Microregistrar Infection Newsletter · Monday 2 November 2026
H5N1 in Washington dairy workers: the hospitalised Yakima County patient has died, and a third human case is confirmed.
The Yakima Health District reported on 1 Nov that the resident hospitalised with severe illness after exposure at a dairy with infected cattle has died. The patient had underlying health conditions; name, sex and age were not released. Close contacts are being monitored. The same release reports a third confirmed human case, also exposed at a Yakima County dairy; this person has not been severely ill or admitted. The district’s page now lists 3 confirmed human cases (the first, reported 15 Oct, was mild; the second, reported 31 Oct, was the fatal case).
HPAI H5N1 was first found in Washington dairy cattle on 8 Oct. Washington State Department of Agriculture data on the district page show 33 Yakima County herds confirmed to 29 Oct. Officials say risk to the public remains low and that human-to-human transmission has never been documented in the US. For UK teams, this is a reminder to take an occupational and travel exposure history (dairy, poultry, raw milk) in severe influenza-like illness and to follow UKHSA’s avian influenza testing and isolation guidance.
Check before quoting: taken from Yakima Health District releases (31 Oct and 1 Nov) and its web page. The releases say “avian influenza” and don’t give the subtype or CDC confirmation for cases 2 and 3. Washington DOH’s statewide table still lists one 2026 dairy-linked case, so it lags the county figures. There’s no CDC or CIDRAP report yet. Ebola could have led today under the once-a-week rule, but today’s Ebola figures come only through relays.
Counted from today’s digest. The Crossref sweep (online 1–2 Nov) found 7 new infection-relevant items (JAC 3, JAC-AMR 3, OFID 1); one non-infection NEJM trial isn’t counted. Journal Watch sent 6 picks today, not 10, because only 6 new PubMed records were indexed over Sunday. Links are unique content links across the issue, not counting our two website links. Another weekend day: GOV.UK showed nothing from UKHSA, MHRA or DHSC after Friday 30 Oct, ECDC posted no news, there was no new WHO DON, and CIDRAP published nothing in the window.
Also today
The other headlines from today’s issue. Each card links to its source and to the full summary.
DRC: 63 new cases for 30 Oct; CFR reported at 51.6%
A DRC government report relayed by FluTrackers gives 63 new cases and 32 deaths for 30 Oct and a case fatality rate of 51.6%, driven by North Kivu and Ituri. Not yet confirmed by WHO.
CLSI vs EUCAST for C. auris: echinocandin calls differ for FKS1 mutants
In 107 international isolates, CDC tentative breakpoints classed 33–44% of FKS1 mutants as non-resistant, whereas all exceeded EUCAST ECOFFs.
aac(6′)-Ib-cr blunts amikacin in “susceptible” KPC K. pneumoniae
AME carriage reduced amikacin killing and survival benefit independently of MIC in time-kill and Galleria models; ceftazidime–avibactam was unaffected.
Phoning the on-call microbiologist speeds sepsis diagnosis
In 327 sepsis-alert patients, early microbiology activation was linked to diagnosis within 24 h (59.6% vs 35.1%; aOR 2.99) and earlier de-escalation.
#MedSafetyWeek starts today
The 2–8 Nov campaign asks patients and clinicians to report suspected side effects, including to vaccines and anti-infectives, via Yellow Card. WHO posted on it this morning.
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 comes from county health district releases; subtype and CDC confirmation for the second and third cases aren’t stated, and the state table lags. All Ebola items are FluTrackers relays: there’s still no new WHO DON since DON622 and no UKHSA outbreaks update, and the 51.6% CFR can’t be checked. Journal Watch supplied 6 picks rather than 10. 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 (2 Nov). The list is unchanged since the 1 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 2 Nov 2026). All nine were reached; only the JAC advance list has something new.
Health Protection Report (UKHSA)
No changeHPR 20(10) of 29 Oct is still the latest issue. HPR volume 20 ›
UK SMI News (RCPath)
No changeStill no open consultations and no new UK SMI documents. No Mail Sorter SMI forwards arrived. Consultations ›
UKHSA organisation page (GOV.UK)
No changeNothing new since Friday 30 Oct. The HCID country risk page hasn’t changed since 22 Oct. UKHSA › · HCID risk ›
Journal of Antimicrobial Chemotherapy
NewThree new JAC articles online 2 Nov: C. auris CLSI vs EUCAST, necrotising soft tissue infection microbiology, and bictegravir pharmacogenetics (see Journals). JAC advance articles ›
Agencies & guidance
Another quiet weekend day for UK and European agencies: nothing new from UKHSA, MHRA, DHSC or ECDC, and no new WHO DON. The main news is from the US, where a Washington dairy-linked H5N1 patient has died. Ebola figures from the DRC came only through relays.
Guidance changes
No new UK infection guidance over the weekend
No new UKHSA, NICE, Green Book or UK SMI guidance appeared in the window. The MMRV catch-up programme (children born 1 January 2020 to 31 August 2022) began on 1 Nov, as covered in yesterday’s issue.
For paediatric ID, virology and IPC teams: expect MMRV catch-up eligibility questions this week.
UKHSA / MHRA / England
No new UKHSA or DHSC infection publications
The latest UKHSA item on GOV.UK is still from Friday 30 Oct. The week 45 flu and COVID-19 surveillance report (data to week 44) is announced but not yet out. There were no Mail Sorter forwards and no new GOV.UK digest emails in the window.
#MedSafetyWeek runs 2–8 November
No new MHRA alerts in the window. The annual campaign encouraging reporting of suspected side effects, including to vaccines and anti-infectives, starts today.
ECDC / Europe
No ECDC news; CDTR archive still at week 42
The ECDC news feed has nothing after 29 Oct. The weekly threats archive still lists week 42 as the latest (weeks 43 and 44 are overdue). ESCMID posted only congress logistics on X.
Global
DRC reports 63 new cases and 32 deaths for 30 Oct; reported CFR rises to 51.6%
- DRC (government, via FluTrackers): 63 new cases and 32 deaths for 30 Oct. The report says the case fatality rate has jumped to 51.6%, driven mainly by North Kivu and Ituri. We can’t tell whether this is a cumulative or recent-period CFR.
- Maternal care: WHO/AFRO highlighted a midwife in Jina, Ituri, maintaining maternity services with training and PPE during the outbreak.
- Kenya and Nigeria: no new case figures were reported in the window.
- UK: no imported cases; UKHSA’s risk assessment is unchanged (low).
There’s no new WHO DON since DON622 (23 Oct), no new UKHSA outbreaks report and no new CIDRAP Ebola article. The latest verified totals are still UKHSA’s (data to 25 Oct). Ebola was eligible to lead today (it hasn’t led since before 25 Oct), but we led with the verified H5N1 death instead.
H5 in a dead dolphin, South Australia
A dead dolphin at Encounter Bay tested positive for H5 bird flu; the relay says South Australia now has 340 confirmed H5 events.
FluTrackers relay; not checked against the South Australian government.
WHO
No new Disease Outbreak News in the window
The latest is still DON622 (Ebola, 23 Oct).
CDC / US
Yakima County: dairy-linked avian influenza death and a third human case
- Death (1 Nov): the resident hospitalised with severe illness after dairy exposure (reported 31 Oct) has died. They had underlying health conditions; close contacts are being monitored.
- Third case: another Yakima County resident exposed to infected dairy cattle; not severely ill or admitted.
- Herds: 33 Yakima County dairy herds positive for HPAI H5N1 to 29 Oct (WSDA, via the district). The per-date table on the district page also adds up to 33.
- Risk: low for the general public; higher for dairy workers and others in close or prolonged contact with infected animals or contaminated environments. No human-to-human transmission has been documented in the US.
For UK clinicians: ask about recent US farm, dairy or raw-milk exposure in returning travellers with severe respiratory illness or conjunctivitis, and follow UKHSA avian influenza testing guidance.
Washington DOH’s statewide table still shows 1 dairy-linked case for 2026, behind the county’s 3. The releases say “avian influenza”; the human subtype and CDC confirmation for cases 2 and 3 aren’t stated.
YHD release, 1 Nov › · YHD release, 31 Oct › · YHD page › · WA DOH › · @FluTrackers ›
No new EID articles; travel notices unchanged
EID’s early-release feed has nothing after 30 Oct. The travel notice list is unchanged, and the HAN archive was blocked again. CIDRAP published nothing in the window. The CDC Ebola travel attestation starts tomorrow (3 Nov).
Journals
New since the 1 Nov issue (online 1–2 Nov), from a Crossref sweep of the 19 watched titles, followed by today’s Journal Watch top picks. The Lancet titles, JAMA, CID, IJID, ICHE, AJIC, J Hosp Infect, J Infect, CMI, ARIC, AAC, JCM and Eurosurveillance had nothing new. JID returned nothing on retry, and NEJM’s one item wasn’t infection-related.
Journal of Antimicrobial Chemotherapy
CLSI vs EUCAST broth microdilution for Candida (Candidozyma) auris
Siopi M, Leventaki S, Pachoulis I and colleagues. 107 international clinical isolates, including azole- and echinocandin-resistant strains. Essential agreement was 100% for amphotericin B, 93% for flucytosine, 81–87% for echinocandins and 44–72% for azoles. Categorical agreement was 92% (anidulafungin) and 94% (micafungin). CDC tentative breakpoints classified 33–44% of FKS1 mutants as non-resistant, whereas all FKS1 mutants exceeded EUCAST ECOFFs.
Takeaway: echinocandin MICs of 0.5–1 mg/L in C. auris may hide FKS1 mutations; know which method and breakpoints your reference laboratory uses, and consider FKS sequencing on failure.
Microbiology and mortality in necrotising soft tissue infections, 16-year cohort
Ji X, Wu Z, Wang K and colleagues. 212 adults (Dec 2008 to May 2025): 90-day mortality 29.7%; Gram-negatives predominated (43.9%). S. pyogenes erythromycin and clindamycin resistance were 75.0% and 62.5%, and 66.7% of E. coli were ESBL-positive. Single-centre data from China; resistance rates come from small isolate numbers.
CYP3A5 and UGT1A1 variants and bictegravir levels in Japanese patients
Yagura H, Hisari A, Nakauchi T and colleagues. In 110 patients, trough bictegravir was 18% higher with homozygous CYP3A5*3 and 69% higher with homozygous or compound heterozygous UGT1A1 variants. UGT1A1 variants were linked to increased appetite.
JAC-AMR and OFID
aac(6′)-Ib-cr reduces amikacin efficacy against phenotypically susceptible KPC K. pneumoniae
Kim J, Seong JE, Lee Y and colleagues. 13 KPC isolates with amikacin MIC ≤4 mg/L (10 AME-positive). AME-positive isolates showed less 24 h killing (2.41 vs 4.28 log10 cfu/mL) and more regrowth. In Galleria, AME status reduced the amikacin effect (adjusted HR 2.09), independently of MIC. Ceftazidime–avibactam’s benefit was unaffected (interaction HR 1.03).
Takeaway: a “susceptible” amikacin MIC may overstate activity in CRKP carrying aac(6′)-Ib-cr. These are in vitro and invertebrate data only.
Azole-resistant A. fumigatus complex in Greece: first TR46 isolate
Siopi M, Vargiami M, Beredaki M and colleagues. 249 isolates: 2% azole-resistant, including all three cryptic species and a pan-azole-resistant TR46/Y121F/T289A isolate from a patient with cystic fibrosis.
Defining appropriate antimicrobial use across One Health
Schermuly A, Scarborough R, Dowson L and colleagues. Four focus groups found structural, economic and educational barriers in human and animal health. The findings will feed into an international Delphi process.
Patients take tick-testing results to their clinicians
Crooker J, Thangamani S. Of 2,560 US respondents, 32.2% used tick pathogen results when seeking care, and 476 thought medication was prescribed on that basis. Detection in a tick doesn’t establish human infection.
Journal Watch top picks (6 today)
Credited to Microregistrar Journal Watch (issue of 2 Nov 2026). Only 6 new PubMed records were indexed for 1–2 Nov, so today’s list has 6 items rather than 10. They are ranked by Journal Watch, and notes restate the abstracts. Items 1 and 6 were also in our 1 Nov issue.
Responsible use of new antibiotics for CRO infections in critically ill patients
Narrative review and expert opinion (Germany). Proposes a coordinated AMS algorithm and an enablement, rather than restrictive, strategy for new antibiotics. Covered in our 1 Nov issue.
Early microbiology laboratory activation in a sepsis alert pathway
Prospective cohort (Spain), 327 patients. Phoning the on-call microbiologist was independently linked to diagnosis within 24 h (59.6% vs 35.1%; aOR 2.99) and earlier de-escalation. There was no difference in mortality or length of stay.
ESwab vs conventional swab vs tissue culture in chronic wounds
Prospective study (US), 63 patients. ESwab and Amies swabs agreed closely (κ 0.86) but poorly with tissue culture. Discordance changed management in only 1 of 21 cases.
Antenatal Group B Streptococcus susceptibility in Greece
89 isolates: erythromycin resistance 58.6%, clindamycin 54.6% and tetracycline 89.8%; 97.8% were benzylpenicillin-susceptible and 50% were multidrug resistant. Penicillin-susceptible isolates at 97.8% means about 2 of 89 were not; the abstract doesn’t explain these.
Aztreonam–durlobactam heteroresistance in ST11-KL25 KPC-2 + NDM-1 K. pneumoniae
Letter (China). There’s no abstract in the PubMed record, so the findings aren’t stated here.
Correction: additional doses of adjuvanted recombinant zoster vaccine 5–6 years after primary vaccination
Published erratum to DOI 10.1093/ofid/ofag282; no other content stated.
On X
Monday light check: searches covering agency and society accounts (UKHSA, WHO, WHO/AFRO, WHO/Europe, ECDC, CDC, MHRA, CIDRAP, ESCMID, IDSA), FluTrackers outbreak relays, and H5N1, C. auris, UK measles and Kenyan Ebola keywords, from 1 Nov 08:10 GMT to this morning. Each item links to the post we read.
Agencies and societies
WHO: #MedSafetyWeek, on why reporting side effects matters. @WHO ›
IDSA: the Science Speaks blog round-up of JID research, including postnatal CMV in preterm infants and post-pandemic IPD rates. @IDSAInfo ›
WHO/AFRO: maternity care continuing in Ituri during the Ebola outbreak. @WHOAFRO ›
No posts from UKHSA, ECDC, CDC, MHRA or CIDRAP in the window.
Outbreaks and AMR
H5N1, Washington: AFluDiary/FluTrackers on the second Yakima County human case (severe) @FluTrackers ›; the death and third case are confirmed in the Yakima Health District release (see lead).
Ebola, DRC: 63 new cases and 32 deaths for 30 Oct; reported CFR 51.6%. @FluTrackers ›
H5, Australia: a dolphin at Encounter Bay tested positive. @FluTrackers ›
CDC AR Threats Report: MedPage Today on C. auris, Acinetobacter, Enterobacterales and N. gonorrhoeae topping the revised list (our 28 Oct lead). @medpagetoday ›
Unverified: FluTrackers and news-share accounts weren’t checked against primary sources, apart from the Washington H5N1 items.
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 (Washington H5N1) | Taken from county health district releases. The human subtype and CDC confirmation for cases 2 and 3 aren’t stated, and Washington DOH’s table (1 dairy-linked case) lags the county’s 3. There’s no CDC or CIDRAP report yet. |
| Ebola | There was no new UKHSA, WHO or CIDRAP update. DRC figures come via FluTrackers, and we can’t tell whether the 51.6% CFR is cumulative or recent. |
| Avian influenza (other) | The Australian dolphin H5 report is a FluTrackers relay. |
| Journals | Crossref abstracts only. JID returned an HTTP 429 error and then nothing on retry. Elsevier titles, the Lancet titles, AAC and JCM returned nothing, possibly because of weekend indexing lag. |
| Journal Watch | The 2 Nov file has 6 picks, not 10 (only 6 new PubMed records). Picks 1 and 6 overlap our 1 Nov issue. Pick 5 has no abstract. GBS percentages are restated from the abstract and weren’t rechecked. |
| X (light) | Light Monday check only. FluTrackers and news-share items are secondary. |
| CDC | The HAN archive was blocked again (stub page). We didn’t check MMWR. |
| ECDC | The CDTR archive still shows week 42 (weeks 43 and 44 are missing). There was no ECDC news in the window. |
| CIDRAP | None of the ten per-topic feeds had an item in the window. All feeds are unchanged since yesterday, and the newest item is from 30 Oct. |
| Moodle | No new entries. We read the sheet only, not the Moodle site itself. |
| Mail Sorter / mailbox | No Mail Sorter forwards and no infection emails in the window. |
Not out yet
- UKHSA: week 45 flu/COVID-19 surveillance report (data to week 44); HCAI monthly data (4 Nov); 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: confirmation of the Washington cases; the Ebola travel attestation starts on 3 Nov.
- Yakima Health District: next scheduled case update today (Monday) at 14:00 Pacific time (22:00 GMT).
- MHRA: #MedSafetyWeek runs 2–8 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 2 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 and measles 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 (unchanged), HAN (blocked), EID early release (none new); Yakima Health District and Washington DOH avian influenza pages
- CIDRAP per-topic feeds (Ebola, measles, avian flu, antimicrobial stewardship, influenza, HAI, COVID-19, pertussis, mpox, C. auris): none in the window
- Journal sweep (Crossref, online 1–2 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 picks, 2 Nov 2026 (6 items)
- X (Monday light check): searches over 1–2 Nov