sheets connector
- UKHSA, MHRA and DHSC on GOV.UK (search API); Green Book, HCID country risk, Health Protection Report, measles and prenatal pertussis pages (content API)
- RCPath UK SMI consultations, UK SMI and Examinations pages; NICE published guidance
- Mail (microregistrar2021@gmail.com, read only): no Mail Sorter forwards; no infection emails in the window
- ECDC: news feed and CDTR archive
- WHO Disease Outbreak News (API)
- CDC: travel notices, HAN (blocked), EID early release (5 new); Yakima Health District avian influenza page
- CIDRAP per-topic feeds (Ebola, measles, avian flu, antimicrobial stewardship, influenza, HAI, COVID-19, pertussis, mpox, C. auris): 3 in-window items (Ebola Quick takes, avian flu, influenza)
- Journal sweep (Crossref, online 2–3 Nov): Lancet Infect Dis, Lancet Microbe, NEJM, JAMA, CID, JID, OFID, IJID, ICHE, AJIC, JAC, JAC-AMR, J Hosp Infect, J Infect, CMI, ARIC, AAC, JCM, Eurosurveillance; EID checked separately
- Microregistrar Journal Watch top 10, 3 Nov 2026
- X (Tuesday light check): searches over 2–3 Nov