Longitudinal Comparison of #Bacterial Diversity and #Antibiotic #Resistance Genes in #NYC #Sewage (mSystems, abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

mSystems. 2019 Aug 6;4(4). pii: e00327-19. doi: 10.1128/mSystems.00327-19.

Longitudinal Comparison of Bacterial Diversity and Antibiotic Resistance Genes in New York City Sewage.

Joseph SM1,2, Battaglia T3, Maritz JM2, Carlton JM2, Blaser MJ3,4.

Author information: 1 New York University School of Medicine, New York, New York, USA susanj13@gmail.com. 2 Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, USA. 3 New York University School of Medicine, New York, New York, USA. 4 Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA.



Bacterial resistance to antibiotics is a pressing health issue around the world, not only in health care settings but also in the community and environment, particularly in crowded urban populations. The aim of our work was to characterize the microbial populations in sewage and the spread of antibiotic resistance within New York City (NYC). Here, we investigated the structure of the microbiome and the prevalence of antibiotic resistance genes in raw sewage samples collected from the fourteen NYC Department of Environmental Protection wastewater treatment plants, distributed across the five NYC boroughs. Sewage, a direct output of anthropogenic activity and a reservoir of microbes, provides an ecological niche to examine the spread of antibiotic resistance. Taxonomic diversity analysis revealed a largely similar and stable bacterial population structure across all the samples, which was found to be similar over three time points in an annual cycle, as well as in the five NYC boroughs. All samples were positive for the presence of the seven antibiotic resistance genes tested, based on real-time quantitative PCR assays, with higher levels observed for tetracycline resistance genes at all time points. For five of the seven genes, abundances were significantly higher in May than in February and August. This study provides characteristics of the NYC sewage resistome in the context of the overall bacterial populations.



Urban sewage or wastewater is a diverse source of bacterial growth, as well as a hot spot for the development of environmental antibiotic resistance, which can in turn influence the health of the residents of the city. As part of a larger study to characterize the urban New York City microbial metagenome, we collected raw sewage samples representing three seasonal time points spanning the five boroughs of NYC and went on to characterize the microbiome and the presence of a range of antibiotic resistance genes. Through this study, we have established a baseline microbial population and antibiotic resistance abundance in NYC sewage which can prove to be very useful in studying the load of antibiotic usage, as well as for developing effective measures in antibiotic stewardship.

Copyright © 2019 Joseph et al.

KEYWORDS: New York City; antibiotic resistance; microbiome; sewage

PMID: 31387933 DOI: 10.1128/mSystems.00327-19

Keywords: Antibiotics; Drugs Resistance; Environmental pollution; USA; NYC.


Activity of #cefepime / #zidebactam (WCK 5222) against #Enterobacteriaceae, #Pseudomonas aeruginosa and #Acinetobacter baumannii endemic to #NYC #medical centres (J Antimicrob Chemother., abstract)

[Source: Journal of Antimicrobial Chemotherapy, full page: (LINK). Abstract, edited.]

Activity of cefepime/zidebactam (WCK 5222) against Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii endemic to New York City medical centres

Zeb Khan, Alejandro Iregui, David Landman, John Quale

Journal of Antimicrobial Chemotherapy, dkz294, https://doi.org/10.1093/jac/dkz294

Published: 11 July 2019




The combination of cefepime and zidebactam (WCK5222), a novel β-lactam enhancer, has demonstrated activity against a wide variety of Gram-negative pathogens and is currently under clinical evaluation.


To examine the activity of cefepime/zidebactam against: (i) a contemporary collection of Gram-negative isolates from New York City; (ii) a collection of carbapenem-resistant clinical isolates; and (iii) a collection of isolates with characterized resistance mechanisms.


Susceptibility tests were performed using broth microdilution for cefepime, zidebactam and cefepime/zidebactam (1:1).


More than 99% of a contemporary collection of Escherichia coli, Klebsiella pneumoniae and Enterobacter spp. had cefepime/zidebactam MICs ≤2 mg/L, the susceptibility breakpoint for cefepime. For K. pneumoniae, the acquisition of blaKPC resulted in increased MICs, although MICs remained ≤2 mg/L for 90% of KPC-possessing isolates. Overall for Pseudomonas aeruginosa, 98% of isolates had MICs ≤8 mg/L and MICs were affected by increased expression of ampC. For carbapenem-resistant P. aeruginosa, 78% of isolates had cefepime/zidebactam MICs ≤8 mg/L. The activity of cefepime/zidebactam against Acinetobacter baumannii was lower, with 85% of all isolates and 34% of carbapenem-resistant isolates with MICs ≤8 mg/L (cefepime interpretative criteria).


Cefepime/zidebactam demonstrated excellent activity against Enterobacteriaceae and P. aeruginosa, although activity was reduced in carbapenem-non-susceptible isolates. The activity against A. baumannii was reduced and studies examining the therapeutic efficacy in strains with high cefepime/zidebactam MICs are warranted.

Topic:  pseudomonas aeruginosa – cefepime – enterobacter – enterobacteriaceae – new york city – acinetobacter baumannii – bacterial carbapenemase resistance blakpc gene – malnutrition-inflammation-cachexia syndrome – carbapenem resistance


© The Author(s) 2019. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email: journals.permissions@oup.com.

This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

Keywords: Antibiotics; Drugs Resistance; Carbapenem; Enterobacteriaceae; Pseudomonas aeruginosa; Acinetobacter baumannii; Cefepine; Zidebactam; USA; NYC.


#Mandatory #Measles #Vaccination in #NYC — Reflections on a Bold Experiment (N Engl J Med., summary)

[Source: The New England Journal of Medicine, full page: (LINK). Summary, edited.]

Mandatory Measles Vaccination in New York City — Reflections on a Bold Experiment

Julie D. Cantor, M.D., J.D.


Though a vaccine has been available for more than 50 years, measles has recently reemerged as a public health threat in the United States. Outbreaks have arisen where vaccination rates have waned, and local governments have responded.

In Detroit, officials and religious leaders of an affected community collaborated, encouraging vaccination to control an outbreak. Los Angeles quarantined people exposed to the virus. New York City and Rockland County have seen the most cases, and their extensive vaccination efforts have included free clinics, meetings with community leaders, and email messages to clinicians. They also issued orders restricting the liberty of people who neither had nor were exposed to the virus.



Disclosure forms provided by the author are available at NEJM.org.

This article was published on June 5, 2019, at NEJM.org.

Author Affiliations: From the UCLA School of Law, Los Angeles.

Keywords: Measles; USA; NYC; Society.


A Single-Center #Experience with a #Pregnant #Immigrant #Population and #Zika Virus Serologic #Screening in #NYC (Am J Perinatol., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Am J Perinatol. 2019 May 30. doi: 10.1055/s-0039-1688819. [Epub ahead of print]

A Single-Center Experience with a Pregnant Immigrant Population and Zika Virus Serologic Screening in New York City.

Merriam AA1, Nhan-Chang CL1, Huerta-Bogdan BI1, Wapner R1, Gyamfi-Bannerman C1.

Author information: 1 Department of Obstetrics and Gynecology, College of Physicians and Surgeons, Columbia University, New York, New York.




Our institution is in an area of New York City with a large population of immigrants from Zika virus endemic areas. With the recent Zika virus outbreak, we sought to examine our center’s experience with screening for Zika virus and outcomes among patients who tested positive for the disease during pregnancy.


We performed a chart review of all pregnant patients who tested positive (positive serum or urine polymerase chain reaction [PCR]) or presumed positive (immunoglobulin M [IgM] enzyme-linked immunosorbent assay [ELISA] positive or IgM ELISA equivocal with positive plaque reduction neutralization test) for Zika virus. All tests were performed by the Department of Health (DOH) and followed Centers for Disease Control and Prevention guidelines in effect at the time of specimen collection. Testing of cord blood, placenta, and/or neonatal blood were/was performed by the DOH for New York County. Prenatal ultrasounds for fetal head size and surveillance for calcifications were performed by maternal-fetal medicine specialists. Infant head ultrasound results were included when available.


Between March 2016 and April 2017, 70 pregnant patients were positive or presumed positive for Zika infection during pregnancy. Of those, 16 women had positive urine or serum PCR and the remaining 54 were presumed positive. Among positive cases, five women tested positive via urine PCR only, nine women tested positive via serum PCR only, and two women had both positive urine and serum PCR. Fifteen of 67 infants (22%) born during the study period were born to mothers with positive urine or serum PCR testing. Sixty-five newborns were clinically normal with normal head measurements. Of the intracranial ultrasound performed, one infant had a grade 1 intraventricular hemorrhage, four had incidental choroid plexus cysts, and one had severe ventriculomegaly that was also noted antenatally. There were 2 positive and 15 equivocal infant serum IgM samples and 1 positive placental PCR from these pregnancies. There were four pregnancy terminations and two cases with fetal anomalies in this population that were split evenly between patients who tested positive and those who tested presumed positive for Zika virus during pregnancy.


We found no differences in pregnancy or neonatal outcomes between women who tested positive and presumed positive for Zika virus during pregnancy. Testing of infants and placenta tissue after delivery was largely inconclusive. Improvement in testing for Zika virus infection is needed to determine which pregnancies are at risk for congenital anomalies. Further research is still needed to determine which children are at risk for poor neurodevelopmental outcomes related to Zika virus and how to best coordinate care among the immigrant population during a new disease epidemic.

Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

PMID: 31146294 DOI: 10.1055/s-0039-1688819

Keywords: Zika Virus; Zika Congenital Syndrome; Pregnancy; USA; NYC; Serology.


#Neonatal #Conjunctivitis Caused by #Neisseria meningitidis US Urethritis Clade, #NY, #USA, August 2017 (Emerg Infect Dis., abstract)

[Source: US Centers for Disease Control and Prevention (CDC), Emerging Infectious Diseases Journal, full page: (LINK). Abstract, edited.]

Volume 25, Number 5—May 2019 / Dispatch

Neonatal Conjunctivitis Caused by Neisseria meningitidis US Urethritis Clade, New York, USA, August 2017

Cecilia B. Kretz1  , Genevieve Bergeron1, Margaret Aldrich, Danielle Bloch, Paula E. Del Rosso, Tanya A. Halse, Belinda Ostrowsky, Qinghuan Liu, Edimarlyn Gonzalez, Enoma Omoregie, Ludwin Chicaiza, Greicy Zayas, Bun Tha, Angela Liang, Jade C. Wang, Michael Levi, Scott Hughes, Kimberlee A. Musser, Don Weiss, and Jennifer L. Rakeman

Author affiliations: Centers for Disease Control and Prevention, Atlanta, Georgia, USA (C.B. Kretz, G. Bergeron); New York City Department of Health and Mental Hygiene; Queens, New York, USA (C.B. Kretz, G. Bergeron, M. Aldrich, D. Bloch, P.E. Del Rosso, Q. Liu, E. Gonzalez, E. Omoregie, L. Chicaiza, G. Zayas, B. Tha, A. Liang, J.C. Wang, S. Hughes, D. Weiss, J.L. Rakeman); Montefiore Medical Center, Bronx, New York, USA (M. Aldrich, B. Ostrowsky, M. Levi); New York State Department of Health, Albany, New York, USA (T.A. Halse, K.A. Musser)



We characterized a case of neonatal conjunctivitis in New York, USA, caused by Neisseria meningitidis by using whole-genome sequencing. The case was a rare occurrence, and the isolate obtained belonged to an emerging clade (N. meningitidis US nongroupable urethritis) associated with an increase in cases of urethritis since 2015.

Keywords: Neisseria meningitidis; Urethritis; Conjunctivitis; USA.


The #Cat’s #Meow: Using Novel #Serological Approaches to Identify Cat-to- #Human #Influenza A(#H7N2) Transmission (J Infect Dis., summary)

[Source: Journal of Infectious Diseases, full page: (LINK). Summary, edited.]

The Cat’s Meow: Using Novel Serological Approaches to Identify Cat-to-Human Influenza A(H7N2) Transmission

Seema Jain, Erin L Murray

The Journal of Infectious Diseases, jiy596, https://doi.org/10.1093/infdis/jiy596

Published: 03 November 2018

(See the major Article by Poirot et al on pages XX-XX)

“What greater gift than the love of a cat?”—Charles Dickens, Great Expectations

Avian influenza viruses have rarely been detected in cats and, until 2016, no cat had ever been documented to have an influenza A(H7N2) virus infection or to transmit the virus to a human. In December 2016, the New York City Department of Health and Mental Hygiene (NYC DOHMH) was alerted about a cat admitted to a Manhattan animal shelter on 12 November 2016 that subsequently died and was confirmed positive for influenza A(H7N2) virus, a low-pathogenic avian influenza virus [1, 2].


Keywords: Avian Influenza; H7N2; Cats; Human; USA; NYC.


Detection of #Avian #Influenza A(#H7N2) Virus #Infection Among #Animal #Shelter #Workers Using a Novel Serological Approach— #NYC, 2016–2017 (J Infect Dis., abstract)

[Source: Journal of Infectious Diseases, full page: (LINK). Abstract, edited.]


Detection of Avian Influenza A(H7N2) Virus Infection Among Animal Shelter Workers Using a Novel Serological Approach—New York City, 2016–2017

Eugenie Poirot, Min Z Levine, Kate Russell, Rebekah J Stewart, Justine M Pompey, Sophia Chiu, Alicia M Fry, Liaini Gross, Fiona P Havers, Zhu-Nan Li, Feng Liu, Aldo Crossa, Christopher T Lee, Vanessa Boshuizen, Jennifer L Rakeman, Sally Slavinski, Scott Harper, L Hannah Gould

The Journal of Infectious Diseases, jiy595, https://doi.org/10.1093/infdis/jiy595

Published: 05 November 2018




In 2016, an influenza A(H7N2) virus outbreak occurred in cats in New York City’s municipal animal shelters. One human infection was initially detected.


We conducted a serological survey using a novel approach to rule out cross-reactive antibodies to other seasonal influenza viruses to determine whether additional A(H7N2) human infections had occurred and to assess exposure risk.


Of 121 shelter workers, one had serological evidence of A(H7N2) infection, corresponding to a seroprevalence of 0.8% (95% confidence interval, .02%–4.5%). Five persons exhibited low positive titers to A(H7N2) virus, indicating possible infection; however, we could not exclude cross-reactive antibody responses to seasonal influenza viruses. The remaining 115 persons were seronegative. The seropositive person reported multiple direct cat exposures without using personal protective equipment and mild illness with subjective fever, runny nose, and sore throat.


We identified a second case of A(H7N2) infection from this outbreak, providing further evidence of cat-to-human transmission of A(H7N2) virus.

influenza, H7N2, outbreak, zoonotic, serology, human infection

Issue Section: Major Article

Keywords: Avian Influenza; H7N2; Cats; Human; USA; NYC.