The Changing Face of the Family Enterobacteriaceae (Order: "Enterobacterales"): New Members, Taxonomic Issues, Geographic Expansion, and New Diseases and Disease Syndromes.

The family Enterobacteriaceae has undergone significant morphogenetic changes in its more than 85-year history, particularly during the past 2 decades (2000 to 2020). The development and introduction of new and novel molecular methods coupled with innovative laboratory techniques have led to many advances. We now know that the global range of enterobacteria is much more expansive than previously recognized, as they play important roles in the environment in vegetative processes and through widespread environmental distribution through insect vectors. In humans, many new species have been described, some associated with specific disease processes. Some established species are now observed in new infectious disease settings and syndromes. The results of molecular taxonomic and phylogenetics studies suggest that the current family Enterobacteriaceae should possibly be divided into seven or more separate families. The logarithmic explosion in the number of enterobacterial species described brings into question the relevancy, need, and mechanisms to potentially identify these taxa. This review covers the progression, transformation, and morphogenesis of the family from the seminal Centers for Disease Control and Prevention publication (J. J. Farmer III, B. R. Davis, F. W. Hickman-Brenner, A. McWhorter, et al., J Clin Microbiol 21:46-76, 1985, https://doi.org/10.1128/JCM.21.1.46-76.1985) to the present.

The Development of a WTC Environmental Health Center Pan-Cancer Database.

(1) Background: Recent studies have reported elevated risks of multiple cancers in the World Trade Center (WTC) affected community members (also called WTC "Survivors"). The large variety of WTC-cancers created a need to develop a comprehensive cancer database. This paper describes the development of a pan-cancer database at the WTC Environmental Health Center (EHC) Data Center. (2) Methods: A new REDCap-based pan-cancer database was created using the pathology reports and available biomarker data of confirmed cancer cases after review by a cancer epidemiologist, a pathologist, physicians and biostatisticians. (3) Results: The WTC EHC pan-cancer database contains cancer characteristics and emerging biomarker information for cancers of individuals enrolled in the WTC EHC and diagnosed after 11 September 2001 and up to 31 December 2019 obtained from WTC EHC clinical records, pathological reports and state cancer registries. As of 31 December 2019, the database included 3440 cancer cases with cancer characteristics and biomarker information. (4) Conclusions: This evolving database represents an important resource for the scientific community facilitating future research about the etiology, heterogeneity, characteristics and outcomes of cancers and comorbid mental health conditions, cancer economics and gene-environment interaction in the unique population of WTC survivors.

Characteristics of Cancer Patients in the World Trade Center Environmental Health Center.

The destruction of the World Trade Center (WTC) towers on 11 September 2001 released many tons of aerosolized dust and smoke with potential for carcinogenic exposures to community members as well as responders. The WTC Environmental Health Center (WTC EHC) is a surveillance and treatment program for a diverse population of community members ("Survivors"), including local residents and workers, present in the NYC disaster area on 9/11 or in the days or weeks following. We report a case series of cancers identified in the WTC EHC as of 31 December 2019. Descriptive characteristics are presented for 2561 cancer patients (excluding non-melanoma skin cancer) and 5377 non-cancer WTC-EHC participants who signed informed consent. We identified a total of 2999 cancer diagnoses in 2561 patients: 2534 solid tumors (84.5%) and 465 lymphoid and hematopoietic tissue cancers (15.5%) with forty-one different cancer types. We describe the distribution, frequency, median age of cancer diagnosis and median latency from 9/11 by cancer site. In addition to common cancer types, rare cancers, including male breast cancers and mesotheliomas have been identified. The current study is the first report on cancer characteristics of enrollees at WTC EHC, a federally designated treatment and surveillance program for local community members affected by the 9/11 terrorist attack on the WTC.

Plesiomonas shigelloides Revisited.

After many years in the family Vibrionaceae, the genus Plesiomonas, represented by a single species, P. shigelloides, currently resides in the family Enterobacteriaceae, although its most appropriate phylogenetic position may yet to be determined. Common environmental reservoirs for plesiomonads include freshwater ecosystems and estuaries and inhabitants of these aquatic environs. Long suspected as being an etiologic agent of bacterial gastroenteritis, convincing evidence supporting this conclusion has accumulated over the past 2 decades in the form of a series of foodborne outbreaks solely or partially attributable to P. shigelloides. The prevalence of P. shigelloides enteritis varies considerably, with higher rates reported from Southeast Asia and Africa and lower numbers from North America and Europe. Reasons for these differences may include hygiene conditions, dietary habits, regional occupations, or other unknown factors. Other human illnesses caused by P. shigelloides include septicemia and central nervous system disease, eye infections, and a variety of miscellaneous ailments. For years, recognizable virulence factors potentially associated with P. shigelloides pathogenicity were lacking; however, several good candidates now have been reported, including a cytotoxic hemolysin, iron acquisition systems, and lipopolysaccharide. While P. shigelloides is easy to identify biochemically, it is often overlooked in stool samples due to its smaller colony size or relatively low prevalence in gastrointestinal samples. However, one FDA-approved PCR-based culture-independent diagnostic test system to detect multiple enteropathogens (FilmArray) includes P. shigelloides on its panel. Plesiomonads produce ß-lactamases but are typically susceptible to many first-line antimicrobial agents, including quinolones and carbapenems.

Using a 2-stage strategy with respondent-driven sampling to recruit a hard-to-reach population for a placebo microbicide gel clinical trial in Nellore, Andhra Pradesh (India).

Traditional recruitment methods for microbicide efficacy trials are labor intensive and may fail to reach high-risk hard-to-reach populations. We report duration of recruitment and lessons learned from a two-stage process to recruit female sex workers (FSWs) into a placebo microbicide trial, and examined characteristics associated with successful recruitment of peers who screened for and enrolled in the trial. FSWs were first recruited via respondent-driven sampling (RDS) to complete a survey and subsequently invited to screen for enrollment into a placebo microbicide trial taking place at a local clinic. It took 6 months to enroll 267 participants into the trial. Successful recruiters of peers who enrolled were more likely to have enrolled themselves (AOR 2.0, CI 1.3-2.9) and less likely to visit Nellore city (AOR 0.5, CI 0.3-0.9). Recruitment of FSWs via a two-stage recruitment strategy with RDS can be a good option for future clinical trials.

Culture-independent diagnostic testing: have we opened Pandora's box for good?

The ability to accurately and quickly identify microbial agents associated with infectious diseases has been a longstanding and continuous goal of diagnostic microbiology laboratories. Over the course of several decades, technology and testing methodologies in this field have gradually evolved from traditional- or classic-based culture and identification approaches to antigen capture systems and more molecular-oriented applications. Recently, these molecular-based applications have signaled a new era in clinical diagnostic microbiology with the commercial introduction of culture-independent diagnostic testing (CIDT) systems. The first major commercial venture into the CIDT arena involves the detection of acute bacterial gastroenteritis. Several commercial products are now on the market globally with at least 4 Food and Drug Administration approved since January of 2013. These new systems offer the direct detection of a variety of enteropathogens quickly without the need for traditional culture. In Greek mythology, Pandora opened a "jar" or "box" out of curiosity thereby releasing all of humanity's evils most notably diseases and plagues according to Hesiod's Theogony. While not ill-intentioned the only thing left in the box was Hope.

The genus Shewanella: from the briny depths below to human pathogen.

The genus Shewanella is currently composed of more than 50 species that inhabit a range of marine environs and ecosystems. Several members of this genus, including S. oneidensis, have been identified that could potentially play key roles in environmental processes such as bioremediation of toxic elements and heavy metals and serving as microbial fuel cells. In contrast to this beneficial role, shewanellae are increasingly being implicated as human pathogens in persons exposed through occupational or recreational activities to marine niches containing shewanellae. Documented illnesses linked to Shewanella include skin and soft tissue infections, bacteremia, and otitis media. At present, it is unclear exactly how many Shewanella species are truly bona fide human pathogens. Recent advances in the taxonomy and phylogenetic relatedness of members of this genus, however, support the concept that most human infections are caused by a single species, S. algae. Some phylogenetic data further suggest that some current members of the genus are not true Shewanella species sensu stricto. The current review summarizes our present knowledge of the distribution, epidemiology, disease spectrum, and identification of microbial species focusing on a clinical perspective.

Expedited partner therapy in federally qualified health centers--New York City, 2012.

BACKGROUND: Management of patients' sex partners is a critical element of sexually transmitted disease (STD) control. Expedited partner therapy (EPT), a practice in which patients deliver medication or a prescription directly to their partners, is one option for partner management. As of 2009, New York State law specifically allows EPT for chlamydial infection. Federally qualified health centers (FQHCs) in New York City (NYC) care for patients at risk for STDs. We describe the policies and practices surrounding EPT and other STD management in NYC FQHCs. METHODS: In 2012, we surveyed medical directors at all NYC FQHC parent entities and clinicians at a sample of their corresponding clinical sites about written policies and actual practices regarding EPT for chlamydial infection and other STD management. RESULTS: Twenty-two entities (22/29; 76%) and 51 sites (51/72; 70%) responded to the survey. More than half of entities have a written policy permitting EPT, and 80% of sites provide EPT. Most entity policies allow EPT for, and most sites provide EPT to, adolescents and adults with both opposite-sex and/or same-sex partners. Most sites use electronic health records and provide EPT by prescriptions, and one third of sites do not provide educational materials with EPT. CONCLUSIONS: Our results indicate widespread EPT provision by NYC FQHCs; however, areas for improvement exist, specifically in following guidelines that recommend providing educational materials with EPT and do not recommend EPT for men with male partners. The use of prescriptions for EPT and electronic health records were identified as potential barriers to EPT provision.

Sexually transmitted infections and reproductive health morbidity in a cohort of female sex workers screened for a microbicide feasibility study in Nellore, India.

UNLABELLED: Women constitute 38% of India's 2.4 million HIV-infected persons. Microbicides are potential HIV-prevention products currently undergoing clinical trials for efficacy. A four-month placebo vaginal gel trial was conducted in Nellore, India to determine the feasibility of recruiting a suitable cohort of female sex workers (FSWs) for a future vaginal microbicide efficacy trial. We report on the HIV and STI prevalence and reproductive health (RH) morbidity of FSWs screened for the trial.   RESULTS: 529 FSWs completed screening procedures; of those 33.6% were found ineligible.  The mean age was 30.9 years; 68.6% women were married and 57.5% were home-based FSWs.  Self-reported symptoms included abnormal vaginal discharge (31.6%), genital itching (3.4%), uterine mass/prolapse (3%) and painful intercourse (2.6%).  Gynecological surgery was reported by 73.2% of participants; of those 10.5% had undergone a hysterectomy. Female sterilization was the most commonly reported contraceptive method. Pelvic examination showed vaginal discharge (50.7%), cervical discharge (5.3%), uterine/vaginal wall prolapse (2.6%), and cervical mass/nodule/vesicles/genital warts (4.2%). Common epithelial findings included erythema (79.1%) and vesicles/bullae (6%); 46% of participants had Papanicolaou tests graded as inflammatory and 1.1% as malignant. HSV-2 was the mostly commonly detected STI (60.7%) followed by HIV (5.3%), syphilis (2.8%), chlamydia (2.2%), gonorrhoea (0.7%) and trichomoniasis (15.5%).  RTIs were more common: bacterial vaginosis (27.8%) and candidiasis (18.9%). CONCLUSIONS:  The low HIV prevalence and high RH morbidity in the population makes this site unsuitable for a future phase 2 or 3 microbicide efficacy trial.  HIV prevention programs targeting this population should include access to RH services.

Female sex workers, male circumcision and HIV: a qualitative study of their understanding, experience, and HIV risk in Zambia.

Several sub-Saharan African countries, including Zambia, have initiated national voluntary medical male circumcision (MC) programs to reduce HIV incidence. In-depth interviews were conducted with twenty female sex workers (FSWs) in Lusaka to examine their understanding of MC and experiences with circumcised clients. Knowledge of MC was derived primarily through informal sources, with very few FSWs reporting exposure to MC educational campaigns. MC was not widely believed to be protective against HIV, however it was viewed by some as protective against STIs. Three FSWs reported having sex with recently circumcised clients, and most reported that men often used their MC status to try to convince FSWs to forego condoms. Findings suggest that FSWs, already at high risk for HIV infection, may face additional pressure toward higher risk behavior as a result of MC. As MC services are expanded, programs should support FSWs' efforts to protect themselves by providing information about what MC can--and cannot--offer for HIV/STI infection prevention.

An evaluation of methods to improve the reporting of adherence in a placebo gel trial in Andhra Pradesh, India.

Female sex workers (FSWs) were recruited for a 4-month placebo vaginal gel trial in Nellore, India. Two experiments explored if prior knowledge of biomarkers for unprotected sex and insertion of gel applicators would yield more accurate self-reports. A third experiment compared self-reports of gel use and adherence levels between FSWs randomly assigned to interactive voice response survey (IVRS) and those assigned to paper diaries. Prior knowledge of biomarkers did not improve accuracy of self-reported condom or gel use, nor did it affect actual adherence. Of those who tested positive for the presence of semenogelin in the vagina, 76% reported no unprotected sex in the previous 48 h. Overall, women reported using gel on 90% of days whereas the biomarker indicated gel use on fewer than 50% of days. Compliance to IVRS was low, despite familiarity with mobile phone technology. Additional explorations with other populations are needed.

Characteristics of female sex workers in southern India willing and unwilling to participate in a placebo gel trial.

Respondent-driven sampling was used to recruit female sex workers (FSWs) for a community survey conducted in southern India. After survey completion, participants were given a brochure describing a clinical trial that entailed daily use of a placebo vaginal gel for four months. This study assessed predictors of screening among survey respondents, predictors of enrollment among those eligible for the trial, and predictors of visit attendance and retention among those enrolled. FSWs who reported having symptoms of sexually transmitted infections (STI), engaging in sex work in the past month, and living in a subdistrict easily accessible by public transportation with a high concentration of FSWs, were more likely to screen. FSWs who had never been tested for HIV were more likely to enroll. This analysis suggests that the primary reason FSWs participated in the trial was a desire for health care-not other factors hypothesized to be important, e.g., HIV risk perception and poverty status.

Increase in extraintestinal infections caused by Salmonella enterica subspecies II-IV.

To garner information regarding site of infection and age and sex of persons infected with Salmonella enterica subspecies II-IV, we retrospectively analyzed data on Salmonella spp. infections in California, USA, 1985-2009. These subspecies were found to cause significantly more frequent invasive disease (e.g., bacteremia) than did Salmonella subspecies I strains.

Expression of ESBL-like activity in infrequently encountered members of the family Enterobacteriaceae.

A collection of 94 unusual members of the Enterobacteriaceae were screened for the presence of extended spectrum ß-lactamases (ESBLs) using the MicroScan ESßL plus dried confirmation panel. Presumptively positive strains were then confirmed for the presence of an ESBL by double disk diffusion, E-test strips (AB Biodisk, Solna, Sweden) and PCR for SHV, TEM, and CTX-M2 genes. Of the 18 strains initially positive on the ESßL panel only three strains (Leminorella grimontii, Klebsiella ozaenae, and Kluyvera ascorbata) were positive by confirmation methods. These results suggest laboratories should be cautious regarding the methodology employed in screening for the presence of ESBLs in enteric bacteria. However, it should be noted that of the 94 strains, 29 were found to be resistant to two or more of the antibiotics present in the MicroScan ESßL plus panel indicating that there are potential treatment issues with these organisms despite their lack of ESBLs.

Clinical and laboratory diagnostic characteristics and cytotoxigenic potential of Hafnia alvei and Hafnia paralvei strains.

A collection of 68 Hafnia strains previously identified to the species level by 16S rRNA gene sequencing were investigated for simple phenotypic properties that could aid in their recognition in the clinical laboratory. Four tests, including malonate utilization, fermentation of salicin and d-arabinose, and expression of ß-glucosidase activity, correctly assigned each strain to either Hafnia alvei or H. paralvei. Antibiotic susceptibility profiles were generated for 35 H. alvei and H. paralvei isolates using Etest strips for 24 antibiotics. All strains were susceptible to aminoglycosides, quinolones, carbapenems, and monobactams. Most of the Hafnia isolates had a colistin MIC of ≥2 µg/ml. Sequencing of an internal ampC gene fragment allowed genotypic differentiation of the two Hafnia species. Approximately 70% of the hafniae tested additionally produced a cytolytic toxin active on Vero cells which may play a role in gastroenteritis.

Assessing the reporting of adherence and sexual activity in a simulated microbicide trial in South Africa: an interview mode experiment using a placebo gel.

Misreporting of adherence undermines detection of an association between product use and HIV infection in microbicide trials. This study investigates whether, in a placebo trial, audio computer-assisted self-interviewing (ACASI) produces more accurate reporting of adherence and sexual behavior than a face-to-face interview (FTFI). At three South African clinics, 849 women were enrolled and instructed to use applicators filled with placebo gel; participants were randomly assigned to FTFI or ACASI. Behavioral reports were validated through two biomarkers that detect product usage and unprotected sex. For most behaviors, ACASI generated significantly higher reporting, although differences by interview mode appeared to diminish over time. ACASI participants were more likely to report having had sex without gel, but reported and tested applicators did not indicate greater honesty about gel insertion with ACASI. While comparisons of reported unprotected sex with the validated biomarker revealed more agreement with ACASI than with FTFI, differences were small.

The genus Aeromonas: taxonomy, pathogenicity, and infection.

Over the past decade, the genus Aeromonas has undergone a number of significant changes of practical importance to clinical microbiologists and scientists alike. In parallel with the molecular revolution in microbiology, several new species have been identified on a phylogenetic basis, and the genome of the type species, A. hydrophila ATCC 7966, has been sequenced. In addition to established disease associations, Aeromonas has been shown to be a significant cause of infections associated with natural disasters (hurricanes, tsunamis, and earthquakes) and has been linked to emerging or new illnesses, including near-drowning events, prostatitis, and hemolytic-uremic syndrome. Despite these achievements, issues still remain regarding the role that Aeromonas plays in bacterial gastroenteritis, the extent to which species identification should be attempted in the clinical laboratory, and laboratory reporting of test results from contaminated body sites containing aeromonads. This article provides an extensive review of these topics, in addition to others, such as taxonomic issues, microbial pathogenicity, and antimicrobial resistance markers.

Hafnia paralvei sp. nov., formerly known as Hafnia alvei hybridization group 2.

It has been shown previously, based largely on DNA-DNA hybridizations and partial 16S rRNA gene sequencing, that Hafnia alvei is genotypically heterogeneous and consists of at least two DNA hybridization groups (HGs). In the present study, the taxonomic status of H. alvei HGs 1 and 2 was reassessed. A panel of 24 reference strains and isolates previously assigned to one of the two HGs in H. alvei was subjected to (GTG)5-PCR fingerprinting; this resulted in the delineation of two (GTG)5-PCR clusters in perfect accordance with the respective HG designations. Based on full 16S rRNA gene sequencing of a selection of reference strains, H. alvei HGs 1 and 2 showed internal sequence similarities of 99.8 and 99.5%, respectively. Between the two groups, sequence similarities ranged from 98.8 to 99.1%. Mean DNA-DNA hybridization values of 74.7-99.9% were obtained within each of the two HGs, whereas cross-hybridizations between members of H. alvei HG 1 (including ATCC 13337T) and HG 2 revealed only 32.7-48.7 % DNA-DNA hybridization. Previously published and new phenotypic data revealed that a combination of malonate assimilation and beta-glucosidase activity enabled correct assignment of Hafnia isolates to one of the two HGs. Collectively, taxonomic data from this study confirm that H. alvei comprises at least two taxa at the species level, of which HG 1 corresponds to H. alvei sensu stricto because it includes the type strain ATCC 13337T. Strains formerly classified as members of H. alvei HG 2 represent a novel species, for which the name Hafnia paralvei sp. nov. is proposed; ATCC 29927T (=CDC 4510-73T =LMG 24706T), the former reference strain of H. alvei HG 2, is designated the type strain.

Usefulness of multilocus polymerase chain reaction followed by electrospray ionization mass spectrometry to identify a diverse panel of bacterial isolates.

Polymerase chain reaction electrospray ionization mass spectrometry (PCR/ESI-MS) was tested for its ability to accurately identify a blinded panel of 156 diverse bacterial isolates, mostly human and/or animal pathogens. Here, 142/156 (91%) isolates were correctly identified to the genus level and 115/156 (74%) were correctly identified to the species level. Only 9% were misidentified. This study shows that multilocus PCR/ESI-MS has the potential to be a useful technique for identifying a broad range of bacteria.